Department Aquatic Ecology

Urbanization is changing Earth's ecosystems by altering the interactions and feedbacks between the fundamental ecological and evolutionary processes that maintain life. Humans in cities alter the eco-evolutionary play by simultaneously changing both the actors and the stage on which the eco-evolutionary play takes place. Urbanization modifies land surfaces, microclimates, habitat connectivity, ecological networks, food webs, species diversity, and species composition. These environmental changes can lead to changes in phenotypic, genetic, and cultural makeup of wild populations that have important consequences for ecosystem function and the essential services that nature provides to human society, such as nutrient cycling, pollination, seed dispersal, food production, and water and air purification. Understanding and monitoring urbanization-induced evolutionary changes is important to inform strategies to achieve sustainability. In the present article, we propose that understanding these dynamics requires rigorous characterization of urbanizing regions as rapidly evolving, tightly coupled human-natural systems. We explore how the emergent properties of urbanization affect eco-evolutionary dynamics across space and time. We identify five key urban drivers of change - habitat modification, connectivity, heterogeneity, novel disturbances, and biotic interactions - and highlight the direct consequences of urbanization-driven eco-evolutionary change for nature's contributions to people. Then, we explore five emerging complexities - landscape complexity, urban discontinuities, socio-ecological heterogeneity, cross-scale interactions, legacies and time lags - that need to be tackled in future research. We propose that the evolving metacommunity concept provides a powerful framework to study urban eco-evolutionary dynamics.

Uncovering biodiversity as an inherent feature of ecosystems and understanding its effects on ecosystem processes is one of the most central goals of ecology. Studying organisms' occurrence and biodiversity patterns in natural ecosystems has spurred the discovery of foundational ecological rules, such as the species–area relationship, and is of general scientific interest. Recent global changes add relevance and urgency to understanding the occurrence and diversity of organisms, and their respective roles in ecosystem processes. While information on ecosystem properties and abiotic environmental conditions are now available at unprecedented, highly-resolved spatial and temporal scales, the most fundamental variable – biodiversity itself – is still often studied in a local perspective, and generally not available at a wide taxonomic breadth, high temporal scale and spatial coverage. This is limiting the capacity and impact of ecology as a field of science. In this forum article, we propose that complete biodiversity assessments should be inclusive across taxonomic and functional groups, across space, and across time to better understand emergent properties, such as ecosystem functioning. We use riverine ecosystems as a case example because they are among the most biodiverse ecosystems worldwide, but are also highly threatened, such that an in-depth understanding of these systems is critically needed. Furthermore, their inherent spatial structure requires a multiscale perspective and consideration of spatial autocorrelation structures commonly ignored in biodiversity–ecosystem functioning studies. We show how recent methodological advances in environmental DNA (eDNA) provide novel opportunities to uncover broad biodiversity and link it to ecosystem processes, with the potential to revolutionize ecology and biodiversity sciences. We then outline a roadmap for using this technique to assess biodiversity in a complete and inclusive manner. Our proposed approach will help to get an understanding of biodiversity and associated ecosystem processes at spatial scales relevant for landscape ecology and environmental managers.

Eine Pilotstudie der Eawag hat an über 300 Standorten im Schweizer Mittelland die Grundwasserfauna untersucht, wobei die Rohwässer in Brunnenstuben durch die Wasserversorgungen selbst beprobt wurden. Anschliessend wurden die gefundenen Organismen morphologisch und teils genetisch bestimmt. An über 60% der Stellen wurden Organismen aus 18 biologischen Ordnungen gefunden. Bei den Grundwasserflohkrebsen wurden neue Arten für die Schweiz und auch für die Wissenschaft entdeckt.

Connecting the selective forces that drive the evolution of phenotypes to their underlying genotypes is key to understanding adaptation, but such connections are rarely tested experimentally. Threespine stickleback (Gasterosteus aculeatus) are a powerful model for such tests because genotypes that underlie putatively adaptive traits have been identified. For example, a regulatory mutation in the Ectodysplasin (Eda) gene causes a reduction in the number of bony armor plates, which occurs rapidly and repeatedly when marine sticklebacks invade freshwater. However, the source of selection on plate loss in freshwater is unknown. Here, we tested whether dietary reduction of phosphorus can account for selection on plate loss due to a growth advantage of low‐plated fish in freshwater. We crossed marine fish heterozygous for the 16 kilobase freshwater Eda haplotype and compared the growth of offspring with different genotypes under contrasting levels of dietary phosphorus in both saltwater and freshwater. Eda genotype was not associated with growth differences in any treatment, or with mechanisms that could mitigate the impacts of phosphorus limitation, such as differential phosphorus deposition, phosphorus excretion, or intestine length. This study highlights the importance of experimentally testing the putative selective forces acting on phenotypes and their underlying genotypes in the wild.

Exploiting a rich data set including both individual fishing activities and ecology, we study how eutrophication and climate warming influence plankton biodiversity in Lake Zürich and the consequent effects on fishers’ behavior and fishery yield. Our analysis indicates that changes in the fishery of Lake Zürich were driven by complex dynamic interactions between fishing efforts, environmental conditions, and lake ecosystem ecology. Results show that nutrient levels and climate warming have both direct and indirect dynamic and nonlinear effects on both fishers’ behavior and lake productivity. Ecological factors such as plankton abundance and diversity affect the dynamics of the fish population, which, in turn, influences fishing effort. The analysis highlights the importance and the interdependence of ecological‐human linkages in aquatic ecosystems.

Background: Organismal fitness can be determined at early life-stages, but phenotypic variation at early life-stages is rarely considered in studies on evolutionary diversification. The trophic apparatus has been shown to contribute to sympatric resource-mediated divergence in several taxa. However, processes underlying diversification in trophic traits are poorly understood. Using phenotypically variable Icelandic Arctic charr (Salvelinus alpinus), we reared offspring from multiple families under standardized laboratory conditions and tested to what extent family (i.e. direct genetic and maternal effects) contributes to offspring morphology at hatching (H) and first feeding (FF). To understand the underlying mechanisms behind early life-stage variation in morphology, we examined how craniofacial shape varied according to family, offspring size, egg size and candidate gene expression.
Results: Craniofacial shape (i.e. the Meckel’s cartilage and hyoid arch) was more variable between families than within families both across and within developmental stages. Differences in craniofacial morphology between developmental stages correlated with offspring size, whilst within developmental stages only shape at FF correlated with offspring size, as well as female mean egg size. Larger offspring and offspring from females with larger eggs consistently had a wider hyoid arch and contracted Meckel’s cartilage in comparison to smaller offspring.
Conclusions: This study provides evidence for family-level variation in early life-stage trophic morphology, indicating the potential for parental effects to facilitate resource polymorphism.

Phytoplankton play a key role in supporting aquatic food webs. However, the effects of ongoing large-scale changes in the concentrations and stoichiometry of important biological compounds [dissolved inorganic N (DIN), total phosphorus (TP), dissolved organic carbon (DOC) and DIN:TP] on the development and nutritional quality of phytoplankton for higher trophic levels are unclear. We conducted lake studies and in situ bioassay experiments in two Swedish mountain regions [Abisko (north) and Jämtland (south)] with different N deposition and where lakes in each region were distributed along a similar gradient in lake DOC (2–7 mg L⁻¹) to assess whether differences in nutrients, DOC and DIN:TP induced differences in phytoplankton quantity [chlorophyll a (Chl-a) and seston carbon (C)] and quality [seston C:N:P stoichiometry and fatty acid (FA) composition]. Using long-term monitoring data from lakes in these two mountain regions, we found declining long-term trends in N deposition and lake DIN and total TP concentrations, but not in lake DIN:TP. Lakes in Abisko received lower N deposition and had lower DIN:TP than those in Jämtland. Phytoplankton was N- to NP-limited in Abisko lakes but NP dual-limited in Jämtland lakes. The N fertilization effects induced by higher DIN:TP were weak on phytoplankton quantity but strong on phytoplankton quality. The phytoplankton had lower eicosapentaenoic acid (EPA) content and higher P content (lower seston C:P) in Abisko compared to in Jämtland. In addition, the quality of the DOC (as indicated by its aromaticity and SUVA) influenced not only the light conditions and the seston C:P ratios, but also the FA composition. We found higher bacteria FA concentrations in seston in Abisko than in Jämtland, despite lower amounts of FA of terrestrial origin in Abisko. Our findings suggest that declining N deposition and enhanced colored terrestrial C loadings leads to lower nutritional quality of basal resources for higher consumers in mountain lakes.

This assessment, by the United Nations Environment Programme (UNEP) Environmental Effects Assessment Panel (EEAP), one of three Panels informing the Parties to the Montreal Protocol, provides an update, since our previous extensive assessment (Photochem. Photobiol. Sci., 2019, 18, 595-828), of recent findings of current and projected interactive environmental effects of ultraviolet (UV) radiation, stratospheric ozone, and climate change. These effects include those on human health, air quality, terrestrial and aquatic ecosystems, biogeochemical cycles, and materials used in construction and other services. The present update evaluates further evidence of the consequences of human activity on climate change that are altering the exposure of organisms and ecosystems to UV radiation. This in turn reveals the interactive effects of many climate change factors with UV radiation that have implications for the atmosphere, feedbacks, contaminant fate and transport, organismal responses, and many outdoor materials including plastics, wood, and fabrics. The universal ratification of the Montreal Protocol, signed by 197 countries, has led to the regulation and phase-out of chemicals that deplete the stratospheric ozone layer. Although this treaty has had unprecedented success in protecting the ozone layer, and hence all life on Earth from damaging UV radiation, it is also making a substantial contribution to reducing climate warming because many of the chemicals under this treaty are greenhouse gases.

Variability in the environment defines the structure and dynamics of all living systems, from organisms to ecosystems. Species have evolved traits and strategies that allow them to detect, exploit and predict the changing environment. These traits allow organisms to maintain steady internal conditions required for physiological functioning through feedback mechanisms that allow internal conditions to remain at or near a set-point despite a fluctuating environment. In addition to feedback, many organisms have evolved feedforward processes, which allow them to adjust in anticipation of an expected future state of the environment. Here we provide a framework describing how feedback and feedforward mechanisms operating within organisms can generate effects across scales of organization, and how they allow living systems to persist in fluctuating environments. Daily, seasonal and multi-year cycles provide cues that organisms use to anticipate changes in physiologically relevant environmental conditions. Using feedforward mechanisms, organisms can exploit correlations in environmental variables to prepare for anticipated future changes. Strategies to obtain, store and act on information about the conditional nature of future events are advantageous and are evidenced in widespread phenotypes such as circadian clocks, social behaviour, diapause and migrations. Humans are altering the ways in which the environment fluctuates, causing correlations between environmental variables to become decoupled, decreasing the reliability of cues. Human-induced environmental change is also altering sensory environments and the ability of organisms to detect cues. Recognizing that living systems combine feedback and feedforward processes is essential to understanding their responses to current and future regimes of environmental fluctuations. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.

Competition for limiting resources is among the most fundamental ecological interactions and has long been considered a key driver of species coexistence and biodiversity. Species' minimum resource requirements, their R*s, are key traits that link individual physiological demands to the outcome of competition. However, a major question remains unanswered - to what extent are species' competitive traits able to evolve in response to resource limitation? To address this knowledge gap, we performed an evolution experiment in which we exposed Chlamydomonas reinhardtii for approximately 285 generations to seven environments in chemostats that differed in resource supply ratios (including nitrogen, phosphorus and light limitation) and salt stress. We then grew the ancestors and descendants in a common garden and quantified their competitive abilities for essential resources. We investigated constraints on trait evolution by testing whether changes in resource requirements for different resources were correlated. Competitive abilities for phosphorus improved in all populations, while competitive abilities for nitrogen and light increased in some populations and decreased in others. In contrast to the common assumption that there are trade-offs between competitive abilities for different resources, we found that improvements in competitive ability for a resource came at no detectable cost. Instead, improvements in competitive ability for multiple resources were either positively correlated or not significantly correlated. Using resource competition theory, we then demonstrated that rapid adaptation in competitive traits altered the predicted outcomes of competition. These results highlight the need to incorporate contemporary evolutionary change into predictions of competitive community dynamics over environmental gradients.
This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

The ABCD conference format (All continents, Balanced gender, low Carbon transport, Diverse backgrounds) mixes live-streamed and pre-recorded talks with in-person ones to reflect a diverse range of viewpoints and reduce the environmental footprint of meetings while also lowering barriers to inclusiveness.

Early detection is paramount for attempts to remove invasive non-native species (INNS). Traditional methods rely on physical sampling and morphological identification, which can be problematic when species are in low densities and/or are cryptic. The use of environmental DNA (eDNA) as a monitoring tool in freshwater systems is becoming increasingly acceptable and widely used for the detection of single species. Here we demonstrate the development and application of standard PCR primers for the detection of two freshwater invasive species which are high priority for monitoring in the UK and elsewhere: the Dreissenid mussels; Dreissena rostriformis bugensis (Andrusov, 1987) and D. polymorpha (Pallas, 1771). We carried out a rigorous validation process for testing the new primers, including DNA detection and degradation experiments in mesocosms, and a field comparison with traditional monitoring protocols. eDNA from single individuals of both mussel species could be detected within four hours of the start of the mesocosm experiment. In field trials, the two mussel species were detected at all sites where the species are known to be present, and eDNA consistently outperformed traditional kick-net sampling for species detection. These results demonstrate the applicability of standard PCR for eDNA detection of freshwater invasive species.

1. The early detection of invasive non-native species (INNS) is important for informing management actions. Established monitoring methods require the collection or observation of specimens, which is unlikely at the beginning of an invasion when densities are likely to be low. Environmental DNA (eDNA) analysis is a highly promising technique for the detection of INNS—particularly during the early stages of an invasion.
2. Here, we compared the use of traditional kick-net sampling with two eDNA approaches (targeted detection using both conventional and quantitative PCR and passive detection via metabarcoding with conserved primers) for detection of quagga mussel, Dreissena rostriformis bugensis, a high priority INNS, along a density gradient on the River Wraysbury, UK
3. . All three molecular tools outperformed traditional sampling in terms of detection. Conventional PCR and qPCR both had 100% detection rate in all samples and outperformed metabarcoding when the target species was at low densities. Additionally, quagga mussel DNA copy number (qPCR) and relative read count (metabarcoding) were significantly influenced by both mussel density and distance from source population, with distance being the most significant predictor.
4. Synthesis and application. All three molecular approaches were more sensitive than traditional kick-net sampling for the detection of the quagga mussel in flowing water, and both qPCR and metabarcoding enabled estimates of relative abundance. Targeted approaches were more sensitive than metabarcoding, but metabarcoding has the advantage of providing information on the wider community and consequently the impacts of INNS.

The adult and metacercaria life stages of a new species of the microphallid genus Atriophallophorus Deblock & Rosé, 1964 are described from specimens collected at Lake Alexandrina (South Island, New Zealand). In addition to molecular analyses of ribosomal and mitochondrial genes, metacercariae of Atriophallophorus winterbourni n. sp. from the snail host Potamopyrgus antipodarum (Gray) were grown in vitro to characterize internal and external morphology of adults using light and scanning electron microscopy and histological techniques. Atriophallophorus winterbourni n. sp. is readily distinguishable from Atriophallophorus coxiellae Smith, 1973 by having a different structure of the prostatic chamber, sub-circular and dorsal to genital atrium, rather than cylindrical, fibrous, elongate and placed between the seminal vesicle and the genital atrium. The new species is most similar to Atriophallophorus minutus (Price, 1934) with regards to the prostatic chamber and the morphometric data, but possesses elongate-oval testes and subtriangular ovary rather than oval and transversely oval in A. minutus. Phylogenetic analyses including sequence data for A. winterbourni n. sp. suggested a congeneric relationship of the new species to a hitherto undescribed metacercariae reported from Australia, both forming a strongly supported clade closely related to Microphallus and Levinseniella. In addition, we provide an amended diagnosis of Atriophallophorus to accommodate the new species and confirm the sinistral interruption of the outer rim of the ventral sucker caused by the protrusion of the dextral parietal atrial scale at the base of the phallus.

Mercury (Hg) is one of the most toxic heavy metals and is known for its persistence in the environment and potential to accumulate along the food chain. In many terrestrial polluted sites, earthworms are in direct contact with Hg contamination by ingesting large quantities of soil. However, little is known about the impact of Hg soil pollution on earthworms' gut microbiome. In this study, two incubation experiments involving earthworms in soils from a long-term Hg-polluted site were conducted to assess: (1) the effect of soil Hg contamination on the diversity and structure of microbial communities in earthworm, cast and soil samples; and (2) how the gut microbiome of different digestive track parts of the earthworm responds to soil Hg contamination. The large accumulation of total Hg and methyl-Hg within the earthworm tissues clearly impacted the bacterial and fungal gut community structures, drastically decreasing the relative abundance of the dominating gut bacterial class Mollicutes. Hg-tolerant taxa were found to be taxonomically widespread but consistent along the different parts of the earthworm digestive tract. This study revealed that although Hg might not directly affect the health of macro-organisms in the food-web such as earthworms, their metabolism and legacy in the soil might be impacted through changes in their gut microbiome.

1. Natural and anthropogenic disturbances commonly alter patterns of biodiversity and ecosystem functioning. However, how networks of interacting species respond to these changes remains poorly understood. We described aquatic food webs using invertebrate and fish community composition, functional traits and stable isotopes from twelve agricultural streams along a landscape disturbance gradient.
2. We predicted that excessive deposition of fine inorganic sediment (sedimentation) associated with agricultural activities would negatively influence aquatic trophic diversity (e.g. reduced vertical and horizontal trophic niche breadths). We hypothesized that multiple mechanisms might cause trophic niche 'compression', as indicated by changes in realized trophic roles.
3. Food-web properties based on consumer stable isotope data (δ¹³C and δ¹⁵N) showed that increasing sediment disturbance was associated with reduced trophic diversity. In particular, the aquatic invertebrate community occupied a smaller area in isotopic niche space along the sedimentation gradient that was best explained by a narrowing of the invertebrate community δ¹³C range.
4. Decreased niche partitioning, driven by increasing habitat homogeneity, environmental filtering and resource scarcity all seemingly lead to greater trophic equivalency caused by the collapse of the autochthonous food-web channel. Bayesian mixing-model analyses supported this contention with invertebrate consumers increasingly reliant on detritus along the sedimentation gradient, and predatory invertebrates relying more on the prey using these basal resources.
5. The narrowing of the fish community δ¹³C range along the sedimentation gradient contributed to an apparent 'trophic shift' towards terrestrial carbon, further indicating the loss of the autochthonous food-web channel. On the vertical trophic niche axis, fish became increasingly separated from aquatic invertebrates with an increase in their estimated trophic position. In combination, these responses were most likely mediated through reduced fish densities and a diminished reliance on aquatic prey.
6. Although species losses remain a major threat to ecosystem integrity, the functional roles of biota that persist dictate how food webs and ecosystem functioning respond to environmental change. Sedimentation was associated with nonlinear reductions in trophic diversity which could affect the functioning and stability of aquatic ecosystems. Our study helps explain how multiple mechanisms may radically reshape food-web properties in response to this type of disturbance.

Multiple anthropogenic drivers are changing ecosystems globally, with a disproportionate and intensifying impact on freshwater habitats. A major impact of urbanization are inputs from wastewater treatment plants (WWTPs). Initially designed to reduce eutrophication and improve water quality, WWTPs increasingly release a multitude of micropollutants (MPs; i.e., synthetic chemicals) and microbes (including antibiotic‐resistant bacteria) to receiving environments. This pollution may have pervasive impacts on biodiversity and ecosystem services. Viewed through multiple lenses of macroecological and ecotoxicological theory, we combined field, flume, and laboratory experiments to determine the effects of wastewater (WW) on microbial communities and organic‐matter processing using a standardized decomposition assay. First, we conducted a mensurative experiment sampling 60 locations above and below WWTP discharges in 20 Swiss streams. Microbial respiration and decomposition rates were positively influenced by WW inputs via warming and nutrient enrichment, but with a notable exception: WW decreased the activation energy of decomposition, indicating a "slowing" of this fundamental ecosystem process in response to temperature. Second, next‐generation sequencing indicated that microbial community structure below WWTPs was altered, with significant compositional turnover, reduced richness, and evidence of negative MP influences. Third, a series of flume experiments confirmed that although diluted WW generally has positive influences on microbial‐mediated processes, the negative effects of MPs are "masked" by nutrient enrichment. Finally, transplant experiments suggested that WW‐borne microbes enhance decomposition rates. Taken together, our results affirm the multiple stressor paradigm by showing that different aspects of WW (warming, nutrients, microbes, and MPs) jointly influence ecosystem functioning in complex ways. Increased respiration rates below WWTPs potentially generate ecosystem "disservices" via greater carbon evasion from streams and rivers. However, toxic MP effects may fundamentally alter ecological scaling relationships, indicating the need for a rapprochement between ecotoxicological and macroecological perspectives.

Predator-prey interactions heavily influence the dynamics of many ecosystems. An increasing body of evidence suggests that rapid evolution and coevolution can alter these interactions, with important ecological implications, by acting on traits determining fitness, including reproduction, anti-predatory defence and foraging efficiency. However, most studies to date have focused only on evolution in the prey species, and the predator traits in (co)evolving systems remain poorly understood. Here, we investigated changes in predator traits after approximately 600 generations in a predator-prey (ciliate-bacteria) evolutionary experiment. Predators independently evolved on seven different prey species, allowing generalization of the predator's evolutionary response. We used highly resolved automated image analysis to quantify changes in predator life history, morphology and behaviour. Consistent with previous studies, we found that prey evolution impaired growth of the predator, although the effect depended on the prey species. By contrast, predator evolution did not cause a clear increase in predator growth when feeding on ancestral prey. However, predator evolution affected morphology and behaviour, increasing size, speed and directionality of movement, which have all been linked to higher prey search efficiency. These results show that in (co)evolving systems, predator adaptation can occur in traits relevant to foraging efficiency without translating into an increased ability of the predator to grow on the ancestral prey type.

The alarming declines of freshwater biodiversity call for efficient biomonitoring at fine spatiotemporal scales, such that conservation measures be grounded upon accurate biodiversity data. Here, we show that combining environmental DNA (eDNA) extracted from stream water samples with models based on hydrological first principles allows upscaling biodiversity estimates for aquatic insects at very high spatial resolution. Our model decouples the diverse upstream contributions to the eDNA data, enabling the reconstruction of taxa distribution patterns. Across a 740-km² basin, we obtain a space-filling biodiversity prediction at a grain size resolution of 1-km long stream sections. The model’s accuracy in matching direct observations of aquatic insects' local occurrence ranges between 57-100%. Our results demonstrate how eDNA can be used for high-resolution biodiversity assessments in rivers with minimal prior knowledge of the system. Our approach allows identification of biodiversity hotspots that could be otherwise overlooked, enabling implementation of focused conservation strategies.

1. Several key processes in freshwater ecology are governed by the connectivity inherent to dendritic river networks. These have extensively been analyzed from a geomorphological and hydrological viewpoint, yet structures classically used in ecological modeling have been poorly representative of the structure of real river basins, often failing to capture well-known scaling features of natural rivers. Pioneering work identified optimal channel networks (OCNs) as spanning trees reproducing all scaling features characteristic of natural stream networks worldwide. While OCNs have been used to create landscapes for studies on metapopulations, biodiversity, and epidemiology, their generation has not been generally accessible.
2. Given the increasing interest in dendritic riverine networks by ecologists and evolutionary biologists, we here present a method to generate OCNs and, to facilitate its application, we provide the R-package OCNet . Owing to the stochastic process generating OCNs, multiple network replicas spanning the same surface can be built; this allows performing computational experiments whose results are irrespective of the particular shape of a single river network. The OCN construct also enables the generation of elevational gradients derived from the optimal network configuration, which can constitute three-dimensional landscapes for spatial studies in both terrestrial and freshwater realms. Moreover, the package provides functions that aggregate OCNs into an arbitrary number of nodes, calculate several descriptors of river networks, and draw relevant network features.
3. We describe the main functionalities of the package and its integration with other R-packages commonly used in spatial ecology. Moreover, we exemplify the generation of OCNs and discuss an application to a metapopulation model for an invasive riverine species.
4. In conclusion, OCNet provides a powerful tool to generate realistic river network analogues for various applications. It thereby allows the design of spatially realistic studies in increasingly impacted ecosystems and enhances our knowledge on spatial processes in freshwater ecology in general.

Stream‐water temperature is a key variable controlling chemical, biological and ecological processes in freshwater environments. Most models focus on a single river cross‐section; however, temperature gradients along stretches and tributaries of a river network are crucial to assess ecohydrological features such as, e.g., aquatic species suitability, growth and feeding rates, or disease transmission. We propose SESTET, a deterministic, spatially‐explicit stream temperature model for a whole river network, based on water and energy budgets at a reach scale and requiring only commonly available spatially distributed datasets, such as morphology and air temperature, as input. Heat exchange processes at the air‐water interface are modelled via the widely used equilibrium temperature concept, while effects of network structure are accounted for through advective heat fluxes. A case study was conducted on the prealpine Wigger river (Switzerland), where water temperatures have been measured in the period 2014‐2018 at eleven spatially distributed locations. Results show the advantages of accounting for water and energy budgets at the reach scale for the entire river network, compared to simpler, lumped formulations. Because our approach fundamentally relies on spatially distributed air temperature fields, adequate spatial interpolation techniques that account for the effects of both elevation and thermal inversion in air temperature are key to a successful application of the model. SESTET allows the assessment of the magnitude of the various components of the heat budget at the reach scale and the derivation of reliable estimates of spatial gradients of mean daily stream temperatures for the whole catchment based on a limited number of conveniently located (namely, spanning the largest possible elevation range) measuring stations. Moreover, accounting for mixing processes and advective fluxes through the river network allows one to trust regionalized values of the parameters controlling the relationship between equilibrium and air temperature, a key feature to generalize the model to data‐scarce catchments.

1. Characterising food-web responses to environmental factors could greatly improve our understanding of environment-biota relationships, and especially in floodplains where trophic interactions can be particularly important during phases of hydrological disconnection. The effects of floodplain hydrology and environmental attributes on structural aspects of biotic assemblages have been extensively studied, but responses at the functional level remain largely unknown.
2. Here, we characterised a central aspect of food-web architecture, the food chain length, as the maximum trophic position within 24 macroinvertebrate communities of parafluvial habitats in the Maggia river floodplain, in Switzerland. We investigated how the food chain length changed with different levels of habitat size, primary productivity and disturbance, the three factors potentially affecting food chain length in both theoretical and empirical studies.
3. We found that food chain length was lower in frequently flooded habitats and immediately after a flood. We also showed that trophic omnivory, where predators fed at lower trophic levels after flooding, and in more frequently flooded habitats, may explain these changes.
4. These findings show that trophic omnivory may explain how predators resist disturbance and are maintained in highly dynamic landscapes. More importantly, given that trophic omnivory may overall weaken trophic linkages and thus increase food-web stability, this suggests that it could be a key mechanism in sustaining biodiversity in river floodplains.

Dinoflagellates can serve as predators or parasites of tintinnid ciliates. Known predators feed on the ciliate from outside the tintinnid lorica, while parasites either grow in the host cytoplasm or feed inside in the lorica while attached to the outside of the host cell. Here we report mixotrophic species of Scrippsiella that enter the lorica to consume the ciliate zooid of Helicostomella subulata from Denmark and multiple tintinnid species from Korea. We contrast morphology and life-history stages of these mixotrophic predators with dinokaryote parasites of tintinnids and address phylogenetic relationships based on rDNA sequences. Mixotrophic Scrippsiella species sometimes attack tintinnids that are simultaneously infected by syndinean dinoflagellates, complicating study of life histories and potentially leading to confusion about trophic status and taxonomy.

Background: Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts.
Results: We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes.
Conclusions: These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.

Genetic diversity is a phenomenon whose existence has fascinated generations of evolutionary biologists. Coevolution of hosts and parasites is a plausible explanation for its existence. Of special interest in this respect is negative frequency-dependent selection between host and parasite genotypes (NFDS). NFDS can create fluctuating selection pressure which repeatedly favours different host and parasite genotypes and hence could maintain genetic diversity.
NFDS between hosts and parasites is a dynamic process and as such is susceptible to interference. I like to visualize the dynamic swings of host and parasite genotype frequencies as a pendulum, swinging from one frequency to another. And much like with a pendulum, also small disturbances, can interfere greatly with the dynamics of host and parasite genotype frequencies.
But before statements about the behavior of a pendulum can be made, the pendulum itself must be examined. How long is the string, how heavy the head? In chapter 1 I introduce a novel agent-based time-forward stochastic simulation for host and parasite co-evolution which allows to simulate life histories of individual agents in great detail. Populations can be simulated by generating groups of such agents. Population-level behaviour then emerges from a multitude of individual-level interactions. This type of simulation allows new and detailed insights into the context-dependency of host-parasite coevolution. [...]

Genetische Diversität ist ein allgegenwärtiges Phänomen dessen Existenz Evolutionsbiologen seit Generationen fasziniert. Häufig wird die Koevolution von Wirtsorganismen mit Parasiten als Erklärung für die vorhandene genetische Diversität herangezogen. Von besonderer Bedeutung ist in diesem Zusammenhang die negativ -genotyp-frequenzabhängige Interaktion, welche einen oszillierenden Selektionsdruck erzeugt, der immer wieder andere Genotypen bevorzugt und somit eine hohe genetische Diversität fördert.
Negativ frequenzabhängige Interaktionen von Wirten und Parasiten sind häufig hochdynamische Prozesse und können also solche leicht beeinflusst werden. Ein Pendel kann gut als Beispiel verwendet werden um das schwingen von einer Wirtsgenotypfrequenz zur nächsten zu visualisieren. Genau wie ein bei einem Pendel können schon kleinste Störungen das dynamische Verhalten von Wirts- und Parasitgenotypfrequenzen verändern.
Bevor nun aber Aussagen über das Verhalten eines Pendels gemacht werden können, muss zuerst das Pendel selbst charakterisiert werden. Wie lange ist der Faden, wie schwer der Kopf des Pendels? In Kapitel 1 präsentiere ich eine neue, individuen-basierte Simulation für Wirt-Parasit Koevolution welche es erlaubt die Lebensgeschichte einzelner Individuen hochdetailiert zu simulieren. Populationen können durch das Erzeugen von Gruppen solcher Individuen simuliert werden. Das Verhalten von Populationen ist somit ein Ergebnis einer Vielzahl von Interaktionen zwischen Individuen. Diese Art Simulation erlaubt einen neuen, detaillierten Blick auf die Kontextabhängigkeit von Wirts-Parasit-Interaktionen. [...]

Despite the increasing ubiquity of biological invasions worldwide, little is known about the scale-dependent effects of nonnative species on real-world ecological dynamics. Here, using an extensive time series dataset of riverine fish communities across different biogeographic regions of the world, we assessed the effects of nonnative species on the temporal variability and synchrony in abundance at different organizational levels (population, metapopulation, community and metacommunity) and spatial scales (stream reach and river basin). At the reach scale, we found that populations of nonnative species were more variable over time than native species, and that this effect scaled up to the community level - significantly destabilizing the dynamics of riverine fish communities. Nonnative species not only contributed to reduced community stability, but also increased variability of native populations. By contrast, we found no effect of nonnative species dominance on local interspecific synchrony among native species. At the basin scale, nonnative metapopulations were again more variable than the native ones. However, neither native metapopulations nor metacommunities showed differences in temporal variability or synchrony as nonnative species dominance increased basin-wide. This suggests a 'dilution effect' where the contribution to regional stability of local native populations from sites displaying low levels of invasion reduced the destabilizing effects of nonnative species. Overall, our results indicate that accounting for the destabilizing effect of nonnative species is critical to understanding native species persistence and community stability.

In many species, individuals can employ alternative reproductive phenotypes, with profound consequences for individual fitness and population dynamics. This is particularly relevant for self-compatible hermaphrodites, which have exceptionally many reproductive options. Here we investigated the occurrence of reproductive phenotypes in the simultaneously hermaphroditic freshwater snail Radix balthica under experimentally simulated conditions of low versus moderate population density. We captured all mating behavior on camera and measured individual female lifetime reproductive success. We found every possible reproductive phenotype: (1) both male and female (i.e., truly hermaphroditic) reproduction, (2) purely female and (3) purely male reproduction, (4) male reproduction combined with self-fertilization and (5) female mating activity, (6) pure self-fertilization without mating and (7-8) two types of reproductive failure. Variation in alternative reproductive phenotypes was explained by mate availability (10.8%) and individual condition, approximated by a snail's mean daily growth rate (17.5%). Increased mate availability resulted in a lower diversity of reproductive phenotypes, in particular increasing the frequency of true hermaphrodites. However, it lowered phenotype-specific fecundities and hence reduced the population growth rate. Snails in better condition were more likely to reproduce as true hermaphrodites or pure females, whereas low-condition snails tended to suffer reproductive failure. Overall, we show substantial variation in alternative reproductive phenotypes in a hermaphrodite, which is possibly in part maintained by fluctuations in population density and thus mate availability, and by variation in individual condition. We also provide evidence of an almost 2-fold increase in clutch size that can be ascribed specifically to mating as a female.

The spread of coronavirus disease 2019 (COVID-19) in Italy prompted drastic measures for transmission containment. We examine the effects of these interventions, based on modeling of the unfolding epidemic. We test modeling options of the spatially explicit type, suggested by the wave of infections spreading from the initial foci to the rest of Italy. We estimate parameters of a metacommunity Susceptible-Exposed-Infected–Recovered (SEIR)-like transmission model that includes a network of 107 provinces connected by mobility at high resolution, and the critical contribution of presymptomatic and asymptomatic transmission. We estimate a generalized reproduction number (R₀ = 3.60 [3.49 to 3.84]), the spectral radius of a suitable next-generation matrix that measures the potential spread in the absence of containment interventions. The model includes the implementation of progressive restrictions after the first case confirmed in Italy (February 21, 2020) and runs until March 25, 2020. We account for uncertainty in epidemiological reporting, and time dependence of human mobility matrices and awareness-dependent exposure probabilities. We draw scenarios of different containment measures and their impact. Results suggest that the sequence of restrictions posed to mobility and human-to-human interactions have reduced transmission by 45% (42 to 49%). Averted hospitalizations are measured by running scenarios obtained by selectively relaxing the imposed restrictions and total about 200,000 individuals (as of March 25, 2020). Although a number of assumptions need to be reexamined, like age structure in social mixing patterns and in the distribution of mobility, hospitalization, and fatality, we conclude that verifiable evidence exists to support the planning of emergency measures.

Landscape's spatial structure has vast implications for the dynamics and distribution of species populations and ecological communities. However, the characterization of the structure of spatial networks has not received nearly as much attention as networks of species interactions counterparts. Recent experiments show the dynamical implications of modularity to buffer perturbations, and theory shows that several other processes might be impacted if spatial networks were modular, from disease transmission to gene flow. Yet the question is, are spatial networks actually modular? Even though some case studies have found modular structures, we lack a general answer to that question. Here, I show that modularity is a naturally emergent property of spatial networks. This finding is further reinforced by analyzing real patchy habitats. Furthermore, I show that there is no need for any other biological process other than dispersal in order to generate a significantly modular spatial network. Modularity is explained by the spatial heterogeneity in the density of habitat fragments. The fact that spatial networks are intrinsically modular might have direct consequences for population and evolutionary dynamics. Modules define the spatial limits of populations and the role each habitat fragment plays in ecological dynamics; they become the relevant scale at which a multitude of processes occur.

Aim: Providing a quantitative overview of ecosystem functioning in a three-dimensional space defined by ecosystem stocks, fluxes and rates, across major ecosystem types and climatic zones.
Location: Global.
Time period: 1966–2019.
Major taxa studied: Ecosystem-level measurements (all organism types).
Methods: We conducted a global quantitative synthesis of a wide range of ecosystem variables related to carbon stocks and fluxes. We gathered a total of 4,479 values from 1,223 individual sites (unique geographical coordinates) reported in the literature (604 studies), covering ecosystem variables including biomass and detritus stocks, gross primary production, ecosystem respiration, detritus decomposition and carbon uptake rates, across eight major aquatic and terrestrial ecosystem types and five broad climatic zones (arctic, boreal, temperate, arid and tropical). We analysed the relationships among variables emerging from the comparisons of stocks, fluxes and rates across ecosystem types and climates.
Results: Within our three-dimensional functioning space, average ecosystems align along a gradient from fast rates–low fluxes and stocks (freshwater and pelagic marine ecosystems) to low rates–high fluxes and stocks (forests), a gradient that we hypothesize results mainly from variation in primary producer characteristics. Moreover, fluxes and rates decrease from warm to colder climates, consistent with the metabolic theory of ecology. However, the strength of climatic effects differs among variables and ecosystem types, resulting, for instance, in opposing effects on net ecosystem production between terrestrial and freshwater ecosystems (positive versus negative effects).
Main conclusions: This large-scale synthesis provides a first quantified cross-ecosystem and cross-climate comparison of multivariate ecosystem functioning. This gives a basis for a mechanistic understanding of the interdependency of different aspects of ecosystem functioning and their sensitivity to global change. To anticipate responses to change at the ecosystem level, further work should investigate potential feedbacks between ecosystem variables at finer scales, which involves site-level quantifications of multivariate functioning and theoretical developments.

In der Schweiz gelangt nach wie vor zu viel Stickstoff und Phosphor in die Umwelt. Kritische Belastungsgrenzen für Stickstoffeinträge in die Umwelt sind vielerorts deutlich überschritten. Vor allem die Stickstoff- und Phosphorüberschüsse der Landwirtschaft und die Stickstoffemissionen des Verkehrs belasten die Umwelt und beeinträchtigen die Biodiversität, die Luft, die Gewässer- und Trinkwasserqualität sowie die Waldfunktionen stark. Zudem verstärken sie den Klimawandel und beeinträchtigen die menschliche Gesundheit. Ursachen wie auch Auswirkungen der übermässigen Einträge sind wissenschaftlich seit Jahrzehnten gut dokumentiert. Allerdings ist kaum eines der diesbezüglichen vom Bundesrat verabschiedeten Reduktionsziele erreicht. Sollen die negativen Effekte auf die Biodiversität und Ökosystemleistungen verringert werden, sind die Ursachen für die übermässigen Einträge dringend anzugehen. Dieses Faktenblatt zeigt hierzu Handlungsansätze auf.

Immune systems have repeatedly diversified in response to parasite diversity. Many animals have outsourced part of their immune defence to defensive symbionts, which should be affected by similar evolutionary pressures as the host's own immune system. Protective symbionts provide efficient and specific protection and respond to changing selection pressure by parasites. Here we use the aphid Aphis fabae, its protective symbiont Hamiltonella defensa, and its parasitoid Lysiphlebus fabarum to test whether parasite diversity can maintain diversity in protective symbionts. We exposed aphid populations with the same initial symbiont composition to parasitoid populations that differed in their diversity. As expected, single parasitoid genotypes mostly favoured a single symbiont that was most protective against that particular parasitoid, while multiple symbionts persisted in aphids exposed to more diverse parasitoid populations, which in turn affected aphid population density and rates of parasitism. Parasite diversity may be crucial to maintaining symbiont diversity in nature.

Changing reproductive strategy from investment in current (asexual eggs) to future (sexual ephippia) reproduction depending on environmental cues is an important fitness trait in zooplankton species like water fleas, Daphnia. Different cues are reported for ephippia production, for example food limitation, changes in photoperiod and temperature, the presence of predators, nutrient depletion or signals of crowding. However, the reliability of these cues strongly depends on the local habitat. In Daphnia galeata, ephippia production might not be subject to any of the environmental cues outlined. Here, we directly test whether changes in crowding alone provides a reliable cue for D. galeata to switch reproductive mode. We conducted life history assays using 10 genotypes of D. galeata from a Swiss Lake to investigate density dependent reproduction and production of ephippia. We started populations at different densities and eliminated competition for food by systematically increasing food availability with population size. Our results suggest that population density depresses population growth rate via a change in energy allocation from current into future reproduction in D. galeata. Thus, signals of crowding produced at high population density constitute a reliable and sufficient cue for D. galeata to switch from asexual to sexual reproduction.

Fishes stocked for recreation and angling can damage freshwater habitats and negatively impact biodiversity. The pond-associated crucian carp (Carassius carassius) is rare across Europe and is stocked for conservation management in England, but its impacts on pond biota are understudied. Freshwater invertebrates contribute substantially to aquatic biodiversity, encompassing many rare and endemic species, but their small size and high abundance complicate their assessment. Practitioners have employed sweep-netting and kick-sampling with microscopy (morphotaxonomy), but specimen size/quality and experience can bias identification. DNA and environmental DNA (eDNA) metabarcoding offer alternative means of invertebrate assessment. We compared invertebrate diversity in ponds (N = 18) with and without crucian carp using morphotaxonomic identification, DNA metabarcoding and eDNA metabarcoding. Five 2L water samples and 3min sweep-net samples were collected at each pond. Inventories produced by morphotaxonomic identification of netted samples, DNA metabarcoding of bulk tissue samples and eDNA metabarcoding of water samples were compared. Alpha diversity was greatest with DNA or eDNA metabarcoding, depending on whether standard or unbiased methods were considered. DNA metabarcoding reflected morphotaxonomic identification, whereas eDNA metabarcoding produced markedly different communities. These complementary tools should be combined for comprehensive invertebrate assessment. Crucian carp presence minimally reduced alpha diversity in ponds, but positively influenced beta diversity through taxon turnover (i.e., ponds with crucian carp contained different invertebrates to fishless ponds). Crucian carp presence contributes to landscape-scale invertebrate diversity, supporting continued conservation management in England. Our results show that molecular tools can enhance freshwater invertebrate assessment and facilitate development of more accurate and ecologically effective pond management strategies.

Cross-ecosystem subsidies are studied with a focus on resource exchange at local ecosystem boundaries. This perspective ignores regional dynamics that can emerge via constraints imposed by the landscape, potentially leading to spatially-dependent effects of subsidies and spatial feedbacks. Using miniaturized landscape analogues of river dendritic and terrestrial lattice spatial networks, we manipulated and studied resource exchange between the two whole networks. We found community composition in dendritic networks depended on the resource pulse from the lattice network, with the strength of this effect declining in larger downstream patches. In turn, this spatially-dependent effect imposed constraints on the lattice network with populations in that network reaching higher densities when connected to more central patches in the dendritic network. Consequently, localized cross-ecosystem fluxes, and their respective effects on recipient ecosystems, must be studied in a perspective taking into account the explicit spatial configuration of the landscape.

Key traits of unicellular species, such as cell size, often follow scale-free or self-similar distributions, hinting at the possibility of an underlying critical process. However, linking such empirical scaling laws to the critical regime of realistic individual-based model classes is difficult. Here, we reveal new empirical scaling evidence associated with a transition in the population and the chlorophyll dynamics of phytoplankton. We offer a possible explanation for these observations by deriving scaling laws in the vicinity of the critical point of a new universality class of non-local cell growth and division models. This "criticality hypothesis" can be tested through new scaling predictions derived for our model class, for the response of chlorophyll distributions to perturbations. The derived scaling laws may also be generalized to other cellular traits and environmental drivers relevant to phytoplankton ecology.

The dietary nutrient composition can affect insects' phenotypes by modulating their physiology. Furthermore, diet can affect gut microbiota composition and abundance, with indirect consequences for the host. In this study, we reared Drosophila melanogaster on five different diets; three with balanced sugar:yeast ratio, but with increasing caloric content (2:2, 8:8, 16:16, in weight %), and two with imbalanced sugar:yeast ratio, either with low sugar and high yeast content (2:16) or vice-versa (16:2). In each of these diets, we compared flies with conventional vs. artificially altered gut microbiota with antibiotics that reduced the bacterial load. The antibiotic treatment also had the surprising effect of increasing the amount of live yeast associated with the flies. We characterized flies from these ten treatments (5 diets × 2 microbiota) in terms of development, body mass, food preference, body reserves, metabolic rate and a range of stress tolerance traits (heat, cold, starvation and desiccation tolerance). Diets, and to a lesser extent antibiotic treatment, affected development rate, weight, and cold tolerance of adult flies. Other traits such as energy reserves, metabolic rate, food preference, or starvation tolerance were affected by diet alone. When detected, the effect of antibiotic treatment was stronger in yeast-poor diets, suggesting that gut bacterial community might help to counterbalance nutritional deficiencies. These results show that changes in dietary factors lead to a global re-organization of fly's physiology and development while the manipulation of gut microorganisms had minor effects that were mainly seen in case of protein restriction.

Larval crowding represents a complex stressful situation arising from inter-individual competition for time- and space-limited resources. The foraging of a large number of individuals may alter the chemical and bacterial composition of food and in turn affect individual's traits. Here we used Drosophila melanogaster to explore these assumptions. First, we used a wide larval density gradient to investigate the impact of crowding on phenotypical traits. We confirmed that high densities increased development time and pupation height, and decreased viability and body mass. Next, we measured concentrations of common metabolic wastes (ammonia, uric acid) and characterized bacterial communities, both in food and in larvae, for three contrasting larval densities (low, medium and high). Ammonia concentration increased in food from medium and high larval densities, but remained low in larvae regardless of the larval density. Uric acid did not accumulate in food but was detected in larvae. Surprisingly, bacterial composition remained stable in guts of larvae whatever their rearing density, although it drastically changed in the food. Overall, these results indicate that crowding deeply affects individuals, and also their abiotic and biotic surroundings. Environmental bacterial communities likely adapt to altered nutritional situations resulting from crowding, putatively acting as scavengers of larval metabolic wastes.

Concentrations of dissolved organic carbon (DOC) have increased recently in many lakes at high latitudes in North America and Europe, but it is unclear what effect this will have on the identity of the limiting nutrient for phytoplankton [nitrogen (N) vs. phosphorus (P)]. Identifying the effect of changing DOC on phytoplankton nutrient limitation is complicated by spatial covariation between atmospheric N deposition and increasing DOC in areas where lake browning occurs. We conducted nutrient-limitation assays in 27 lakes from three sites along gradients of climate and atmospheric N deposition in Sweden. Within each site, lakes were selected to represent the range of DOC concentrations. We also conducted statistical analyses of large-scale lake survey data (n = 4768 lakes divided into 47 regions) to investigate relationships between DOC and nutrient stoichiometry while controlling for differences in N deposition. Our findings confirmed that most lakes were dual-limited by both N and P in the south, whereas northern lakes were primarily N-limited. Throughout Sweden the ratio of dissolved inorganic nitrogen (DIN) to total phosphorus (TP) declined with increasing DOC in most regions, suggesting that browner lakes are more likely to be N limited. These results were not supported by our nutrient limitation assays, which identified no relationship between DOC and relative strength of limitation by N or P. Increased DOC also resulted in significant increases in both total and inorganic N and P fractions, suggesting that other factors such as light limitation or increased top-down control become more important as DOC increases.

Ecological stoichiometry is concerned with the ratios of different elements, particularly carbon, nitrogen, and phosphorus. Ratios by their nature do not respond symmetrically to changes in the numerator and denominator and do not follow normal distributions; however, researchers frequently fail to consider these properties in their analyses, which has biased reported results. Calculating means, variance, or linear slopes based on untransformed ratios results in biased results. I demonstrate the consequences of these errors for inferences from stoichiometric analyses using simple examples and several large monitoring data sets. I then review 100 studies in ecological stoichiometry and find that misuse of ratio data is common, with 93% of studies containing at least one error. These errors may be problematic, particularly in large-scale meta-analyses summarizing data over large ranges. Fortunately, most of these mistakes can be easily avoided by first log transforming elemental ratios. I therefore recommend that, to ensure robust and reproducible results, researchers in ecological stoichiometry should adopt a convention of presenting stoichiometric ratio data as the logarithm of molar ratios in the future. The widespread use of untransformed nitrogen to phosphorus ratio as an indicator of nutrient limitation has likely exaggerated the importance of phosphorus limitation, particularly in freshwater systems.

Ecological pyramids represent the distribution of abundance and biomass of living organisms across body-sizes. Our understanding of their expected shape relies on the assumption of invariant steady-state conditions. However, most of the world’s ecosystems experience disturbances that keep them far from such a steady state. Here, using the allometric scaling between population growth rate and body-size, we predict the response of size-abundance pyramids within a trophic guild to any combination of disturbance frequency and intensity affecting all species in a similar way. We show that disturbances narrow the base of size-abundance pyramids, lower their height and decrease total community biomass in a nonlinear way. An experimental test using microbial communities demonstrates that the model captures well the effect of disturbances on empirical pyramids. Overall, we demonstrate both theoretically and experimentally how disturbances that are not size-selective can nonetheless have disproportionate impacts on large species.

Current global change is associated with an increase in disturbance frequency and intensity, with the potential to trigger population collapses and to cause permanent transitions to new ecosystem states. However, our understanding of ecosystem responses to disturbances is still incomplete. Specifically, there is a mismatch between the diversity of disturbance regimes experienced by ecosystems and the one-dimensional description of disturbances used in most studies on ecological stability. To fill this gap, we conducted a full factorial experiment on microbial communities, where we varied the frequency and intensity of disturbances affecting species mortality, resulting in 20 different disturbance regimes. We explored the direct and long-term effects of these disturbance regimes on community biomass. While most communities were able to recover biomass and composition states similar to undisturbed controls after a halt of the disturbances, we identified some disturbance thresholds that had long-lasting legacies on communities. Using a model based on logistic growth, we identified qualitatively the sets of disturbance frequency and intensity that had equivalent long-term negative impacts on experimental communities. Our results show that an increase in disturbance intensity is a bigger threat for biodiversity and biomass recovery than the occurrence of more frequent but less intense disturbances.

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; "CESTES". Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology.

The importance of functional diversity for the functioning and behaviour of microbial communities is clear, yet the widespread incorporation of functional diversity measurements into environmental microbiology study designs remains surprisingly limited. This may, at least to some extent, be a consequence of the unique conceptual and methodological challenges to measuring functional diversity in microbial communities. To facilitate the increased incorporation of functional diversity measurements into environmental microbiology study designs, we review here the process and some key caveats for measuring functional diversity and provide specific examples. We highlight three main decision points and provide guidance to making these decisions based on the underlying mechanisms for how functional diversity relates to an ecosystem process or property of interest. We discuss the selection of an appropriate type of functional trait, selection of the specificity at which functional diversity will be measured, and selection of an appropriate metric for estimating functional diversity from quantitative measures of those traits. We further discuss decisions regarding the use of one- or multi-dimensional measures of functional diversity and how advances in the field of trait-based community ecology could be applied or adapted to address questions in environmental microbiology.

The Convention on Biological Diversity, and the Nagoya Protocol in particular, provide a framework for the fair and equitable sharing of benefits arising from the utilization of biological resources and traditional knowledge, and ultimately aim to promote capacity-building in the developing world. However, measuring capacity-building is a challenging task due to its intangible nature. By compiling and analyzing a database of scientific peer-reviewed publications over a period of 50 y (1965 to 2015), we investigated capacity-building in global marine natural product discovery. We used publication and authorship metrics to assess how the capacity to become scientifically proficient, prolific, and independent has changed in bioprospecting countries. Our results show that marine bioprospecting is a dynamically growing field of research with continuously increasing numbers of participating countries, publications, and scientists. Yet despite longstanding efforts to promote equitability and scientific independence, not all countries have similarly increased their capacity to explore marine biodiversity within their national jurisdiction areas. Although developing countries show an increasing trend in the number of publications, a few developed countries still account for almost one-half of all publications in the field. Multiple lines of evidence suggest that economic capacity affects how well countries with species-rich marine ecosystems can scientifically explore those resources. Overall, the capacity-building data analyzed here provides a timely contribution to the ongoing international debate about access to and benefit-sharing of biological resources for countries exploring biodiversity within and outside their national jurisdiction areas.

Biodiversity loss and climate warming are occurring in concert, with potentially profound impacts on ecosystem functioning. We currently know very little about the combined effects of these changes on the links between the community structure, dynamics and the resulting in situ CO₂ concentrations in freshwater ecosystems. Here we aimed to determine both individual and combined effects of temperature and non-resource diversity (species inedible for a given consumer) on CO₂ concentration. Our analysis further aimed to establish both direct effects on CO₂ concentrations and potential indirect effects that occur via changes to the phytoplankton and zooplankton biomasses. Our results showed that there were no interactive effects of changes in temperature and diversity on CO₂ concentration in the water. Instead, independent increases in either temperature or non-resource diversity resulted in a substantial reduction in CO₂ concentrations, particularly at the highest non-resource diversity. The effects of non-resource diversity and warming on CO₂ were indirect, resulting largely from the positive impacts on total biomass of primary producers. Our study is the first to experimentally partition the impacts of temperature and diversity on the consumer–resource dynamics and associated changes to CO₂ concentrations. It provides new mechanistic insights into the role of diverse plankton communities for ecosystem functioning and their importance in regulating CO₂ dynamics under ongoing climate warming.

Human-induced global change dramatically alters individual aspects of river biodiversity, such as taxonomic, phylogenetic or functional diversity, and is predicted to lead to losses of associated ecosystem functions. Understanding these losses and dependencies are critical to human well-being. Until now, however, most studies have only looked either at individual organismal groups or single functions, and little is known on the effect of human activities on multitrophic biodiversity and on ecosystem multifunctionality in riverine ecosystem. Here we profiled biodiversity from bacteria to invertebrates based on environmental DNA (hereafter, 'eDNA') samples across a major river catchment in China, and analysed their dependencies with multiple ecosystem functions, especially linked to C/N/P-cycling. Firstly, we found a spatial cross-taxon congruence pattern of communities' structure in the network of the Shaying river, which was related to strong environmental filtering due to human land use. Secondly, human land use explained the decline of multitrophic and multifaceted biodiversity and ecosystem functions, but increased functional redundancy in the riverine ecosystem. Thirdly, biodiversity and ecosystem function relationships at an integrative level showed a concave-up (non-saturating) shape. Finally, structural equation modeling suggested that land use affects ecosystem functions through biodiversity-mediated pathways, including biodiversity loss and altered community interdependence in multitrophic groups. Our study highlights the value of a complete and inclusive assessment of biodiversity and ecosystem functions for an integrated land-use management of riverine ecosystems.

A major focus of ecology is to understand and predict ecosystem function across scales. Many ecosystem functions are measured only at local scales, while their effects occur at a landscape level. Here we investigate how landscape-scale predictions of ecosystem function depend on intraspecific competition, a fine-scale process, by manipulating intraspecific density of shredding macroinvertebrates and examining effects on leaf litter decomposition, a key function in freshwater ecosystems. For two species, we found that per capita leaf processing rates declined with increasing density following power functions with negative exponents, likely due to interference competition. To demonstrate consequences of this nonlinearity, we scaled up estimates of leaf litter processing from shredder abundance surveys in 10 replicated headwater streams. In accordance with Jensen's inequality, applying density-dependent consumption rates reduced estimates of catchment-scale leaf consumption by an order of magnitude relative to density-independent rates. Density-dependent consumption estimates aligned closely with metabolic requirements in catchments with large - but not small - shredder populations. Importantly, shredder abundance was not limited by leaf litter availability, and catchment-level leaf litter supply was much higher than estimated consumption. Thus leaf litter processing was not limited by resource supply. Our work highlights the need for scaling up, which accounts for intraspecific interactions.

Caullerya mesnili is a common and virulent parasite of the water flea, Daphnia. It was classified within the Haplosporidia (Rhizaria) for over a century. However, a recent molecular phylogeny based on the 18S rRNA gene suggested it belonged to the Ichthyosporea, a class of protists closely related to animals within the Opisthokonta clade. The exact phylogenetic position of C. mesnili remained uncertain because it appeared in the 18S rRNA tree with a very long branch and separated from all other taxa, suggesting that its position could be artifactual. A better understanding of its phylogenetic position has been constrained by a lack of molecular markers and the difficulty of obtaining a suitable quantity and quality of DNA from in vitro cultures, as this intracellular parasite cannot be cultured without its host. We isolated and collected spores of C. mesnili and sequenced genomic libraries. Phylogenetic analyses of a newly generated multi-protein data set (22 proteins, 4,998 amino acids) and of sequences from the 18S rRNA gene both placed C. mesnili within the Ichthyophonida sub-clade of Ichthyosporea, as sister-taxon to Abeoforma whisleri and Pirum gemmata. Our study highlights the utility of metagenomic approaches for obtaining genomic information from intracellular parasites and for more accurate phylogenetic placement in evolutionary studies.

We report on a novel RNA virus infecting the wasp Lysiphlebus fabarum, a parasitoid of aphids. This virus, tentatively named "Lysiphlebus fabarum virus" (LysV), was discovered in transcriptome sequences of wasps from an experimental evolution study in which the parasitoids were allowed to adapt to aphid hosts (Aphis fabae) with or without resistance-conferring endosymbionts. Based on phylogenetic analyses of the viral RNA-dependent RNA polymerase (RdRp), LysV belongs to the Iflaviridae family in the order of the Picornavirales, with the closest known relatives all being parasitoid wasp-infecting viruses. We developed an endpoint PCR and a more sensitive qPCR assay to screen for LysV in field samples and laboratory lines. These screens verified the occurrence of LysV in wild parasitoids and identified the likely wild-source population for lab infections in Western Switzerland. Three viral haplotypes could be distinguished in wild populations, of which two were found in the laboratory. Both vertical and horizontal transmission of LysV were demonstrated experimentally, and repeated sampling of laboratory populations suggests that the virus can form persistent infections without obvious symptoms in infected wasps.

Wastewater treatment plant (WWTP) effluents release not only chemical constituents in watersheds, but also contain microorganisms. Thus, an understanding of what microorganisms are released and how they change microbial communities within natural streams is needed. To characterize the community shifts in streams receiving WWTP effluent, we sampled water-column microorganisms from upstream, downstream, and the effluent of WWTPs located on 23 headwater streams in which no other effluent was released upstream. We characterized the bacterial community by sequencing the V3-V4 region of the 16S rRNA gene. We hypothesized that the downstream community profile would be a hydraulic mixture between the two sources (i.e., upstream and effluent). In ordination analyses, the downstream bacterial community profile was a mixture between the upstream and effluent. For 14 of the sites, the main contribution (>50%) to the downstream community originated from bacteria in the WWTP effluent and significant shifts in relative abundance of specific sequence variants were detected. These shifts in sequence variants may serve as general bioindicators of wastewater-effluent influenced streams, with a human-gut related Ruminococcus genus displaying the highest shift (30-fold higher abundances downstream). However, not all taxa composition changes were predicted based on hydraulic mixing alone. Specifically, the decrease of Cyanobacteria/Chloroplast reads was not adequately described by hydraulic mixing. The potential alteration of stream microbial communities via a high inflow of human-gut related bacteria and a decrease in autotrophic functional groups resulting from WWTP effluent creates the potential for general shifts in stream ecosystem function.

1. Climate change has the potential to shape the future of infectious diseases, both directly and indirectly. In aquatic systems, for example, elevated temperatures can modulate the infectivity of waterborne parasites and affect the immune response of zooplanktonic hosts. Moreover, lake warming causes shifts in the communities of primary producers towards cyanobacterial dominance, thus lowering the quality of zooplankton diet. This may further affect host fitness, resulting in suboptimal resources available for parasite growth.
2. Previous experimental studies have demonstrated the respective effects of temperature and host diet on infection outcomes, using the zooplankter Daphnia and its microparasites as model systems. Although cyanobacteria blooms and heat waves are concurrent events in nature, few attempts have been made to combine both stressors in experimental settings.
3. Here, we raised the zooplankter Daphnia (two genotypes) under a full factorial design with varying levels of temperature (the standard 19°C and elevated 23°C), food quality (Scenedesmus obliquus as high-quality green algae, Microcystis aeruginosa and Planktothrix agardhii as low-quality cyanobacteria) and exposed them to the parasitic yeast Metschnikowia bicuspidata. We recorded life history parameters of the host as well as parasite traits related to transmission.
4. The combination of low-quality cyanobacterial diets and elevated temperature resulted in additive detrimental effects on host fecundity. Low-quality diets reduced parasite output, while temperature effects were context dependent. Overall, we argue that the combined effects of elevated water temperature and poor-quality diets may decrease epidemics of a common fungal parasite under a climate change scenario.

Drawing insights from multiple disciplines is essential for finding integrative solutions that are required to tackle complex environmental problems. Human activities are causing unprecedented influence on global ecosystems, culminating in the loss of species and fundamental changes in the selective environments of organisms across the tree of life. Our collective understanding about biological evolution can help identify and mitigate many of the environmental problems in the Anthropocene. To this end, we propose a stronger integration of environmental sciences with evolutionary biology.

Many microbial symbionts have multiple phenotypic consequences for their animal hosts. However, the ways in which different symbiont-mediated phenotypes combine to affect fitness are not well understood. We investigated whether there are correlations between different symbiont-mediated phenotypes. We used the symbiont Spiroplasma, a striking example of a bacterial symbiont conferring diverse phenotypes on insect hosts. We took 11 strains of Spiroplasma infecting pea aphids (Acyrthosiphon pisum) and assessed their ability to provide protection against the fungal pathogen Pandora neoaphidis and the parasitoids Aphidius ervi and Praon volucre. We also assessed effects on male offspring production for five of the Spiroplasma strains. All but one of the Spiroplasma strains provided very strong protection against the parasitoid P. volucre. As previously reported, variable protection against P. neoaphidis and A. ervi was also present; male-killing was likewise a variable phenotype. We find no evidence of any correlation, positive or negative, between the different phenotypes, nor was there any evidence of an effect of symbiont phylogeny on protective phenotype. We conclude that multiple symbiont-mediated phenotypes can evolve independently from one another without trade-offs between them.

Abiotic stress is a major force of selection that organisms are constantly facing. While the evolutionary effects of various stressors have been broadly studied, it is only more recently that the relevance of interactions between evolution and underlying ecological conditions, that is, eco‐evolutionary feedbacks, have been highlighted. Here, we experimentally investigated how populations adapt to pH‐stress under high population densities. Using the protist species Tetrahymena thermophila, we studied how four different genotypes evolved in response to stressfully low pH conditions and high population densities. We found that genotypes underwent evolutionary changes, some shifting up and others shifting down their intrinsic rates of increase (r₀). Overall, evolution at low pH led to the convergence of r₀ and intraspecific competitive ability (α) across the four genotypes. Given the strong correlation between r₀ and α, we argue that this convergence was a consequence of selection for increased density‐dependent fitness at low pH under the experienced high density conditions. Increased density‐dependent fitness was either attained through increase in r₀, or decrease of α, depending on the genetic background. In conclusion, we show that demography can influence the direction of evolution under abiotic stress.

At species' range edges, individuals often face novel environmental conditions that may limit range expansion until populations adapt. The potential to adapt depends on genetic variation upon which selection can act. However, populations at species' range edges are often genetically depauperate. One mechanism increasing genetic variation is reshuffling existing variation through sex. Sex, however, can potentially limit adaptation by breaking up existing beneficial allele combinations (recombination load). The gene swamping hypothesis predicts this is specifically the case when populations expand along an abiotic gradient and asymmetric dispersal leads to numerous maladapted dispersers from the range core swamping the range edge. We used the ciliate Tetrahymena thermophila as a model for testing the gene swamping hypothesis. We performed replicated range expansions in landscapes with or without a pH-gradient, while simultaneously manipulating the occurrence of gene flow and sexual versus asexual reproduction. We show that sex accelerated evolution of local adaptation in the absence of gene flow, but hindered it in the presence of gene flow. However, sex affected adaptation independently of the pH-gradient, indicating that both abiotic gradients and the biotic gradient in population density lead to gene swamping. Overall, our results show that gene swamping alters adaptation in life-history strategies.

Environmental DNA (eDNA) metabarcoding is raising expectations for biomonitoring of organisms that have hitherto been neglected. To bypass current limitations in taxonomic assignments due to incomplete or erroneous reference databases, taxonomy-free approaches are proposed for biomonitoring at the level of operational taxonomic units (OTUs). This is challenging, because OTUs cannot be annotated and directly compared against classically derived taxonomic data. The application of good stringency treatments to infer the validity of OTUs and clear understanding of the consequences of such treatments is especially relevant for biodiversity assessments. We investigated how common practices of stringency filtering affect eDNA diversity estimates in the statistical framework of Hill numbers. We collected water eDNA samples at 61 sites across a 740-km² river catchment, reflecting a spatially realistic scenario in biomonitoring. After bioinformatic processing of the data, we studied how different stringency treatments affect conclusions with respect to biodiversity at the catchment and site levels. The applied stringency treatments were based on the consistent appearance of OTUs across filter replicates, a relative abundance cut-off and rarefaction. We detected large differences in diversity estimates when accounting for presence/absence only, such that detected diversity at the catchment scale differed by an order of magnitude between the treatments. These differences disappeared when using stringency treatments with increasing weighting of the OTU abundances. Our study demonstrated the usefulness of Hill numbers for biodiversity analyses and comparisons of eDNA data sets that strongly differ in diversity. We recommend best practice for data stringency filtering for biomonitoring using eDNA.

In the current era of the Anthropocene, biodiversity is facing a devastating decline with especially severe e ects on freshwater systems due to human induced habitat degradation such as pollution or introduction of invasive species. Understanding the state but also change of biodiversity in a timely manner is thereby needed to gain the necessary information upon which policy and stakeholder actions can be implemented. Metabarcoding of environmental DNA (eDNA) has been proposed as a game changer by offering the possibility to acquire such biodiversity data at an unprecedented spatial and taxonomic resolution. [...]

Current high-input and high-output food systems have many negative consequences for producers, consumers, and natural environments worldwide. Projections based on the increasing wealth of low- and middle-income countries suggest that meat consumption will continue to grow, which will only increase pressure on the environment. It remains unclear how to develop a sustainable food system that is beneficial to all actors and contributes to a global system capable of feeding 9-10 billion people by 2050.

More than one‐third of the world's rivers cease to flow and go dry on a periodic basis—so‐called intermittent rivers. The frequency and duration of flow intermittency in running waters are increasing due to climate change and water demands for human use. Intermittency effects on stream biodiversity and ecosystem functioning are dramatic and are expected to become increasingly prevalent in alpine landscapes in the near future. This project used modified field sensors to measure flow intermittency, temperature, and water origin (groundwater, precipitation, glacier) at high spatio‐temporal resolution throughout an alpine fluvial network (Val Roseg, Switzerland). We continuously recorded water presence in 30 tributary streams and validated sensor performance with field‐collected measures. Three different flow regimes were observed in the network, including periodically intermittent, seasonally intermittent, and permanently flowing streams. Twenty‐four streams (80% of recorded streams) dried at least once during the sampling period. Principal components analysis along with generalized additive models showed alpine streams with low average temperature and high conductivity (groundwater‐fed) were prone to permanent flow, whereas streams with higher average temperature and low conductivity (glacier‐fed) typically had intermittent flow. The field sensors proved precise for simultaneously measuring flow intermittency, temperature, and water origin at high resolution throughout the river network. Overall, this approach provides an effective way to develop eco‐hydrological models that examine the effects of flow intermittency on biodiversity and ecosystem functioning in riverine networks.

Coordinated distributed experiments (CDEs) enable the study of large-scale ecological patterns in geographically dispersed areas, while simultaneously providing broad academic and personal benefits for the participants. However, the effective involvement of early-career researchers (ECRs) presents major challenges. Here, we analyze the benefits and challenges of the first CDE exclusively led and conducted by ECRs (i.e. ECR-CDE), which sets a baseline for similar CDEs, and we provide recommendations for successful CDE execution. ECR-CDEs achieve most of the outcomes identified in conventional CDEs as well as extensive benefits for the young cohort of researchers, including: (i) receiving scientific credit, (ii) peer-training in new concepts and methods, (iii) developing leadership and communication skills, (iv) promoting a peer network among ECRs, and (v) building on individual engagement and independence. We also discuss the challenges of ECR-CDEs, which are mainly derived from the lack of independence and instability of the participants, and we suggest mechanisms to address them, such as resource re-allocation and communication strategies. We conclude that ECR-CDEs can be a relevant tool to empower ECRs across disciplines by fostering their training, networking and personal well-being.

Das Biomonitoring aquatischer Lebensräume wird derzeit durch Verfahren, die auf Umwelt-DNA (eDNA) basieren, verändert. Diese neuen Instrumente überwinden gewisse Beschränkungen herkömmlicher Biomonitoringmethoden und erlauben eine nichtinvasive Probenahme, eine breite taxonomische Auflösung, eine hohe Sensitivität und die Möglichkeit, Prozesse zu automatisieren. Allerdings stellen die komplett neue Herangehensweise und die rasche Entwicklung der neuen Technologie Herausforderungen für ihre Einführung in die Praxis dar. In dieser Publikation werden die Grundsätze der eDNA-Technologie erläutert und die Vorteile und Beschränkungen vorgestellt. Es werden mögliche Anwendungen von eDNA-Tools für das Monitoring und die Bewertung aquatischer Ökosysteme aufgezeigt und detaillierte Protokolle und bewährte Praktiken für die Verarbeitung von eDNA-Proben vorgestellt.

Aquatic biomonitoring is currently transformed by environmental DNA (eDNA) based approaches. These new tools overcome some limitations of traditional biomonitoring and allow non-invasive sampling, broad taxonomic coverage, high sensitivity, and the possibility to automation. However, the disruptive character and rapid developments of the new technology challenge its implementation. This publication explains the principles of the eDNA technology and presents its advantages and limitations. It shows possible applications of eDNA tools in monitoring and assessment of aquatic ecosystems, and provides detailed protocols and best practices for processing eDNA samples.

Aquatic biomonitoring is currently transformed by environmental DNA (eDNA) based approaches. These new tools overcome some limitations of traditional biomonitoring and allow non-invasive sampling, broad taxonomic coverage, high sensitivity, and the possibility to automation. However, the disruptive character and rapid developments of the new technology challenge its implementation. This publication explains the principles of the eDNA technology and presents its advantages and limitations. It shows possible applications of eDNA tools in monitoring and assessment of aquatic ecosystems, and provides detailed protocols and best practices for processing eDNA samples.

Das Biomonitoring aquatischer Lebensräume wird derzeit durch Verfahren, die auf Umwelt-DNA (eDNA) basieren, verändert. Diese neuen Instrumente überwinden gewisse Beschränkungen herkömmlicher Biomonitoringmethoden und erlauben eine nichtinva-sive Probenahme, eine breite taxonomische Auflösung, eine hohe Sensitivität und die Möglichkeit, Prozesse zu automatisieren. Allerdings stellen die komplett neue Heran-gehensweise und die rasche Entwicklung der neuen Technologie Herausforderungen für ihre Einführung in die Praxis dar. In dieser Publikation werden die Grundsätze der eDNA-Technologie erläutert und die Vorteile und Beschränkungen vorgestellt. Es werden mögliche Anwendungen von eDNA-Tools für das Monitoring und die Bewertung aqua-tischer Ökosysteme aufgezeigt und detaillierte Protokolle und bewährte Praktiken für die Verarbeitung von eDNA-Proben vorgestellt.

The last decade brought a spectacular development of so-called environmental (e)DNA studies. In general, “environmental DNA” is defined as DNA isolated from environmental samples, in contrast to genomic DNA that is extracted directly from specimens. However, the variety of different sources of eDNA and the range of taxonomic groups that are targeted by eDNA studies is large, which has led to some discussion about the breadth of the eDNA concept. In particular, there is a recent trend to restrict the use of the term “eDNA” to the DNA of macro-organisms, which are not physically present in environmental samples. In this paper, we argue that such a distinction may not be ideal, because the eDNA signal can come from organisms across the whole tree of life. Consequently, we advocate that the term “eDNA” should be used in its generic sense, as originally defined, encompassing the DNA of all organisms present in environmental samples, including microbial, meiofaunal and macrobial taxa. We first suggest specifying the environmental origin of the DNA sample, such as water eDNA, sediment eDNA or soil eDNA. A second specification would then define the taxonomic group targeted through polymerase chain reaction amplification, such as fish eDNA, invertebrate eDNA and bacterial eDNA. This terminology does also not require assumptions about the specific state of the DNA sampled (intracellular or extracellular). We hope that such terminology will help better define the scope of eDNA studies, especially for environmental managers, who use them as reference in routine biomonitoring and bioassessment.

Les approches fondées sur l’ADN environnemental (ADNe) sont en passe de transformer la biosurveillance aquatique. Ces nouveaux outils permettent d’outrepasser les limites de la surveillance biologique traditionnelle : ils permettent d’effectuer un échantillonnage non invasif, de couvrir un large éventail taxonomique et offrent une sensibilité élevée ainsi que des possibilités d’automatisation. Cependant, le caractère révolutionnaire et les développements rapides de cette nouvelle technologie entravent sa mise en oeuvre. La présente publication explique les principes des méthodes ADNe, en présente les avantages et les limites et formule des suggestions concernant les standards et les pratiques de routine. En outre, elle montre les utilisations possibles des outils fondés sur l’ADNe dans la surveillance et l’évaluation des écosystèmes aquatiques, expose des études de cas spécifiques et propose des protocoles détaillés ainsi que des exemples de bonnes pratiques pour le traitement des échantillons d’ADNe.

Aquatic biomonitoring is currently transformed by environmental DNA (eDNA) based approaches. These new tools overcome some limitations of traditional biomonitoring and allow non-invasive sampling, broad taxonomic coverage, high sensitivity, and the possibility to automation. However, the disruptive character and rapid developments of the new technology challenge its implementation. This publication explains the principles of the eDNA technology and presents its advantages and limitations. It shows possible applications of eDNA tools in monitoring and assessment of aquatic ecosystems, and provides detailed protocols and best practices for processing eDNA samples.

The increasing urbanization process is hypothesized to drastically alter (semi-)natural environments with a concomitant major decline in species abundance and diversity. Yet, studies on this effect of urbanization, and the spatial scale at which it acts, are at present inconclusive due to the large heterogeneity in taxonomic groups and spatial scales at which this relationship has been investigated among studies. Comprehensive studies analysing this relationship across multiple animal groups and at multiple spatial scales are rare, hampering the assessment of how biodiversity generally responds to urbanization. We studied aquatic (cladocerans), limno-terrestrial (bdelloid rotifers) and terrestrial (butterflies, ground beetles, ground- and web spiders, macro-moths, orthopterans and snails) invertebrate groups using a hierarchical spatial design, wherein three local-scale (200 m × 200 m) urbanization levels were repeatedly sampled across three landscape-scale (3 km × 3 km) urbanization levels. We tested for local and landscape urbanization effects on abundance and species richness of each group, whereby total richness was partitioned into the average richness of local communities and the richness due to variation among local communities. Abundances of the terrestrial active dispersers declined in response to local urbanization, with reductions up to 85% for butterflies, while passive dispersers did not show any clear trend. Species richness also declined with increasing levels of urbanization, but responses were highly heterogeneous among the different groups with respect to the richness component and the spatial scale at which urbanization impacts richness. Depending on the group, species richness declined due to biotic homogenization and/or local species loss. This resulted in an overall decrease in total richness across groups in urban areas. These results provide strong support to the general negative impact of urbanization on abundance and species richness within habitat patches and highlight the importance of considering multiple spatial scales and taxa to assess the impacts of urbanization on biodiversity.

Globally, lake surface water temperatures have warmed rapidly relative to air temperatures, but changes in deepwater temperatures and vertical thermal structure are still largely unknown. We have compiled the most comprehensive data set to date of long-term (1970–2009) summertime vertical temperature profiles in lakes across the world to examine trends and drivers of whole-lake vertical thermal structure. We found significant increases in surface water temperatures across lakes at an average rate of + 0.37 °C decade⁻¹, comparable to changes reported previously for other lakes, and similarly consistent trends of increasing water column stability (+ 0.08 kg m⁻³ decade⁻¹). In contrast, however, deepwater temperature trends showed little change on average (+ 0.06 °C decade⁻¹), but had high variability across lakes, with trends in individual lakes ranging from − 0.68 °C decade⁻¹ to + 0.65 °C decade⁻¹. The variability in deepwater temperature trends was not explained by trends in either surface water temperatures or thermal stability within lakes, and only 8.4% was explained by lake thermal region or local lake characteristics in a random forest analysis. These findings suggest that external drivers beyond our tested lake characteristics are important in explaining long-term trends in thermal structure, such as local to regional climate patterns or additional external anthropogenic influences.

Biomass distribution among size classes follows a power law where the Log-abundance of taxa scales to Log-size with a slope that responds to environmental abiotic and biotic conditions. The interactions between ecological mechanisms controlling the slope of locally realized size-abundance relationships (SAR) are however not well understood. Here we tested how warming, nutrient levels, and grazing affect the slope of phytoplankton community SARs in decadal time-series from eight Swiss lakes of the peri-alpine region, which underwent environmental forcing due to climate change and oligotrophication. We expected rising temperature to have a negative effect on slope (favoring small phytoplankton), and increasing nutrient levels and grazing pressure to have a positive effect (benefiting large phytoplankton). Using a random forest approach to extract robust patterns from the noisy data, we found that the effects of temperature (direct and indirect through water column stability), nutrient availability (phosphorus and total biomass), and large herbivore (copepods and daphnids) grazing and selectivity on slope were non-linear and interactive. Increasing water temperature or total grazing pressure, and decreasing phosphorus levels, had a positive effect on slope (favoring large phytoplankton, which are predominantly mixotrophic in the lake dataset). Our results therefore showed patterns that were opposite to the expected long-term effects of temperature and nutrient levels, and support a paradigm in which (i) small phototrophic phytoplankton appear to be favored under high nutrients levels, low temperature and low grazing, and (ii) large mixotrophic algae are favored under oligotrophic conditions when temperature and grazing pressure are high. The effects of temperature were stronger under nutrient limitation, and the effects of nutrients and grazing were stronger at high temperature. Our study shows that the phytoplankton local SARs in lakes respond to both the independent and the interactive effects of resources, grazing and water temperature in a complex, unexpected way, and observations from long-term studies can deviate significantly from general theoretical expectations.

Organisms living in hot, arid environments face important risks associated with hyperthermia and dehydration which are expected to become more severe with climate change. To mitigate these risks, individuals often modify behaviour, e.g. reducing activity and seeking shade. These behavioural modifications may affect interactions between individuals, with consequences for the social structure of groups. We tested whether the social structure of cooperative groups of sociable weavers Philetairus socius varied with environmental temperature. We recorded the nature and frequency of interactions at feeders positioned beneath three sociable weaver colonies (n = 49 identified birds) in the Kalahari Desert with respect to environmental temperatures over a 30-day period. Using random forest models, we examined whether thermal conditions predicted variation in social network structure. We also conducted focal observations of individual weavers to assess functional links between temperature, intensity of heat dissipation behaviour (panting) and immediate effects on social behaviour. Our results suggest that the social structure of weaver colonies becomes less cohesive and more fragmented at extreme and variable environmental temperatures. These changes in network structure appear to be linked with individuals’ heat dissipation behaviour: extreme and variable temperatures were associated with increased panting, which was significantly correlated with an immediate reduction in the frequency of association. Collectively, our results indicate that interactions within groups could be disturbed by environmental temperature variation and extremes. Changing temperature regimes could therefore affect the functioning of animal societies by altering social networks.

Beaver populations are increasing throughout Europe and especially in Switzerland. Beaver are major ecological engineers of fluvial systems, dramatically influencing river morphology, ecohydrology and, consequently, aquatic and terrestrial biota. This study compared macroinvertebrate assemblages and trophic structure at two beaver complexes with contrasting topography in Switzerland over an annual cycle. One complex (Marthalen) was in a low gradient open basin, whereas the other complex (Flaach) flowed through a higher gradient ravine-like basin. Both complexes were embedded in an overall agricultural landscape matrix. Water physico-chemistry differed between the two complexes with nitrogen, phosphorus, and DOC being higher at Marthalen than at Flaach. Both complexes showed strong seasonality in physico-chemistry, but retention of nutrients (N, P) was highest in summer and only at Marthalen. Both complexes also showed strong seasonality in macroinvertebrate assemblages, although assemblages differed substantially between complexes. At Marthalen, macroinvertebrate assemblages were predominantly lentic in character at 'pool' sites within the complex. At Flaach, lotic macroinvertebrate assemblages were common at most sites with some lentic taxa also being present. Dietary shifts based on carbon/nitrogen stable isotopes occurred in spring and summer among sites at both complexes (autochthonous resource use increasing over allochthonous resource use downstream), although being most pronounced at Marthalen. In contrast, similar resource use across sites occurred in winter within both complexes. Although beaver significantly influenced fluvial dynamics and macroinvertebrate assemblage structure at both complexes, this influence was most pronounced at Marthalen where beaver caused the system to become more wetland in character, e.g., via higher hydraulic residence time, than at Flaach. We conclude that topography can shape beaver effects on fluvial systems and resident biota.

There is increasing demand for sustainable pest management to reduce harmful effects of pesticides on the environment and human health. For pest aphids, biological control with parasitoid wasps provides a welcome alternative, particularly in greenhouses. However, aphids are frequently infected with the heritable bacterial endosymbiont Hamiltonella defensa, which increases resistance to parasitoids and thereby hampers biological control. Using the black bean aphid (Aphis fabae) and its main parasitoid Lysiphlebus fabarum, we tested whether prior adaptation of parasitoids can improve the control of symbiont‐protected pests. We had parasitoid lines adapted to two different strains of H. defensa by experimental evolution, as well as parasitoids evolved on H. defensa‐free aphids. We compared their ability to control caged aphid populations comprising 60% unprotected and 40% H. defensa‐protected aphids, with both H. defensa strains present in the populations. Parasitoids that were not adapted to H. defensa had virtually no effect on aphid population dynamics compared to parasitoid‐free controls, but one of the adapted lines and a mixture of both adapted lines controlled aphids successfully, strongly benefitting plant growth. Selection by parasitoids altered aphid population composition in a very specific manner. Aphid populations became dominated by H. defensa‐protected aphids in the presence of parasitoids, and each adapted parasitoid line selected for the H. defensa strain it was not adapted to. This study shows, for the first time, that prior adaptation of parasitoids improves biological control of symbiont‐protected pests, but the high specificity of parasitoid counter‐resistance may represent a challenge for its implementation.

Due to the growing amount of data from in-situ sensors in environmental monitoring, it becomes necessary to automatically detect anomalous data points. Nowadays, this is mainly performed using supervised machine learning models, which need a fully labelled data set for their training process. However, the process of labelling data is typically cumbersome and, as a result, a hindrance to the adoption of machine learning methods for automated anomaly detection. In this work, we propose to address this challenge by means of active learning. This method consists of querying the domain expert for the labels of only a selected subset of the full data set. We show that this reduces the time and costs associated to labelling while delivering the same or similar anomaly detection performances. Finally, we also show that machine learning models providing a nonlinear classification boundary are to be recommended for anomaly detection in complex environmental data sets.

Dispersal is an essential process in population and community dynamics, but is difficult to measure in the field. In freshwater ecosystems, information on biological traits related to organisms’ morphology, life history and behaviour provides useful dispersal proxies, but information remains scattered or unpublished for many taxa. We compiled information on multiple dispersal-related biological traits of European aquatic macroinvertebrates in a unique resource, the DISPERSE database. DISPERSE includes nine dispersal-related traits subdivided into 39 trait categories for 480 taxa, including Annelida, Mollusca, Platyhelminthes, and Arthropoda such as Crustacea and Insecta, generally at the genus level. Information within DISPERSE can be used to address fundamental research questions in metapopulation ecology, metacommunity ecology, macroecology and evolutionary ecology. Information on dispersal proxies can be applied to improve predictions of ecological responses to global change, and to inform improvements to biomonitoring, conservation and management strategies. The diverse sources used in DISPERSE complement existing trait databases by providing new information on dispersal traits, most of which would not otherwise be accessible to the scientific community.

Genetically specific interactions between hosts and parasites can lead to coevolutionary fluctuations in their genotype frequencies over time. Such fluctuating selection dynamics are, however, expected to occur only under specific circumstances (e.g., high fitness costs of infection to the hosts). The outcomes of host–parasite interactions are typically affected by environmental/ecological factors, which could modify coevolutionary dynamics. For instance, individual hosts are often infected with more than one parasite species and interactions between them can alter host and parasite performance. We examined the potential effects of coinfections by genetically specific (i.e., coevolving) and nonspecific (i.e., generalist) parasite species on fluctuating selection dynamics using numerical simulations. We modeled coevolution (a) when hosts are exposed to a single parasite species that must genetically match the host to infect, (b) when hosts are also exposed to a generalist parasite that increases fitness costs to the hosts, and (c) when coinfecting parasites compete for the shared host resources. Our results show that coinfections can enhance fluctuating selection dynamics when they increase fitness costs to the hosts. Under resource competition, coinfections can either enhance or suppress fluctuating selection dynamics, depending on the characteristics (i.e., fecundity, fitness costs induced to the hosts) of the interacting parasites.

Emergent diseases are contributing to the decline of various freshwater species already facing multiple threats of anthropogenic origin, such as habitat degradation, climate change and species introductions. One of the most ecologically important diseases is the crayfish plague, caused by the oomycete Aphanomyces astaci, responsible for widespread population collapses of native European freshwater crayfish species. The chytrid fungus Batrachochytrium dendrobatidis is another highly problematic pathogen and major contributor of amphibian declines worldwide, its spread being promoted by animal trade. Saprolegnia parasitica, closely related to A. astaci and causal agent of Saprolegniosis, widely occurs in freshwater habitats and can cause high mortality outbreaks in fish. Proliferative kidney disease (PKD), caused by the myxozoan Tetracapsuloides bryosalmonae, severely impacts wild salmonid stocks and trout farms. Due to its temperature-dependent development, climate change is expected to increase the disease's impact on host populations. [...]

Viele Süsswasserarten werden, nebst anthropogenen Beeinflussungen, wie Verschlechterung des Lebensraumes, Klimawandel und invasive Arteinführungen, durch neuaufkommende Krankheiten bedroht. Eine der gefährlichsten Krankheiten ist die Krebspest, welche vom Eipilz Aphanomyces astaci verursacht wird und den Kollaps vieler europäischer Flusskrebspopulationen herbeigeführt hat. Der Chytridpilz Batrachochytrium dendrobatidis ist ein weiterer problematischer Krankheitserreger, deren Verbreitung durch den internationalen Tierhandel begünstigt wird und mitverantwortlich ist für Rückgänge von Amphibienpopulationen weltweit. Die mit A. astaci nah verwandte Saprolegnia parasitica, Verursacherin von Saprolegniose, kommt in fast allen Süsswassergewässern vor und kann hohe Mortalitäten in Fischbeständen verursachen. Die Proliferative Nierenkrankheit (PKD), mit dem Myxozoten Tetracapsuloides bryosalmonae als Erreger, hat grosse negative Auswirkungen auf sowohl wilde Salmonide als auch in Fischzuchten. Durch ihre temperaturbedingte Entwicklung wird eine weitere Ausbreitung durch die Klimaerwärmung erwartet. [...]

Monitoring the occurrence and density of parasites and pathogens can identify high infection-risk areas and facilitates disease control and eradication measures. Environmental DNA (eDNA) techniques are increasingly used for pathogen detection due to their relative ease of application. Since many factors affect the reliability and efficacy of eDNA-based detection, rigorous validation and assessment of method limitations is a crucial first step. We evaluated an eDNA detection method using in situ filtration of large-volume water samples, developed to detect and quantify aquatic wildlife parasites by quantitative PCR (qPCR). We assessed method reliability using Batrachochytrium dendrobatidis, a pathogenic fungus of amphibians and the myxozoan Tetracapsuloides bryosalmonae, causative agent of salmonid proliferative kidney disease, in a controlled experimental setup. Different amounts of parasite spores were added to tanks containing either clean tap water or water from a semi-natural mesocosm community. Overall detection rates were higher than 80%, but detection was not consistent among replicate samples. Within-tank variation in detection emphasises the need for increased site-level replication when dealing with parasites and pathogens. Estimated parasite DNA concentrations in water samples were highly variable, and a significant increase with higher spore concentrations was observed only for B. dendrobatidis. Despite evidence for PCR inhibition in DNA extractions from mesocosm water samples, the type of water did not affect detection rates significantly. Direct spiking controls revealed that the filtration step reduced detection sensitivity. Our study identifies sensitive quantification and sufficient replication as major remaining challenges for the eDNA-based methods for detection of parasites in water.

Flow intermittency occurs naturally in alpine streams. However, changing rainfall patterns and glacier retreat are predicted to increase the occurrence of flow intermittency in alpine catchments, with largely unknown effects on ecosystem structure and function. We conducted a flow manipulation experiment within a headwater stream of Val Roseg, a glacierized alpine catchment, to determine the effects of increased flow intermittency on aquatic macroinvertebrates, periphyton, benthic organic matter, and trophic structure. Compared to an adjacent reference channel, an increase in flow intermittency reduced macroinvertebrate density, taxa richness, and the proportion of rheophilic taxa. Density and richness remained low in the manipulated channel after resumption of natural flow. Flow intermittency did not affect organic matter standing stocks, but increased assimilation of periphyton by aquatic macroinvertebrates. Predation on aquatic invertebrates by riparian spiders also increased. We attribute many of these patterns to the timing of drying, which likely excluded summer-growing cohorts of rheophilic, aerial dispersers. This study suggests that reductions in summer glacial melt and rainfall events might increase flow intermittency and lead to fundamental changes in diversity and function of alpine fluvial networks.

Sexually selected ornaments range from highly dynamic traits to those that are fixed during development and relatively static throughout sexual maturity. Ornaments along this continuum differ in the information they provide about the qualities of potential mates, such as their parasite resistance. Dynamic ornaments enable real-time assessment of the bearer's condition: they can reflect an individual's current infection status, or they can reflect resistance to recent infections. Static ornaments, however, are not affected by recent infection but may instead indicate an individual's genetically determined resistance, even in the absence of infection. Given the typically aggregated distribution of parasites among hosts, infection is unlikely to affect the ornaments of the vast majority of individuals in a population: static ornaments may therefore be the more reliable indicators of parasite resistance. To test this hypothesis, we quantified the ornaments of male guppies (Poecilia reticulata) before experimentally infecting them with Gyrodactylus turnbulli. Males with more left-right symmetrical black coloration and those with larger areas of orange coloration, both static ornaments, were more resistant. However, males with more saturated orange coloration, a dynamic ornament, were less resistant. Female guppies often prefer symmetrical males with larger orange ornaments, suggesting that parasite-mediated natural and sexual selection act in concert on these traits.

In many regions across the globe, extreme weather events such as storms have increased in frequency, intensity, and duration due to climate change. Ecological theory predicts that such extreme events should have large impacts on ecosystem structure and function. High winds and precipitation associated with storms can affect lakes via short-term runoff events from watersheds and physical mixing of the water column. In addition, lakes connected to rivers and streams will also experience flushing due to high flow rates. Although we have a well-developed understanding of how wind and precipitation events can alter lake physical processes and some aspects of biogeochemical cycling, our mechanistic understanding of the emergent responses of phytoplankton communities is poor. Here we provide a comprehensive synthesis that identifies how storms interact with lake and watershed attributes and their antecedent conditions to generate changes in lake physical and chemical environments. Such changes can restructure phytoplankton communities and their dynamics, as well as result in altered ecological function (e.g., carbon, nutrient and energy cycling) in the short- and long-term. We summarize the current understanding of storm-induced phytoplankton dynamics, identify knowledge gaps with a systematic review of the literature, and suggest future research directions across a gradient of lake types and environmental conditions.

Proliferative kidney disease (PKD) is an emerging disease of salmonids, which is exacerbating with increasing water temperature. Its causative agent, the myxozoan parasite Tetracapsuloides bryosalmonae , exploits freshwater bryozoans as primary hosts and salmonids as intermediate hosts. Our experiments showed that the manipulation of exposure concentrations of infective malacospores had relatively minor impacts for the disease outcomes in the fish host. In this study, brown trout (Salmo trutta ) were exposed to three different exposure concentrations of T. bryosalmonae malacospores: (a) a single low parasite concentration (LC), (b) a single high parasite concentration (HC) and (c) three times a low concentration (repeat exposure, RE). Parasite dynamics in the fish host and release of fish malacospores were quantified and fish kidney histopathology was evaluated to determine PKD pathogenesis. Infection prevalence was always lower in the LC group than in the other groups over the course of the study. While the parasite proliferation phase was slower in the LC group, the maximum parasite burden did not differ significantly amongst treatments. The onset of fish malacospore release (day 45 post‐exposure), indicated by detection of T. bryosalmonae DNA in the tank water, occurred at the same time point for all groups. Reduced intensity of kidney pathological development was observed in the LC treatment indicating lower disease severity. While the LC treatment resulted in reduced outcomes across several infection parameters (infection prevalence, parasite proliferation, total fish malacospores released), the overall differences were small. The RE and HC treatment outcomes were for most parameters comparable. Our results suggest that repeated exposure, as is likely to occur in the wild during the summer months, might play a more important role in the dynamics of PKD as an emerging infectious disease than the actual concentration of spores.

River reaches downstream of dams with constant residual discharge often lack sediment supply and periodic high flows due to dam sediment retention and flow regulation, respectively. To test a novel multi-deposit methodology for defining environmental flows for activating the dynamics of the river morphology downstream of dams, a flood was released from Rossens Dam in Switzerland. This event was combined for the first time with a multi-deposit configuration of sediment replenishment consisting of four artificial deposits allocated as alternate bars along the riverbanks as a restoration measure. To validate the sediment transport behaviour observed in laboratory tests, stones were equipped with radiofrequency identification (RFID) passive integrated transponder (PIT) tags, a fixed antenna was installed at the river bed and a mobile antenna was used to enable the investigation of the erosion, transport and deposition of replenished sediments. The duration of the erosion period was determined for the tracked stones, and average transport velocities were found to be on the order of 10^-3 m/s. To estimate the erosion efficiency of the flood, defined as the eroded tagged stones compared with the released water volume, the hydrograph was divided into different periods: rising limb, constant peak discharge, decreasing limb. During the rising limb of the flood, which lasted for 20% of the total flood duration, more than 40% of the PIT tags were transported. The defined erosion efficiency is a measure to support the hydrographic design of artificial flood releases from dams. The deposition of tagged stones resulted in a repeating cluster formation, as expected from previous laboratory experiments, creating an increase in hydraulic habitat diversity. Comparison of the results obtained in the field and from laboratory experiments confirmed the robustness of the multi-deposit sediment replenishment method. Combined with the knowledge gained on the erosion efficiency, these results could motivate further applications and research into multi-deposit sediment replenishment techniques as a habitat-oriented river restoration measure.

Environmental change can alter species' abundances within communities consistently; for example, increasing all abundances by the same percentage, or more idiosyncratically. Here, we show how comparing effects of temperature on species grown in isolation and when grown together helps our understanding of how ecological communities more generally respond to environmental change. In particular, we find that the shape of the feasibility domain (the parameter space of carrying capacities compatible with positive species' abundances) helps to explain the composition of experimental microbial communities under changing environmental conditions. First, we introduce a measure to quantify the asymmetry of a community’s feasibility domain using the column vectors of the corresponding interaction matrix. These column vectors describe the effects each species has on all other species in the community (hereafter referred to as species' multidimensional effects). We show that as the asymmetry of the feasibility domain increases the relationship between species' abundance when grown together and when grown in isolation weakens. We then show that microbial communities experiencing different temperature environments exhibit patterns consistent with this theory. Specifically, communities at warmer temperatures show relatively more asymmetry; thus, the idiosyncrasy of responses is higher compared with that in communities at cooler temperatures. These results suggest that while species’ interactions are typically defined at the pairwise level, multispecies dynamics can be better understood by focusing on the effects of these interactions at the community level.

The majority of variation in six traits critical to the growth, survival and reproduction of plant species is thought to be organised along just two dimensions, corresponding to strategies of plant size and resource acquisition. However, it is unknown whether global plant trait relationships extend to climatic extremes, and if these interspecific relationships are confounded by trait variation within species. We test whether trait relationships extend to the cold extremes of life on Earth using the largest database of tundra plant traits yet compiled. We show that tundra plants demonstrate remarkably similar resource economic traits, but not size traits, compared to global distributions, and exhibit the same two dimensions of trait variation. Three quarters of trait variation occurs among species, mirroring global estimates of interspecific trait variation. Plant trait relationships are thus generalizable to the edge of global trait-space, informing prediction of plant community change in a warming world.

Many studies document genetic and phenotypic trait changes of species in response to climate change, or document how evolution of individual species can impact population abundances and community composition. An integration of population and community‐level responses requires, however, a multiple species approach. Here we quantify among‐ and within‐species differences in thermal tolerance and life‐history traits in three co‐occurring Daphnia species upon exposure to a naturally occurring heat wave. Populations of randomly isolated clones of Daphnia magna, Daphnia pulicaria, and Daphnia galeata from the same pond were exposed to a natural heat wave in outdoor mesocosms. We subsequently conducted a common garden experiment in the laboratory using clonal lineages isolated at the end of the mesocosm selection experiment, at two rearing temperatures, measuring thermal tolerance and life‐history traits. We find pronounced plasticity responses to higher rearing thermal regime in each study species. We observe only few significant microevolutionary responses involving evolution of plasticity in D. pulicaria. Yet in terms of effect size, evolutionary trait change within species contributes more than 25% to total trait change in response to the heat wave for a majority of the trait × species combinations. The relative importance of intraspecific to interspecific variation varies widely among traits. Our results show that the relative importance of interspecific variation, phenotypic plasticity, and evolutionary trait change differs strongly depending on the set of species and traits studied. Taking into account this variation at different levels of biological organization is important to predict community‐wide responses to global change.

Ab 2020 wird für die Wirkungskontrolle von Fliessgewässerrevitalisierungen schweizweit ein einheitliches Gerüst vorgegeben, das aus zwei Elementen besteht - der Wirkungskontrolle STANDARD und der Wirkungskontrolle VERTIEFT. Die Ende 2019 erschienene Praxisdokumentation erklärt das konkrete Vorgehen und beschreibt 10 Indikator-Sets für die Erhebungen im Feld. Dank einheitlichen Erhebungen können zukünftig Erfahrungen aus unterschiedlichen Projekten und Projektkontexten einander gegenübergestellt werden. Der Schritt von der projektspezifischen Einzelfallbetrachtung zur projektübergreifenden Übersicht ermöglicht ein umfassenderes, allgemein gültigeres Verständnis der ablaufenden Prozesse sowie der Faktoren, die die Wirkung von Revitalisierungen hemmen oder fördern (z. B. revitalisierte Länge, Fragmentierung). Erkenntnisse aus der Wirkungskontrolle sollen in konkrete Handlungsempfehlungen übersetzt werden. Damit können zukünftige Revitalisierungen noch kosteneffektiver werden und einen wesentlichen Beitrag zur Erhaltung und zur Förderung der heimischen Biodiversität leisten.

Amphipods are a highly diverse group of aquatic invertebrates with >10,000 described species globally. About 20% of these are freshwater species, with half of them found in the West Palaearctic. Amphipods inhabit almost all freshwater ecosystems, including lakes, rivers, streams, as well as cave and groundwater systems, and can be the dominant macroinvertebrates in these habitats. They exhibit essential roles in the functioning of aquatic ecosystems, contributing to leaf litter breakdown and serving as important prey for fish. Furthermore, they are commonly used as indicator taxa for biomonitoring and in ecotoxicological studies. Many amphipod communities are currently undergoing rapid changes due to various drivers of global change, and some amphipod species are among the most successful nonnative invasive invertebrates.
Despite their ecological and economic significance, the knowledge on amphipods in Switzerland was hitherto limited, and until now no checklist, distribution maps, or broadscale estimates on genetic, functional, and morphological diversity of all amphipod species in Switzerland existed. All hitherto available literature on the ecology, faunistics, and taxonomy of amphipods in Central Europe is either outdated by many decades (Chevreux & Fage, 1925; Schellenberg, 1942), does not cover all species (Ginet, 1995; Eggers & Martens, 2001, Piscart & Bollache, 2012), or is only targeting neighboring countries (Vornatscher, 1965; Karaman, 1993; Eggers & Martens, 2001; Piscart & Bollache, 2012, Zettler & Zettler, 2017). This lack of appropriate baseline information on the ecology, distribution and faunistics of amphipods in Switzerland is a serious limitation for fundamental ecological research, impedes appropriate conservation strategies, and limits the use and application of amphipods as indicator taxa.

Alpine landscapes are being transformed through the rapid recession of glaciers, resulting in the development of numerous non-glacial headwater streams inhabited by a diverse assemblage of macroinvertebrates. We examined spatial patterns in biodiversity and rarity of macroinvertebrates in 41 non-glacial streams from five glacierized catchments in the Swiss Alps undergoing rapid glacial recession over the last decades. Water physico-chemistry and food resources (periphyton, benthic organic matter) varied widely among streams within each catchment, while no significant differences occurred among catchments. Variability in community composition was similar among streams within each catchment but differed among catchments, reflecting differences in catchment-scale species pools due to biogeographical context and season. Overall, 101 taxa from ca 33,000 individuals collected were identified in the streams with 7–33 taxa found in individual streams. Some 64% of the taxa comprised less than 5% of the total abundances at the streams (rare in abundance) with 78% of the taxa being represented by less than 5% of the most common taxon (Baetis sp.), whereas 47% of the taxa were found in less than 10% of the streams (rare in distribution). No taxon was found at all sites (maximum presence at 85% of the sites), while 15% of the taxa were found at 50% of the sites or more. However, analyzing the rank-abundance distribution showed that rarity was less prevalent than previously shown in other ecosystems. The results indicated that community assembly of alpine headwater streams is a complex interaction between environmental properties (habitat filtering), habitat stability coupled with dispersal (source sink dynamics), and time since deglaciation (island biogeography). Integrating these processes is essential towards understanding ongoing colonization events in headwater streams of alpine catchments as glaciers continue to recede.

Parasites can shape the structure and function of ecosystems by influencing both the density and traits of their hosts. Such changes in ecosystems are particularly likely when the host is a predator that mediates the dynamics of trophic cascades. Here, we experimentally tested how parasite load of a small predatory fish, the threespine stickleback, can affect the occurrence and strength of trophic cascades and ecosystem functioning. In a factorial mesocosm experiment, we manipulated the density of stickleback (low vs. high), and the level of parasite load (natural vs. reduced). In addition, we used two stickleback populations from different lineages: an eastern European lineage with a more pelagic phenotype (Lake Constance) and a western European lineage with a more benthic phenotype (Lake Geneva). We found that stickleback caused trophic cascades in the pelagic but not the benthic food chain. Evidence for pelagic trophic cascades was stronger in treatments where parasite load of stickleback was reduced with an antihelmintic medication, and where fish originated from Lake Constance (i.e., the more pelagic lineage). A structural equation model revealed that differences in stickleback lineage and parasite load were most likely to impact trophic cascades via changes in the composition, rather than overall biomass, of zooplankton communities. Overall, our results provide experimental evidence that parasites of predators can influence the cascading effects of fish on lower trophic levels with consequences on ecosystem functioning.

Intermittent rivers and ephemeral streams (IRES) encompass fluvial ecosystems that eventually stop flowing and run dry at some point in space and time. During the dry phase, channels of IRES consist mainly of dry riverbeds (DRBs), prevalent yet widely unexplored ecotones between dry and wet phases that can strongly influence the biogeochemistry of fluvial networks. DRBs are often overlooked because they do not strictly belong to either domain of soil or freshwater science. Due to this dual character of DRBs, we suggest that concepts and knowledge from soil science can be used to expand the understanding of IRES biogeochemistry. Based on this idea, we propose that DRBs can be conceptually understood as early stage soils exhibiting many similarities with soils through two main forces: i) time since last sediment transport event, and ii) the development status of stabilizing structures (e.g. soil crusts and/or vascular plants). Our analysis suggests that while DRBs and soils may differ in master physical attributes (e.g. soil horizons vs fluvial sedimentary facies), they become rapidly comparable in terms of microbial communities and biogeochemical processes. We further propose that drivers of DRBs biogeochemistry are similar to those of soils and, hence, concepts and methods used in soil science are transferable to DRBs research. Finally, our paper presents future research directions to advance the knowledge of DRBs and to understand their role in the biogeochemistry of intermittent fluvial networks.

The presence of a multitude of bioactive organic pollutants collectively classified as pharmaceuticals and personal care products (PPCPs) in freshwaters is of concern, considering that ecological assessments of their potential impacts on natural systems are still scarce. In this field experiment we tested whether a single pulse exposure to a mixture of 12 pharmaceuticals and personal care products, which are commonly found in European inland waters, can influence the size distributions of natural lake phytoplankton communities. Size is one of the most influential determinants of community structure and functioning, particularly in planktonic communities and food webs. Using an in-situ microcosm approach, phytoplankton communities in two lakes with different nutrient levels (mesotrophic and eutrophic) were exposed to a concentration gradient of the PPCPs mixture at five levels. We tested whether sub-lethal PPCPs doses affect the scaling of organisms' abundances with their size, and the slope of these size spectra, which describe changes in the abundances of small relative to large phytoplankton. Our results showed that a large proportion (approximately 80%) of the dataset followed a power-law distribution, thus suggesting evidence of scale invariance of abundances, as expected in steady state ecosystems. PPCPs were however found to induce significant changes in the size spectra and community structure of natural phytoplankton assemblages. The two highest treatment levels of PPCPs were associated with decreased abundance of the most dominant size class (nano-phytoplankton: 2–5 μm), leading to a flattening of the size spectra slope. These results suggest that a pulse exposure to PPCPs induce changes that potentially lead to unsteady ecosystem states and cascading effects in the aquatic food webs, by favoring larger non-edible algae at the expense of small edible species. We propose higher susceptibility due to higher surface to volume ratio in small species as the likely cause of these structural changes.

Freshwaters are increasingly exposed to complex mixtures of pharmaceutical and personal care products (PPCPs) from municipal wastewater, which are known to alter freshwater communities' structure and functioning. However, their interaction with other disturbances and whether their combined effects can impact ecological resilience (i.e., the ability of a system to tolerate disturbances without altering the system's original structure and processes) remain unexplored. Using in situ mesocosms in 2 lakes with different nutrient levels (mesotrophic and eutrophic), we assessed whether a pulse exposure to sublethal concentrations of 12 PPCPs affects the ecological resilience of natural phytoplankton communities that experienced an abrupt environmental change involving the destabilization of the water column through mixing. Such mixing events are predicted to increase as the effects of climate change unfold, leading to more frequent storms, which disrupt stratification in lakes and force communities to restructure. We assessed their combined effects on community metrics (biomass, species richness, and composition) and their relative resilience using 4 indicators (cross‐scale, within‐scale, aggregation length, and gap length), inferred from phytoplankton communities by discontinuity analysis. The mixing disturbance alone had negligible effects on the community metrics, but when combined with chemical contaminants significant changes were measured: reducing total biomass, species richness, and altered community composition of phytoplankton. Once these changes occurred, they persisted until the end of the experiment (day 20), when the communities’ structures from the 2 highest exposure levels diverged from the controls. The resilience indicators were not affected by PPCPs but differed significantly between lakes, with lower resilience found in the eutrophic lake. Thus, PPCPs can significantly alter community structures and reinforce mechanisms that maintain ecosystems in a "degraded state."

Aim: How do factors such as space, time, climate and other ecological drivers influence food web structure and dynamics? Collections of well‐studied food webs and replicate food webs from the same system that span biogeographical and ecological gradients now enable detailed, quantitative investigation of such questions and help integrate food web ecology and macroecology. Here, we integrate macroecology and food web ecology by focusing on how ecogeographical rules [the latitudinal diversity gradient (LDG), Bergmann's rule, the island rule and Rapoport's rule] are associated with the architecture of food webs.
Location: Global.
Time period: Current.
Major taxa studied: All taxa.
Methods: We discuss the implications of each ecogeographical rule for food webs, present predictions for how food web structure will vary with each rule, assess empirical support where available, and discuss how food webs may influence ecogeographical rules. Finally, we recommend systems and approaches for further advancing this research agenda.
Results: We derived testable predictions for some ecogeographical rules (e.g. LDG, Rapoport's rule), while for others (e.g., Bergmann's and island rules) it is less clear how we would expect food webs to change over macroecological scales. Based on the LDG, we found weak support for both positive and negative relationships between food chain length and latitude and for increased generality and linkage density at higher latitudes. Based on Rapoport's rule, we found support for the prediction that species turnover in food webs is inversely related to latitude.
Main conclusions: The macroecology of food webs goes beyond traditional approaches to biodiversity at macroecological scales by focusing on trophic interactions among species. The collection of food web data for different types of ecosystems across biogeographical gradients is key to advance this research agenda. Further, considering food web interactions as a selection pressure that drives or disrupts ecogeographical rules has the potential to address both mechanisms of and deviations from these macroecological relationships. For these reasons, further integration of macroecology and food webs will help ecologists better understand the assembly, maintenance and change of ecosystems across space and time.

Changes in stratospheric ozone and climate over the past 40-plus years have altered the solar ultraviolet (UV) radiation conditions at the Earth's surface. Ozone depletion has also contributed to climate change across the Southern Hemisphere. These changes are interacting in complex ways to affect human health, food and water security, and ecosystem services. Many adverse effects of high UV exposure have been avoided thanks to the Montreal Protocol with its Amendments and Adjustments, which have effectively controlled the production and use of ozone-depleting substances. This international treaty has also played an important role in mitigating climate change. Climate change is modifying UV exposure and affecting how people and ecosystems respond to UV; these effects will become more pronounced in the future. The interactions between stratospheric ozone, climate and UV radiation will therefore shift over time; however, the Montreal Protocol will continue to have far-reaching benefits for human well-being and environmental sustainability.

Gene expression during development shapes the phenotypes of individuals. Althoughembryonic gene expression can have lasting effects on developmental trajectories,few studies consider the role of maternal effects, such as egg size, on gene expression.Using qPCR, we characterize relative expression of 14 growth and/or skeletalpromoting genes across embryonic development in Arctic charr (Salvelinus alpinus).We test to what extent their relative expression is correlated with egg size and size atearly life-stages within the study population. We predict smaller individuals to havehigher expression of growth and skeletal promoting genes, due to less maternalresources (i.e., yolk) and prioritization of energy toward ossification. We foundexpression levels to vary across developmental stages and only three genes (Mmp9,Star, and Sgk1) correlated with individual size at a given developmental stage.Contrary to our hypothesis, expression of Mmp9 and Star showed a non-linearrelationship with size (at post fertilization and hatching, respectively), whilst Sgk1was higher in larger embryos at hatching. Interestingly, these genes are alsoassociated with craniofacial divergence of Arctic charr morphs. Our results indicatethat early life-stage variation in gene expression, concomitant to maternal effects, caninfluence developmental plasticity and potentially the evolution of resourcepolymorphism in fishes.

Climate change is one of the largest and possibly most impactful ongoing but also future environmental drivers. Understanding effects of climate change on aquatic ecosystems and their function is thus of high importance. Within the framework of the Hydro-CH2018 project, the Swiss Federal Office for the Environment (FOEN) initiated a synthesis of climate change effects on water quality and the ecological status of freshwater ecosystems. The present report is the result of these synthesis efforts.

Our goal was to summarize available knowledge on how climatic change affects freshwater ecosystems in Switzerland. The work was performed between fall 2017 and fall 2018. We aimed to provide a synthesis of existing knowledge that is as consistent and complete as possible, but also to identify possible knowledge gaps. The work is based on extensive literature surveys and expert interviews. Whenever possible, we included quantitative conclusions. At the same time, we also wanted to be specific and relevant for natural Swiss water systems, so we also included qualitative effects and case studies. While many of the major ongoing and expected effects of climate change on aquatic systems are already well known, we also faced several challenges. For example: (i) some effects of climate change are still only partly understood, (ii) many of the focal endpoints, both with respect to water quality and ecological status, are not only affected by climate change, but also by other anthropogenic drivers, and disentangling these drivers is challenging if not infeasible, (iii) specific effects can be dependent on specific local factors, and (iv) the research field is so vast that the available resources for this one-year synthesis did not allow us to go into as much detail and data analysis as the topic would deserve. As a result, our report is a snapshot of scientific knowledge, at the period of realization, of the effects of climate change on aquatic ecosystems in Switzerland, set into the context of other environmental drivers.

While we see that climate change will have major effects on Swiss water systems, we also identify possible ways of mitigating these effects. We thereby hope that our synthesis is not only an overview of current and future changes, but will also help in policy- and decisionmaking about how to best deal with these changes and challenges.

Over the last decade, steady advancements have been made in the use of DNA-based methods for detection of species in a wide range of ecosystems. This progress has culminated in molecular monitoring methods being employed for the detection of several species for enforceable management purposes of endangered, invasive, and illegally harvested species worldwide. However, the routine application of DNA-based methods to monitor whole communities (typically a metabarcoding approach) in order to assess the status of ecosystems continues to be limited. In aquatic ecosystems, the limited use is particularly true for macroinvertebrate communities. As part of the DNAqua-Net consortium, a structured discussion was initiated with the aim to identify potential molecular methods for freshwater macroinvertebrate community assessment and identify important knowledge gaps for their routine application. We focus on three complementary DNA sources that can be metabarcoded: 1) DNA from homogenised samples (bulk DNA), 2) DNA extracted from sample preservative (fixative DNA), and 3) environmental DNA (eDNA) from water or sediment. We provide a brief overview of metabarcoding macroinvertebrate communities from each DNA source and identify challenges for their application to routine monitoring. To advance the utilisation of DNA-based monitoring for macroinvertebrates, we propose an experimental design template for a series of methodological calibration tests. The template compares sources of DNA with the goal of identifying the effects of molecular processing steps on precision and accuracy. Furthermore, the same samples will be morphologically analysed, which will enable the benchmarking of molecular to traditional processing approaches. In doing so we hope to highlight pathways for the development of DNA-based methods for the monitoring of freshwater macroinvertebrates.

Effector proteins play crucial roles in determining the outcome of various plant-parasite interactions. Aphids inject salivary effector proteins into plants to facilitate phloem feeding, but some proteins might trigger defense responses in certain plants. The pea aphid, Acyrthosiphon pisum, forms multiple biotypes, and each biotype is specialized to feed on a small number of closely related legume species. Interestingly, all the previously identified biotypes can feed on Vicia faba; hence, it serves as a universal host plant of A. pisum. We hypothesized that the salivary effector proteins have a key role in determining the compatibility between specific host species and A. pisum biotypes and that each biotype produces saliva containing a specific mixture of effector proteins due to differential expression of encoding genes. As the first step to address these hypotheses, we conducted two sets of RNA-seq experiments. RNA-seq analysis of dissected salivary glands (SGs) from reference alfalfa- and pea-specialized A. pisum lines revealed common and line-specific repertoires of candidate salivary effector genes. Based on the results, we created an extended catalogue of A. pisum salivary effector candidates. Next, we used aphid head samples, which contain SGs, to examine biotype-specific expression patterns of candidate salivary genes. RNA-seq analysis of head samples of alfalfa- and pea-specialized biotypes, each represented by three genetically distinct aphid lines reared on either a universal or specific host plant, showed that a majority of the candidate salivary effector genes was expressed in both biotypes at a similar level. Nonetheless, we identified small sets of genes that were differentially regulated in a biotype-specific manner. Little host plant effect (universal vs. specific) was observed on the expression of candidate salivary genes. Analysis of previously obtained genome re-sequenced data of the two biotypes revealed the copy number variations that might explain the differential expression of some candidate salivary genes. In addition, at least four candidate effector genes that were present in the alfalfa biotype but might not be encoded in the pea biotype were identified. This work sets the stage for future functional characterization of candidate genes potentially involved in the determination of plant specificity of pea aphid biotypes.

Water pollution is ubiquitous globally, yet how the effects of pollutants propagate through natural ecosystems remains poorly understood. This is because the interactive effects of multiple stressors are generally hard to predict. Agriculture and municipal wastewater treatment plants (WWTPs) are often major sources of contaminants for streams, but their relative importance and the role of different pollutants (e.g. nutrients or pesticides) are largely unknown. Using a 'real world experiment' with sampling locations up- and downstream of WWTPs, we studied how effluent discharges affected water quality and macroinvertebrate communities in 23 Swiss streams across a broad land-use gradient.
Variation partitioning of community composition revealed that overall water quality explained approximately 30% of community variability, whereby nutrients and pesticides each independently explained 10% and 2%, respectively. Excluding oligochaetes (which were highly abundant downstream of the WWTPs) from the analyses, resulted in a relatively stronger influence (3%) of pesticides on the macroinvertebrate community composition, whereas nutrients had no influence. Generally, the macroinvertebrate community composition downstream of the WWTPs strongly reflected the upstream conditions, likely due to a combination of efficient treatment processes, environmental filtering and organismal dispersal. Wastewater impacts were most prominently by the Saprobic index, whereas the SPEAR index (a trait-based macroinvertebrate metrics reflecting sensitivity to pesticides) revealed a strong impact of arable cropping but only a weak impact of wastewater.
Overall, our results indicate that agriculture can have a stronger impact on headwater stream macroinvertebrate communities than discharges from WWTP. Yet, effects of wastewater-born micropollutants were clearly quantifiable among all other influence factors. Improving our ability to further quantify the impacts of micropollutants requires highly-resolved water quality and taxonomic data with adequate spatial and temporal sampling. These improvements would help to better account for the underlying causal pathways that drive observed biological responses, such as episodic contaminant peaks and dispersal-related processes.

Floods are necessary for the functioning of floodplain ecosystems. Ultimately, flood effects on biota are spatially complex and unfold at various time scales. Yet, biodiversity conservation in regulated floodplains requires a sound quantification of the main pathways how floods affect riverine ecosystems. Here, we investigated the relative effects of flood frequency, magnitude, and time elapsed since the last flood on macroinvertebrate communities of 24 parafluvial habitats in the Maggia river floodplain, Switzerland. Parafluvial habitats were sampled seasonally over 1 year, and a combination of 2D hydrodynamic modelling and piecewise structural equation modelling was used to quantify the direct and indirect effects of local hydrological metrics on macroinvertebrate communities. We found that high flood frequency favoured rheophilic species (EPT taxa) over other groups (Coleoptera, Diptera) and prevented strong competitive interactions and competitive exclusion by maintaining low food resource levels. Importantly, we found that parafluvial habitats exhibited more lentic‐like characteristics as time passed after a flood, which caused EPT taxa to be relatively more abundant and taxa richness higher immediately after flood disturbance. Lastly, overall taxa richness increased over time after a flood and even more so after larger floods. Our results suggest that variation in flood magnitude, frequency, and return period maximizes beta diversity within floodplain riverscapes due to the independent and spatially interactive responses of parafluvial habitats.

Floodplain ecosystems are some of the most biodiverse ecosystems on earth. This level of biodiversity is sustained by a great diversity of habitats and ecological niches, resulting from the interaction between the natural flow and sediment regimes. However, the ecological integrity of floodplains is rapidly deteriorating worldwide because of human activities. Flow regulation for hydropower production is one of the main drivers of ecological degradation in freshwaters and in floodplains in particular. Dams, impoundments and diversions result in a simplification of the natural flow regime, which becomes less variable, this in turn drives a simplification of the riverscape and a decrease in its biodiversity and ecological functioning. The general aim of this thesis is to investigate how communities of aquatic macroinvertebrates are shaped by hydrology in an alluvial floodplain in order to refine our understanding of hydrology – biodiversity linkages in complex ecosystems. To achieve this aim, I conducted an extensive field survey and an innovative field experiment on the Maggia River floodplain, in southern Switzerland. First, I investigated how different flooding regimes and recent flooding history lead to different community structures amongst floodplain habitats. I found that frequent flooding favored rheophilic species over more lentic groups, and limited strong competitive interactions to occur by maintaining low periphyton standing crops. Then, I developed a novel experimental setup, where 24 ponds were excavated out of two gravel bars in the floodplain, and monitored macroinvertebrate metacommunity assembly over 45 days. I showed that the interaction between the local environment and the degree of connectivity to the regional species pool can lead to different assembly trajectories through time. The findings of the experiment were then broadly compared to the temporal changes in metacommunity organization observed in the natural habitats. There, I found that local environmental conditions and the degree of landscape connectivity greatly affected metacommunity structure. Most importantly, I showed that metacommunity organization changed in time during post-disturbance metacommunity assembly, and that the temporal shifts between the main structuring processes differed with the dispersal ability of species. Finally, I used stable isotope analyses to calculate the food chain length within macroinvertebrate communities, and assessed how it responded to gradients of habitat size, productivity and disturbance regime. There, I showed that flooding reduced food chain length, because predators were feeding at lower trophic levels in frequently disturbed habitats. Overall, this study shows that maintaining flow variability and spatial heterogeneity in flood disturbance is key to sustaining floodplain aquatic biodiversity. My research also contributes to the field of metacommunity ecology by showing that metacommunity organization is highly variable in time and especially during assembly after disturbance.

Cotton-strip bioassays are increasingly used to assess ecosystem integrity because they provide a standardized measure of organic-matter decomposition – a fundamental ecosystem process. However, several different cotton-strip assays are routinely used, complicating the interpretation of results across studies, and hindering broader synthesis. Here, we compare the decay rates and assemblages of bacteria and fungi colonizing the three most commonly used cotton materials: Artist’s canvas, Calico cloth, and Empa fabric. Cotton strips from each material type were incubated in 10 streams that span a wide range of physicochemical properties across five ecoregions. Additionally, to evaluate responses to environmental stress without potentially confounding biogeographical effects, we deployed identical bioassays in five streams across an acidification gradient within a single ecoregion.
Across all streams decomposition rates (as tensile strength loss [TSL]) differed among the three cotton materials; Calico cloth decomposed fastest (time to 50% TSL [T₅₀] = 16.7 d), followed by the Empa fabric (T₅₀ = 18.3 d) and then Artist’s canvas (T₅₀ = 21.4 d). Despite these differences, rates of TSL of the three cotton materials responded consistently to variation in environmental conditions; TSL of each fabric increased with stream temperature, dissolved-nutrient concentrations and acid-neutralizing capacity, although Artist’s canvas and Calico cloth were more sensitive than Empa fabric. Microbial communities were similar among the materials, and values of community structure (e.g., phylotype richness and diversity) were comparable to those reported for decaying leaves in streams from the same region, the major natural basal carbon resource in forested-stream ecosystems. We present linear calibrations among pairs of assays so that past and future studies can be expressed in a "common currency" (e.g., Artist’s-fabric equivalents) ‘past and future studies’ repeated two times in the sentence. Lastly, given its relatively low within-site variability, and the large number of streams where it has been used (>700 across the globe), we recommend Artist’s fabric for future work. These results show that cotton provides an effective and realistic standardized substrate for studying heterotrophic microbial assemblages, and acts as a reasonable proxy for more chemically complex forms of detritus. These findings add to growing evidence that cotton-strip bioassays are simple, effective and easily standardized indicators of heterotrophic microbial activity and the ecosystem processes that result.

There is growing concern over tipping points arising in ecosystems because of the crossing of environmental thresholds. Tipping points lead to abrupt and possibly irreversible shifts between alternative ecosystem states, potentially incurring high societal costs. Trait variation in populations is central to the biotic feedbacks that maintain alternative ecosystem states, as they govern the responses of populations to environmental change that could stabilize or destabilize ecosystem states. However, we know little about how evolutionary changes in trait distributions over time affect the occurrence of tipping points and even less about how big-scale ecological shifts reciprocally interact with trait dynamics. We argue that interactions between ecological and evolutionary processes should be taken into account in order to understand the balance of feedbacks governing tipping points in nature.

1. The field of eco-evolutionary dynamics is developing rapidly, with a growing number of well-designed experiments quantifying the impact of evolution on ecological processes and patterns, ranging from population demography to community composition and ecosystem functioning. The key challenge remains to transfer the insights of these proof-of-principle experiments to natural settings, where multiple species interact and the dynamics are far more complex than those studied in most experiments.
2. Here, we discuss potential pitfalls of building a framework on eco-evolutionary dynamics that is based on data on single species studied in isolation from interspecific interactions, which can lead to both under- and overestimation of the impact of evolution on ecological processes. Underestimation of evolution-driven ecological changes could occur in a single-species approach when the focal species is involved in co-evolutionary dynamics, whereas overestimation might occur due to increased rates of evolution following ecological release of the focal species.
3. In order to develop a multi-species perspective on eco-evolutionary dynamics, we discuss the need for a broad-sense definition of “eco-evolutionary feedbacks” that includes any reciprocal interaction between ecological and evolutionary processes, next to a narrow-sense definition that refers to interactions that directly feed back on the interactor that evolves.
4. We discuss the challenges and opportunities of using more natural settings in eco-evolutionary studies by gradually adding complexity: (a) multiple interacting species within a guild, (b) food web interactions and (c) evolving metacommunities in multiple habitat patches in a landscape. A literature survey indicated that only a few studies on microbial systems so far developed a truly multi-species approach in their analysis of eco-evolutionary dynamics, and mostly so in artificially constructed communities.
5. Finally, we provide a road map of methods to study eco-evolutionary dynamics in more natural settings. Eco-evolutionary studies involving multiple species are necessarily demanding and might require intensive collaboration among research teams, but are highly needed.

Eutrophication of shallow lakes often triggers a series of cascading ecological effects. Among these are shifts in the zooplankton community structure due to phytoplankton changes, or shifts in the fish community reducing size-selective feeding of planktivorous fish. In such conditions, larger zooplankton (e.g. Daphnia) can have a selective advantage. Re-oligotrophication can reverse such food-web interactions. Europe’s largest wetland system (the Danube Delta) went through a period of eutrophication and is now slowly recovering again. However, changes in the Daphnia populations triggered by eutrophication in this system have remained unstudied. We used different sampling strategies to screen 24 lakes (which differ in their ecological state) for the presence of Daphnia as well as for biotic and abiotic parameters potentially explaining Daphnia abundance. Daphnia densities were surprisingly low. We found D. magna ephippia in the sediment, but no D. magna in the water column. Microsatellite analyses on pelagic Daphnia populations confirmed the presence of the D. longispina complex and provided evidence for significant hybridisation events. FluoroProbe data showed that Daphnia was mainly present in lakes with a higher phytoplankton production. Our study provides insights into the spatial and temporal distribution of Daphnia in a very dynamic wetland system.

Understanding how different food resources sustain stream food webs is fundamental towards increasing our knowledge on trophic structure and energy flow pathways in fluvial ecosystems.
Food webs in small mountain streams are sustained by autochthonous (instream primary production) and allochthonous (inputs from the terrestrial ecosystem) organic resources, with their relative importance highly dependent on catchment land cover. This study aimed to understand how catchment land cover determines food resource type (autochthonous, allochthonous) and quantity in mountain streams, and how this affects energy flow pathways and food web structure. We hypothesised that food resource type and quantity would reflect catchment land cover.
Thus, changes in food resources would lead to shifts in macroinvertebrate assimilation of autochthonous and allochthonous food resources and consequently in dominant energy flow pathways. We further hypothesised that changes in food resources will have strong effects on dominant feeding groups and community biomass distribution among taxa in food webs.
Energy flow pathways were quantified by combining macroinvertebrate biomass measures and assimilation of food resources estimated from δ²H and δ¹⁵N in 10 streams along a forest cover gradient, located in the Cantabrian Mountains (northern Spain).
Results showed that grassland/shrub dominated streams had a higher proportion autochthonous food resources and a lower proportion of allochthonous food resources, whereas forested streams showed the opposite pattern. Changes in food resources with forest cover resulted in shifts in food resource assimilation and dominant energy flow pathways. Forested streams were mainly sustained by allochthonous resources, while streams flowing through grassland/shrub landscapes were mostly sustained by autochthonous resources.
Food resource assimilation differed between feeding groups. Detritivores showed a fixed assimilation of allochthonous resources independent of resource quantity, while omnivore assimilation was determined by the dominant food resource. This was reflected in food‐web structure. There was an increase in detritivore biomass and conservation of omnivore biomass with increasing forest cover, leading to a more equal distribution of community biomass among macroinvertebrates comprising individual food webs.
The dependence of stream food webs on dominant food resources highlights the importance of catchment land cover in determining energy flow pathways and food web structure in low order mountain streams. These findings will improve our predictions on the effects of land cover change on the functioning of mountain stream ecosystems.

The family Moitessieriidae is poorly known, as its members, inhabiting exclusively subterranean waters, are often known only from few minute, empty shells. Molecular studies on their relationships confirmed the distinctness of this family. Their monophyly, however, remained doubtful, since the Moitessieriidae did not form a distinct clade in the phylogenetic tree based on the most commonly applied mitochondrial cytochrome oxidase subunit I (COI), and the representative of the family Cochliopidae occupied a position among the moitessieriid clades. In the present paper two new nuclear loci, namely histone H3 gene and ribosomal internal transcribed spacer ITS2, have been applied to resolve the status of the Moitessieriidae. The resulting phylogenies show the Moitessieriidae as a distinct, well supported clade, confirming thus their monophyly.

Species that successfully colonized subterranean environments are subject to two opposing selection processes. Stringent abiotic factors select for convergent adaptations, such as loss of eyes and pigments, while interspecific competition drives between-species divergence. Subterranean species can resolve opposing selection by adaptation to physically different microhabitats. Yet, species frequently co-occur in physically homogeneous subterranean habitats, like interstitial. These co-occurrences in such a narrow ecological context can be explained either by equalizing mechanisms, in which neither of the co-occurring species has a competitive advantage, or by more complex niche models that include species' differentiation along a trophic niche axis. We tested these hypotheses using the amphipod genus Niphargus. We analysed Europe-wide co-occurrence records of Niphargus species from interstitial habitats, split into six independent large-scale regions. Firstly, we addressed whether species' pairwise co-occurrences are random using a probabilistic model. Secondly, we tested whether species cluster into distinct functional–morphological groups and whether ecologically or phylogenetically distinct species are more likely to co-occur. We found that 68% of species co-occurrences were not different from random expectation, indicating that most species had access to most sites within each region. The remaining 32% co-occurred either significantly more or less often than expected by chance. Cluster analysis of functional morphological characters showed that interstitial species belong to two feeding types, micro- and macrofeeders, likely representing two peaks of the interstitial adaptive landscape, and hinting that niche divergence, as a mechanism allowing coexistence, is favoured. Finally, we found that the number of co-occurrences increases with increasing differentiation of functional morphology, but not phylogenetic differences. We conclude that ecological differentiation may be important in shaping such interstitial communities.

Individual-level variation arising from responses to environmental gradients influences population and community dynamics. How such responses empirically relate to the mechanisms that govern species coexistence is, however, poorly understood. Previous results from lake phytoplankton communities suggested that the evenness of organismal traits in multiple dimensions increases with resource limitation, possibly due to resource partitioning at the individual level. Here we experimentally tested the emergence of this pattern by growing two phytoplankton species (Pseudokirchneriella subcapitata and Microcystis aeruginosa) under a gradient of light intensity, in monoculture and jointly. Under low light (resource) conditions, the populations diversified into a wide range of phenotypes, which were evenly distributed in multidimensional trait space (defined by four pigment-related trait dimensions), consistent with the observed field pattern. Our interpretation is that under conditions of light limitation, individual phytoplankton cells alter photosynthetic traits to reduce overlap in light acquisition, acquiring unexploited resources and thereby likely maximising individual success. Our results provide prime experimental evidence that resource limitation increases the evenness of conspecific and heterospecific microbial phenotypes along trait axes, advancing our understanding of trait-based coexistence.

The seasonal dynamics and spatial variability of macroinvertebrate assemblages in Alpine streams are becoming better understood. However, the implications of this knowledge for indices used in monitoring programs have yet to be fully considered. Establishing the ecological status of such streams using macroinvertebrates may then be difficult if what is expected to be found, and where, varies across small distances between streams at a given altitude, or between years in response to different climatic characteristics. In this paper, we evaluated the degree of spatial variability in macroinvertebrate abundance and diversity for 14 tributaries at similar altitude that feed a 6-km reach of an Alpine stream, and how this spatial variability differs within and between years. Environmental variables and macroinvertebrates were sampled on 10 dates for assessment. The data showed that differences in environmental characteristics over relatively short distances lead to between tributary differences in the “windows of opportunity” and hence when a tributary should be sampled for monitoring purposes. Superimposed on this spatial variability was inter-annual variability linked to climate differences that shifted this “window of opportunity” in time, and thus altered when monitoring was optimal for any one tributary in any one year. If biological indices are not rendered sensitivity to these variations, the results obtained may reflect more natural variability than possible human impacts.

In Alpine streams, humans have strongly modified the interactions between hydraulic processes, geomorphology and aquatic life through dams, flow abstraction at water intakes and river channel engineering. To mitigate these impacts, research has addressed both minimum flows and flow variability to sustain aquatic ecosystems. Whilst such environmental flows might work downstream of dams, this may not be the case for water intakes. Intakes, generally much smaller than dams, are designed to abstract water and to leave sediment behind. Sediment accumulation then results in the need to flush intakes periodically, often more frequently than daily in some highly glaciated basins. Sediment delivery downstream is then maintained through short duration floods with very high sediment loads. Here we tested the hypothesis that sediment flushing, and the associated high frequency of bed disturbance, controls in-stream habitat and macroinvertebrate assemblages. We collected macroinvertebrates over a 17-month period from an Alpine stream as well as a set of lateral unperturbed tributaries that served as controls. In contrast to established conceptual models, our results showed that the stream is largely void of life during summer, but that populations recover rapidly as the frequency of intake flushing falls in early autumn, producing richer and larger populations in winter and early spring. The recovery in autumn may be due to the recruitment of individuals from tributaries. We conclude that intake flushing in summer inverts expected summer-winter macroinvertebrate abundances, and questions the extent to which environmental flows in intake-impacted Alpine streams will lead to improvements in instream macrofauna unless sediment also is managed.

Understanding the effects of global warming on trait variation and trophic structure is a crucial challenge in the 21st century. However, there is a lack of general patterns that can be used to predict trait variation and community trophic structure under the ongoing environmental change. We investigated the responses of body size and community trophic structure of zooplankton to climate related factors (e.g., temperature). Isotopic niche breadth was applied to investigate the community trophic structure across a 1‐year study from a subtropical reservoir (Tingxi Reservoir) in southeastern China. Body size and community isotopic niche breadth of zooplankton were larger during water mixing than stratification periods and correlated significantly with water temperature change along the time series. The contributions of intra‐ and intertaxonomic components to body size and community trophic structure variation showed significant relationships with the temperature change going from the mixing to stratification periods. Water temperature imposed direct effect on body size, while direct and indirect effect on the community trophic structure of zooplankton occurred through trophic redundancy along time series. Water temperature and community properties (e.g., body size, trophic redundancy, or trophic interaction) showed complex interactions and integrated to influence community trophic structure of zooplankton. Our results can expand the knowledge of how elevated temperature will alter individual trait and community trophic structure under future climate change.

1. Network connectivity is a key feature of rivers that affects patterns and processes in lotic ecosystems. Few studies have considered how changes in river reach connectivity might affect ecosystem attributes at a whole river network scale. The use of population dynamics models of keystone species at a river network scale allows exploration of how the effects of altered natural connectivity patterns might propagate through a river network.
2. In this study, we present a metapopulation model to estimate the spatial distribution of the population density of brown trout (Salmo trutta), an ecologically and socioeconomically important top predator, in a river network in northern Spain. The model accounts for the presence of barriers that limit longitudinal connectivity in upstream and downstream directions. The model estimates the spatial distribution of densities of three age‐classes (young‐of‐the‐year, juveniles, and adults) in all river reaches that make up the network based on topology, connectivity and population dynamics (e.g. age‐class specific mortality, spawning, age‐class dispersal, and spawning migration patterns).
3. Seventy‐five percent of the modelled population densities fell within the 95% confidence intervals of the empirical data (84.6% for young‐of‐the‐year, 69.2% for juveniles, and 69.2% for adults) collected in 13 reaches. The simulated removal of all longitudinal barriers to migration in the river network (re‐naturalisation of the whole catchment) produced a modelled increase in brown trout density in the most downstream reaches of the river network and lowered fish densities in the upstream portion of the network when bias in juvenile and adult movement direction was assumed. Furthermore, the simulated removal of a single obstacle affected fish density even in distant tributaries.
4. The proposed model is an appropriate tool for the evaluation of spatial patterns of brown trout density at a river network scale and for the assessment of the impact of altered connectivity. This might help simulate the results of management strategies regarding river connectivity and show where population decreases or increases could be expected, although empirical knowledge of overall trout movement in the studied river networks is required for drawing realistic scenarios.

1. Theoretical models pertaining to feedbacks between ecological and evolutionary processes are prevalent in multiple biological fields. An integrative overview is currently lacking, due to little crosstalk between the fields and the use of different methodological approaches.
2. Here, we review a wide range of models of eco‐evolutionary feedbacks and highlight their underlying assumptions. We discuss models where feedbacks occur both within and between hierarchical levels of ecosystems, including populations, communities and abiotic environments, and consider feedbacks across spatial scales.
3. Identifying the commonalities among feedback models, and the underlying assumptions, helps us better understand the mechanistic basis of eco‐evolutionary feedbacks. Eco‐evolutionary feedbacks can be readily modelled by coupling demographic and evolutionary formalisms. We provide an overview of these approaches and suggest future integrative modelling avenues.
4. Our overview highlights that eco‐evolutionary feedbacks have been incorporated in theoretical work for nearly a century. Yet, this work does not always include the notion of rapid evolution or concurrent ecological and evolutionary time scales. We show the importance of density‐ and frequency‐dependent selection for feedbacks, as well as the importance of dispersal as a central linking trait between ecology and evolution in a spatial context.

Insects commonly possess heritable microbial symbionts that increase their resistance to particular parasites. A diverse community of defensive symbionts may thus provide hosts with effective and specific protection against multiple parasites, although costs might constrain the accumulation of many symbionts. In parallel to the allelic diversity in the MHC complex of the vertebrate immune system, parasite diversity could be the driving force behind symbiont diversity. There is indeed evidence that parasites have the ability to drive frequencies of defensive symbionts in their hosts, and that these symbionts influence parasite communities, but direct evidence that parasite diversity can promote symbiont diversity is still lacking. We provide suggestions to investigate this potential link.

Host manipulation is a parasite-induced alteration of a host's phenotype that increases parasite fitness. However, if genetically encoded in the parasite, it should be under selection in the parasite. Such host manipulation has often been assumed to be energetically costly, which should restrict its evolution. Evidence of such costs, however, remains elusive. The trophically transmitted cestode Schistocephalus solidus manipulates the activity of its first intermediate copepod host to reduce its predation susceptibility before the parasite is ready for transmission. Thereafter, S. solidus increases host activity to facilitate transmission to its subsequent fish host. I selected S. solidus for or against host manipulation over three generations to investigate the evolvability of manipulation and identify potential trade-offs. Host manipulation responded to selection, confirming that this trait is heritable in the parasite and hence can present an extended phenotype. Changes in host manipulation were not restrained by any obvious costs.

Many parasites alter their host's phenotype in a manner that enhances their own fitness beyond the benefits they would gain from normal exploitation. Such host manipulation is rarely consistent with the host's best interests resulting in suboptimal and often fatal behavior from the host's perspective. In this case, hosts should evolve resistance to host manipulation. The cestode Schistocephalus solidus manipulates the behavior of its first intermediate copepod host to reduce its predation susceptibility and avoid fatal premature predation before the parasite is ready for transmission to its subsequent host. Thereafter, S. solidus increases host activity to facilitate transmission. If successful, this host manipulation is necessarily fatal for the host. I selected the copepod Macrocyclops albidus, a first intermediate host of S. solidus, for resistance or susceptibility to host manipulation to investigate their evolvability. Selection on the host indeed increased host manipulation in susceptible and reduced host manipulation in resistant selection lines. Interestingly, this seemed to be at least partly due to changes in the baseline levels of the modified trait (activity) rather than actual changes in resistance or susceptibility to host manipulation. Hence, hosts seem restricted in how rapidly and efficiently they can evolve resistance to host manipulation.

Species interactions lie at the heart of many theories of macroevolution, from adaptive radiation to the Red Queen. Although some theories describe the imprint that interactions will have over long time scales, we are still missing a comprehensive understanding of the effects of interactions on macroevolution. Current research shows strong evidence for the impact of interactions on macroevolutionary patterns of trait evolution and diversification, yet many macroevolutionary studies have only a tenuous relationship to ecological studies of interactions over shorter time scales. We review current research in this area, highlighting approaches that explicitly model species interactions and connect them to broad‐scale macroevolutionary patterns. We also suggest that progress has been made by taking an integrative interdisciplinary look at individual clades. We focus on African cichlids as a case study of how this approach can be fruitful. Overall, while the evidence for species interactions shaping macroevolution is strong, further work using integrative and model‐based approaches is needed to spur progress towards understanding the complex dynamics that structure communities over time and space.
 

Environmental DNA (eDNA) analysis is a rapid, non-invasive, cost-efficient biodiversity monitoring tool with enormous potential to inform aquatic conservation and management. Development is ongoing, with strong commercial interest, and new uses are continually being discovered. General applications of eDNA and guidelines for best practice in freshwater systems have been established, but habitat-specific assessments are lacking. Ponds are highly diverse, yet understudied systems that could benefit from eDNA monitoring. However, eDNA applications in ponds and methodological constraints specific to these environments remain unaddressed. Following a stakeholder workshop in 2017, researchers combined knowledge and expertise to review these applications and challenges that must be addressed for the future and consistency of eDNA monitoring in ponds. The greatest challenges for pond eDNA surveys are representative sampling, eDNA capture, and potential PCR inhibition. We provide recommendations for sampling, eDNA capture, inhibition testing, and laboratory practice, which should aid new and ongoing eDNA projects in ponds. If implemented, these recommendations will contribute towards an eventual broad standardisation of eDNA research and practice, with room to tailor workflows for optimal analysis and different applications. Such standardisation will provide more robust, comparable, and ecologically meaningful data to enable effective conservation and management of pond biodiversity.

Moving beyond species count data is an essential step to better understand the effects of environmental perturbations on biodiversity and ecosystem functions, and to eventually better predict the strength and direction of those effects. Here, coupling an integrative path analysis approach with data from an extensive countrywide monitoring program, we tested the main spatial, environmental and anthropogenic drivers of change in the functional structure of aquatic macroinvertebrate communities along the entire Swiss Rhine river catchment. Functional structure was largely driven by inherent altitudinal variation influencing and cascading to regional scaled factors such as land use change and position in the riverine network, which, in turn, transformed local habitat structure variables. Those cascading effects across scales propagated through the biotic community, first affecting prey and, in turn, predators. Our results illustrate how seemingly less important local factors can act as essential transmission belts, propagating through direct and indirect pathways across scales to generate the specific context in which each functional group will strive or not, leading to characteristic landscape wide variations in functional community structure.

Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so.The factors causing this variation among lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene Fads2 in stickleback lineages that subsequently colonized and radiated in freshwater habitats, but not in close relatives that failed to colonize.Transgenic manipulation of Fads2 in marine stickleback increased their ability to synthesize DHA and survive on DHA-deficient diets. Multiple freshwater ray-finned fishes also show a convergent increase in Fads2 copies, indicating its key role in freshwater colonization.

Heritable bacterial endosymbionts are common in aphids (Hemiptera: Aphididae), and they can influence ecologically important traits of their hosts. It is generally assumed that their persistence in a population is dependent on a balance between the costs and benefits they confer. A good example is Hamiltonella defensa Moran et al., a facultative symbiont that provides a benefit by strongly increasing aphid resistance to parasitoid wasps, but becomes costly to the host in the absence of parasitoids. Regiella insecticola Moran et al. is another common symbiont of aphids and generally does not influence resistance to parasitoids. In the green peach aphid, Myzus persicae (Sulzer), however, one strain (R5.15) was discovered that behaves like H. defensa in that it provides strong protection against parasitoid wasps. Here we compare R5.15‐infected and uninfected lines of three M. persicae clones to test whether this protective symbiont is costly as well, i.e., whether it has any negative effects on aphid life‐history traits. Furthermore, we transferred R5.15 to two other aphid species, the pea aphid, Acyrthosiphon pisum (Harris), and the black bean aphid, Aphis fabae Scopoli, where this strain is also protective against parasitoids and where we could compare its effects with those of additional, non‐protective strains of R. insecticola. Negative effects of R5.15 on host survival and lifetime reproduction were limited and frequently non‐significant, and these effects were comparable or in one case weaker than those of R. insecticola strains that are not protective against parasitoid wasps. Unless the benefit of protection is counteracted by detrimental effects on traits that were not considered in this study, R. insecticola strain R5.15 should have a high potential to spread in aphid populations.

Coinfections by multiple parasites predominate in the wild. Interactions between parasites can be antagonistic, neutral, or facilitative, and they can have significant implications for epidemiology, disease dynamics, and evolution of virulence. Coinfections commonly result from sequential exposure of hosts to different parasites. We argue that the sequential nature of coinfections is important for the consequences of infection in both natural and man-made environments. Coinfections accumulate during host lifespan, determining the structure of the parasite infracommunity. Interactions within the parasite community and their joint effect on the host individual potentially shape evolution of parasite life‐history traits and transmission biology. Overall, sequential coinfections have the potential to change evolutionary and epidemiological outcomes of host–parasite interactions widely across plant and animal systems.

Microsatellites (simple sequence repeats, SSRs) still remain popular molecular markers for studying neutral genetic variation. Two alternative models outline how new microsatellite alleles evolve. Infinite alleles model (IAM) assumes that all possible alleles are equally likely to result from a mutation, while stepwise mutation model (SMM) describes microsatellite evolution as stepwise adding or subtracting single repeat units. Genetic relationships between individuals can be analyzed in higher precision when assuming the SMM scenario with allele size differences as a proxy of genetic distance. If population structure is not predetermined in advance, an empirical data analysis usually includes (a) estimating proximity between individual SSR profiles with a selected dissimilarity measure and (b) determining putative genetic structure of a given set of individuals using methods of clustering and/or ordination for the obtained dissimilarity matrix. We developed new dissimilarity indices between SSR profiles of haploid, diploid, or polyploid organisms assuming different mutation models and compared the performance of these indices for determining genetic structure with population data and with simulations. More specifically, we compared SMM with a constant or variable mutation rate at different SSR loci to IAM using data from natural populations of a freshwater bryozoan Cristatella mucedo (diploid), wheat leaf rust Puccinia triticina (dikaryon), and wheat powdery mildew Blumeria graminis (monokaryon). We show that inferences about population genetic structure are sensitive to the assumed mutation model. With simulations, we found that Bruvo's distance performs generally poorly, while the new metrics are capturing the differences in the genetic structure of the populations.

Global climate change imposes a serious threat to natural populations of many species. Estimates of the effects of climate change‐mediated environmental stresses are, however, often based only on their direct effects on organisms, and neglect the potential transgenerational (e.g. maternal) effects.
We tested whether high temperature (i.e. an experimental heatwave), which is known to reduce the performance of adult Lymnaea stagnalis snails, affects the produced offspring (eggs and hatchlings) through maternal effects, and how strong these effects are compared with the effects of direct exposure of offspring to high temperature. We examined the effect of maternal thermal environment (15°C versus 25°C) on per offspring investment (egg size), and the role of both maternal and offspring thermal environments (15°C versus 25°C) on hatching success and developmental time of eggs, offspring survival after hatching, and hatchling size at the age of 5 weeks.
Exposure of mothers to high temperature reduced the size of oviposited eggs, increased their hatching success, and also made the onset of hatching earlier. However, high maternal temperature reduced the survival and the final size of hatched juveniles. Direct exposure of offspring to high temperature reduced their survival (both eggs and hatchlings) but increased the developmental rate and growth of those individuals that survived. Interestingly, the magnitude of maternal effects on hatching success of eggs and hatchling survival were similar to the direct effects of high temperature.
Our results indicate that heatwaves can affect natural populations through transgenerational maternal effects and that the magnitude of those effects can be equally strong to the direct effects of temperature, although this depends on the trait considered. These findings highlight the importance of considering the transgenerational effects of climate warming when estimating its effects in the wild.

Global climate change affects natural populations of many species by increasing the average temperature and the frequency of extreme weather events (e.g. summer heat waves). The ability of organisms to cope with these environmental changes can, however, depend on their genetic properties. For instance, genetic load owing to inbreeding could alter organisms' responses to climate change-mediated environmental changes but such effects are often overlooked. We investigated the effects of an experimental heat wave (25°C versus 15°C) on life history (reproduction, size) and constitutive immune defence traits (phenoloxidase-like and antibacterial activity of haemolymph) in relation to inbreeding by manipulating the mating type (outcrossing, self-fertilization) in two populations of a hermaphroditic freshwater snail, Lymnaea stagnalis. High temperature increased reproduction and size of snails but impaired their immune function. In one of the two study populations, inbreeding reduced reproductive output of snails indicating inbreeding depression. Furthermore, this effect did not depend on the temperature snails were exposed to. Our results suggest that L. stagnalis snails can be negatively affected by inbreeding but it may not alter their responses to heat waves.

Resource competition theory is a conceptual framework that provides mechanistic insights into competition and community assembly of species with different resource requirements. However, there has been little exploration of how resource requirements depend on other environmental factors, including temperature. Changes in resource requirements as influenced by environmental temperature would imply that climate warming can alter the outcomes of competition and community assembly.
We experimentally demonstrate that environmental temperature alters the minimum light and nitrogen requirements – as well as other growth parameters – of six widespread phytoplankton species from distinct taxonomic groups. We found that species require the most nitrogen at the highest temperatures while light requirements tend to be lowest at intermediate temperatures, although there are substantial interspecific differences in the exact shape of this relationship.
We also experimentally parameterize two competition models, which we use to illustrate how temperature, through its effects on species’ traits, alters competitive hierarchies in multispecies assemblages, determining community dynamics.
Developing a mechanistic understanding of how temperature influences the ability to compete for limiting resources is a critical step towards improving forecasts of community dynamics under climate warming.

The fate of dissolved organic carbon (DOC) is partly determined by its availability to microbial degradation. Organisms at upper trophic levels could influence the bioavailability of DOC via cascading effects on primary producers and bacteria. Here we experimentally tested whether the presence of fish in aquatic food webs can indirectly affect the composition of the DOC pool. We found that fish had strong positive effects on phytoplankton biomass that affected the dynamics of DOC composition. Specifically, fish increased protein-like, algae-derived DOC mid-experiment, concurrent with the strongest fish-induced increase in phytoplankton biomass. Fish also increased bacterial abundance, altered the community composition and diversity of bacteria, and temporarily increased DOC compounds with fluorescence properties indicative of microbially-reprocessed organic matter. Overall, our experiment revealed that fish can positively influence the substrate (algae-produced DOC) and the key players (bacteria) of the microbial carbon pump. Consequently, fish could contribute to carbon sequestration by stimulating both the production of bioavailable DOC and the microbial degradation of bioavailable to persistent DOC. We propose this as a novel mechanism whereby the loss of predators from global ecosystems could alter carbon cycling.

Leaf litter processing is an essential ecosystem function in freshwater systems, since much of the carbon and nutrients moving through freshwater food webs come from the surrounding terrestrial ecosystems. Thus, it is important to understand how the species performing this function differ, especially because many native species are being replaced by non-native species in aquatic ecosystems. We used a field experiment to examine leaf consumption rates of two common shredding macroinvertebrates (the native Gammarus fossarum and the non-native Gammarus roeselii). Leaves from three species, varying in resource quality, were added both in leaf monocultures and as a three-species mixture. Biomass-adjusted daily consumption rates were similar between the two amphipod species, and each consumed nitrogen-rich alder leaves faster than oak or beech leaves. However, because adult G. roeselii are approximately twice the size of G. fossarum, this led to systematic, though nonsignificant, differences in consumption rates at the per-capita or population level. Furthermore, we found nuanced effects of decomposer identity on leaf decomposition in mixtures. Only G. roeselii showed increased consumption of the preferred resource (alder) in the mixture, while G. fossarum consumed all leaves at the same proportional rates as in monocultures. This is an important distinction, as most measures of macroinvertebrate leaf shredding are made in the laboratory with only a single leaf resource available. Our results, based on a field experiment which could control the presence of dominant macroinvertebrates while still providing natural, biologically realistic context, suggest that even functionally similar species may subtly shift ecosystem processes.

Dispersal can strongly influence ecological and evolutionary dynamics. Besides the direct contribution of dispersal to population dynamics, dispersers often differ in their phenotypic attributes from non-dispersers, which leads to dispersal syndromes. The consequences of such dispersal syndromes have been widely explored at the population and community level; however, to date, ecosystem-level effects remain unclear. Here, we examine whether dispersing and resident individuals of two different aquatic keystone invertebrate species have different contributions to detrital processing, a key function in freshwater ecosystems. Using experimental two-patch systems, we found no difference in leaf consumption rates with dispersal status of the common native species Gammarus fossarum. In Dikerogammarus villosus, however, a Ponto-Caspian species now expanding throughout Europe, dispersers consumed leaf litter at roughly three times the rate of non-dispersers. Furthermore, this put the contribution of dispersing D. villosus to leaf litter processing on par with native G. fossarum, after adjusting for differences in organismal size. Given that leaf litter decomposition is a key function in aquatic ecosystems, and the rapid species turnover in freshwater habitats with range expansions of non-native species, this finding suggests that dispersal syndromes may have important consequences for ecosystem functioning.

This thesis investigates meta-ecosystem processes in streams. It specifically considers decomposition, a key ecosystem function, and how it is governed by terrestrial and aquatic landscapes and communities. Using a combination of field surveys, laboratory and field experiments, and statistical modeling, this thesis shows that the local distribution of freshwater biodiversity results from a combination of deterministic and stochastic processes, while the amount and identity of terrestrial subsidies entering streams at the reach scale is controlled by human land use decisions. Finally, this thesis scales mechanisms operating at the between-individual level up to the landscape level to provide estimates of ecosystem functioning in entire stream catchments.

Switzerland plans to restore 4000 km of rivers by 2090. Despite the immense investment costs, river restoration benefits have not been valued in monetary terms, and a cost-benefit analysis (CBA) does not exist for any river restoration project in Switzerland. We apply stated preference methods to elicit public preferences and willingness to pay for restoring two specific but representative river sites. The benefits of restoration are compared with its costs. Upscaling the results to the national level shows that the government budget allocated for river restoration (CHF 1200/m) is insufficient to cover the costs of local restoration projects. However, the surveyed local populations are willing to pay substantially more for restoring rivers in their area of residence than they are legally obliged to do. The CBA results demonstrate that the benefits outweigh the costs in the two case studies, and hence that restoration efforts are justified from an economic point of view. A sensitivity analysis shows that the main results and conclusions do not change when we change some of the key assumptions underlying the CBA.

Interactions between species can structure populations and communities, affect the flow of energy and matter within and across ecosystem boundaries, and shape the biotic and abiotic environment. Thereby, species interactions can also feed back on the participating species themselves, and on other members of the community. Complex interaction networks can arise that may influence the stability of ecosystems and potentially make them resilient against external perturbation. However, species interactions are not static: through endlessly recurring interplay with their environment, species, and thus, their interactions with other species, are subject to evolutionary change. [...]

Wechselwirkungen zwischen Arten können Populationen und Gemeinschaften strukturieren, den Energie- und Materialfluss innerhalb und über die Ökosystemgrenzen hinweg beeinflussen, und die biotische und abiotische Umgebung modifizieren. Dabei können Wechselwirkungen auch auf die beteiligten Arten selbst, sowie auf andere Mitglieder der Gemeinschaft zurückwirken und komplexe Netzwerke aus Wechselwirkungen bilden. Durch diese Wechselwirkungen können vorhandene Arten die Stabilität ihrer Ökosysteme beeinflussen, und sie möglicherweise widerstandsfähig gegen Störungen von außen machen. Wechselwirkungen zwischen Arten sind jedoch nicht statisch: durch das endlos wiederkehrende Zusammenspiel mit ihrer Umwelt unterliegen intra- und, interspezifische Wechselwirkungen mit anderen Arten evolutionären Dynamiken. [...]

The heritable endosymbiont Spiroplasma infects many insects and has repeatedly evolved the ability to protect its hosts against different parasites. Defenses do not come for free to the host, and theory predicts that more costly symbionts need to provide stronger benefits to persist in host populations. We investigated the costs and benefits of Spiroplasma infections in pea aphids (Acyrthosiphon pisum), testing 12 bacterial strains from three different clades. Virtually all strains decreased aphid lifespan and reproduction, but only two had a (weak) protective effect against the parasitoid Aphidius ervi, an important natural enemy of pea aphids. Spiroplasma‐induced fitness costs were variable, with strains from the most slowly evolving clade reaching higher titers and curtailing aphid lifespan more strongly than other strains. Some Spiroplasma strains shared their host with a second endosymbiont, Regiella insecticola. Although the result of an unfortunate handling error, these co‐infections proved instructive, because they showed that the cost of infection with Spiroplasma may be attenuated in the presence of Regiella. These results suggest that mechanisms other than protection against A. ervi maintain pea aphid infections with diverse strains of Spiroplasma, and that studying them in isolation will not provide a complete picture of their effects on host fitness.

Virtually all higher organisms form holobionts with associated microbiota. To understand the biology of holobionts we need to know how species assemble and interact. Controlled experiments are suited to study interactions between particular symbionts, but they only accommodate a tiny portion of the diversity within each species. Alternatively, interactions can be inferred by testing if associations among symbionts in the field are more or less frequent than expected under random assortment. However, random assortment may not be a valid null hypothesis for maternally transmitted symbionts since drift alone can result in associations. Here we analyse a European field survey of endosymbionts in pea aphids (Acyrthosiphon pisum), confirming that symbiont associations are pervasive. To interpret them, we develop a model simulating the effect of drift on symbiont associations. We show that drift induces apparently non‐random assortment, even though horizontal transmissions and maternal transmission failures tend to randomise symbiont associations. We also use this model in the approximate Bayesian computation framework to re‐visit the association between Spiroplasma and Wolbachia in Drosophila neotestacea reported by Jaenike et al. (2010a). New field data reported here reveal that this association has disappeared in the investigated location, yet a significant interaction between Spiroplasma and Wolbachia can still be inferred. Our study confirms that negative and positive associations are pervasive and often induced by symbiont‐symbiont interactions. Nevertheless, some associations are also likely to be driven by drift. This possibility needs to be considered when performing such analyses, and our model is helpful for this purpose.

Sex determination has evolved in a variety of ways and can depend on environmental and genetic signals. A widespread form of genetic sex determination is haplodiploidy, where unfertilized, haploid eggs develop into males and fertilized diploid eggs into females. One of the molecular mechanisms underlying haplodiploidy in Hymenoptera, the large insect order comprising ants, bees, and wasps, is complementary sex determination (CSD). In species with CSD, heterozygosity at one or several loci induces female development. Here, we identify the genomic regions putatively underlying multilocus CSD in the parasitoid wasp Lysiphlebus fabarum using restriction-site associated DNA sequencing. By analyzing segregation patterns at polymorphic sites among 331 diploid males and females, we identify up to four CSD candidate regions, all on different chromosomes. None of the candidate regions feature evidence for homology with the csd gene from the honey bee, the only species in which CSD has been characterized, suggesting that CSD in L. fabarum is regulated via a novel molecular mechanism. Moreover, no homology is shared between the candidate loci, in contrast to the idea that multilocus CSD should emerge from duplications of an ancestral single-locus system. Taken together, our results suggest that the molecular mechanisms underlying CSD in Hymenoptera are not conserved between species, raising the question as to whether CSD may have evolved multiple times independently in the group.

Disentangling the relative importance of deterministic and stochastic processes in shaping natural communities is central to ecology. Studies about community assembly over broad temporal and spatial scales in aquatic microorganisms are scarce. Here, we used 16S rDNA sequence data from lake sediments to test for community assembly patterns in cyanobacterial phylogenies across ten European peri-Alpine lakes and over a century of eutrophication and climate warming. We studied phylogenetic similarity in cyanobacterial assemblages over spatial and temporal distance, and over environmental gradients, comparing detected patterns with theoretical expectations from deterministic and stochastic processes. We found limited evidence for deviation of lake communities from a random assembly model and no significant effects of geographic distance on phylogenetic similarity, suggesting no dispersal limitation and high levels of stochastic assembly. We detected a weak influence of phosphorus, but no significant effect of nitrogen levels on deviation of community phylogenies from random. We found however a significant decay of phylogenetic similarity for non-random communities over a gradient of air temperature and water column stability. We show how phylogenetic data from sedimentary archives can improve our understanding of microbial community assembly processes, and support previous evidence that climate warming has been the strongest environmental driver of cyanobacterial community assembly over the past century.

The phylum Cyanobacteria comprises a non-photosynthetic lineage. The diversity anddistribution of non-photosynthetic cyanobacteria (NCY) across aquatic environmentsare currently unknown, including their ecology. Here, we report about composition andphylogenetic diversity of two clades of NCY in ten lakes of the European peri-Alpineregion, over the past ~100 years. Using 16S rDNA sequences obtained from datedsediment cores, we found almost equal proportion of taxa assigned to Melainabacteriaand the deepest-branching group Sericytochromatia (ML635J-21) (63 total detectedtaxa). The topology of our reconstructed phylogenies reflected evolutionary relationshipsexpected from previous work, that is, a clear separation between the deepest branchingSericytochromatia, the Melainabacteria, and the photosynthetic cyanobacteria clades.While different lakes harbored distinct NCY communities, the diversity of NCYassemblages within and between lakes (alpha and beta diversity) did not significantlychange over the last century. This is in contrast with what was previously reportedfor photosynthetic cyanobacteria. Unchanged community phylogenetic similarity overgeographic distance indicated no dispersal limitation of NCY at the regional scale. Ourresults solicit studies linking in-lake environmental factors to the composition of thesemicroorganisms’ communities, whose assembly appeared not to have been influencedby large-scale anthropogenic environmental changes. This is the first attempt to studythe diversity and distribution of NCY taxa across temperate lakes. It provides a firststep towards understanding their distribution and ecological function in pelagic aquatichabitats, where these organisms seem to be prevalent.

Assessing individual components of biodiversity, such as local or regional taxon richness, and differences in community composition is a long‐standing challenge in ecology. It is especially relevant in spatially structured and diverse ecosystems. Environmental DNA (eDNA) has been suggested as a novel technique to detect taxa and therefore may allow to accurately measure biodiversity. However, we do not yet fully understand the comparability of eDNA‐based assessments to classical morphological approaches. We assessed may‐, stone‐, and caddisfly genera with two contemporary methods, namely eDNA sampling followed by molecular identification and kicknet sampling followed by morphological identification. We sampled 61 sites distributed over a large river network, allowing a comparison of various diversity measures from the catchment to site levels and providing insights into how these measures relate to network properties. We extended our data with historical morphological records of total diversity at the catchment level. At the catchment scale, identification based on eDNA and kicknet samples detected similar proportions of the overall and cumulative historically documented richness (gamma diversity), 42% and 46%, respectively. We detected a good overlap (62%) between genera identified from eDNA and kicknet samples at the regional scale. At the local scale, we found highly congruent values of local taxon richness (alpha diversity) between eDNA and kicknet samples. Richness of eDNA was positively related to discharge, a descriptor of network position, while kicknet was not. Beta diversity, a measure of dissimilarity between sites, was comparable for the two contemporary methods and is driven by species replacement and not by nestedness. Although eDNA approaches are still in their infancy and optimization regarding sampling design and laboratory work is still needed, our results indicate that it can capture different components of diversity, proving its potential utility as a new tool for large sampling campaigns across hitherto understudied complete river catchments.

A major challenge in ecology is to understand determinants of ecosystem functioning and stability in the face of disturbance. Some important species can strongly shape community structure and ecosystem functioning, but their impacts and interactions on ecosystem-level responses to disturbance are less well known. Shallow ponds provide a model system in which to study the effects of such species because some taxa mitigate transitions between alternative ecosystem states caused by eutrophication. We performed pond experiments to test how two foundation species (a macrophyte and a mussel) affected the biomass of planktonic primary producers and its stability in response to nutrient additions. Individually, each species reduced phytoplankton biomass and tended to increase rates of recovery from disturbance, but together the species reversed these effects, particularly with larger nutrient additions. This reversal was mediated by high cyanobacterial dominance of the community and a resulting loss of trait evenness. Effects of the foundation species on primary producer biomass were associated with effects on other ecosystem properties, including turbidity and dissolved oxygen. Our work highlights the important role of foundation species and their interactive effects in determining responses of ecosystem functioning to disturbance.

During past decades, many lakes underwent drastic human‐caused changes in trophic state with strong implications for population dynamics and food web processes. We investigated the influence of trophic state on nutrient allocation into Daphnia resting eggs. The production of resting eggs is an important survival strategy, allowing Daphnia to cope with unfavorable environmental conditions. Allocation of essential nutrients into resting eggs may crucially influence embryonic development and offspring survival and thus is of great ecological and evolutionary interest. The capacity of Daphnia to adjust the allocation of nutrients into resting eggs may depend on the dietary nutrient supply, which may vary with trophic state‐related changes in the phytoplankton community composition. Resting eggs were isolated from sediment cores taken from Lake Constance, a large prealpine lake with a distinct eutrophication and reoligotrophication history, and analyzed for elemental (carbon, nitrogen, and phosphorus) and biochemical (sterols and fatty acids) nutrients. Carbon allocation into Daphnia resting eggs continuously decreased over time, irrespective of changes in trophic state. The allocation of nitrogen into Daphnia resting eggs followed the changes in trophic state, that is, nitrogen concentrations in resting eggs increased with eutrophication and decreased again with reoligotrophication. The allocation of phosphorus, sterols and long‐chain polyunsaturated fatty acids, such as eicosapentaenoic acid, into Daphnia resting eggs did not change significantly over time. Changes in trophic state strikingly influenced all trophic levels in Lake Constance. However, nutrient allocation into Daphnia resting eggs was mostly resilient to changes in lake trophic state.

Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.

The persistence of ecological systems in changing environments requires energy, materials, and information. Although the importance of information to ecological function has been widely recognized, the fundamental principles of ecological science as commonly expressed do not reflect this central role of information processing. We articulate five fundamental principles of ecology that integrate information with energy and material constraints across scales of organization in living systems. We show how these principles outline new theoretical and empirical research challenges, and offer one novel attempt to incorporate them in a theoretical model. To provide adequate background for the principles, we review major concepts and identify common themes and key differences in information theories spanning physics, biology and semiotics. We structured our review around a series of questions about the role information may play in ecological systems: (i) what is information? (ii) how is information related to uncertainty? (iii) what is information processing? (iv) does information processing link ecological systems across scales? We highlight two aspects of information that capture its dual roles: syntactic information defining the processes that encode, filter and process information stored in biological structure and semiotic information associated with structures and their context. We argue that the principles of information in living systems promote a unified approach to understanding living systems in terms of first principles of biology and physics, and promote much needed theoretical and empirical advances in ecological research to unify understanding across disciplines and scales.
 

Freshwater environments are fragmented and heterogeneous in space and time. Long term persistence thus necessitates at least occasional dispersal of aquatic organisms to locate suitable habitats. However, the insubstantial movements of many require zoochory-hitchhiking a ride with more mobile animals. We review evidence for waterbird-mediated zoochory of freshwater bryozoans, a group that provides an excellent model for addressing this issue. The feasibility of long distance transport by waterbirds of bryozoan propagules (statoblasts) is evaluated in relation to statoblast resistance to extreme conditions and waterbird gut retention times, flight durations and distances. We highlight genetic evidence for colonization following waterbird-mediated transport. The consequences of zoochory for biodiversity are manifold. Taxa that release statoblasts show lower levels of genetic differentiation, genetic divergence and haplotype diversity than those whose statoblasts are retained in situ (hence less available for zoochory). Zoochory may also disseminate pathogens and parasites when infected host stages are transported. Such co-dispersal may explain some disease distributions and is supported by viability of infected statoblasts. Zoochory can also be expected to influence local and regional population and community dynamics, food web structure and stability, and organismal distributions, and abundances. Finally, zoochory may influence host-parasite coevolution and disease dynamics across the landscape with the benefits to parasites depending on their life history (e.g., simple vs. complex life cycles, generalists vs. specialists). Our synthesis highlights the complex ecological and evolutionary impacts of zoochory of freshwater organisms and raises questions for future research.

The cost of males should give asexual females an advantage when in competition with sexual females. In addition, high‐fecundity asexual genotypes should have an advantage over low‐fecundity clones, leading to reduction in clonal diversity over time. To evaluate fitness components in a natural population, we measured the annual reproductive rate of individual sexual and asexual female Potamopyrgus antipodarum, a New Zealand freshwater snail, in field enclosures that excluded competitors and predators. We used allozyme genotyping to assign the asexual females to particular clonal genotypes. We found that the most fecund asexual clones had similar or higher fecundity as the top 10% of sexual families, suggesting that fecundity selection, even without the cost of males, would lead to replacement of the sexual population by clones. Consequently, we expected that the clones with the highest fecundity would dominate the natural population. Counter to this prediction, we found that high annual reproductive rates did not correlate with the frequency of clones in the natural population. When we exposed the same clones to parasites in the laboratory, we found that resistance to infection was positively correlated with the frequency of clones in the population. The correlation between fecundity and parasite resistance was negative, suggesting a trade‐off between these two traits. Our results thus suggest that parasite resistance is an important short‐term predictor of the success of asexual P. antipodarum in this population.

Successfully predicting the future states of systems that are complex, stochastic, and potentially chaotic is a major challenge. Model forecasting error (FE) is the usual measure of success; however model predictions provide no insights into the potential for improvement. In short, the realized predictability of a specific model is uninformative about whether the system is inherently predictable or whether the chosen model is a poor match for the system and our observations thereof. Ideally, model proficiency would be judged with respect to the systems' intrinsic predictability, the highest achievable predictability given the degree to which system dynamics are the result of deterministic vs. stochastic processes. Intrinsic predictability may be quantified with permutation entropy (PE), a model-free, information-theoretic measure of the complexity of a time series. By means of simulations, we show that a correlation exists between estimated PE and FE and show how stochasticity, process error, and chaotic dynamics affect the relationship. This relationship is verified for a data set of 461 empirical ecological time series. We show how deviations from the expected PE–FE relationship are related to covariates of data quality and the nonlinearity of ecological dynamics. These results demonstrate a theoretically grounded basis for a model-free evaluation of a system's intrinsic predictability. Identifying the gap between the intrinsic and realized predictability of time series will enable researchers to understand whether forecasting proficiency is limited by the quality and quantity of their data or the ability of the chosen forecasting model to explain the data. Intrinsic predictability also provides a model-free baseline of forecasting proficiency against which modeling efforts can be evaluated.

The growing threat of global climate change has led to a profusion of studies examining the effects of warming on biota. Despite the potential importance of natural variability such as diurnal temperature fluctuations, most experimental studies on warming are conducted under stable temperatures. Here, we investigated whether the responses of an aquatic invertebrate grazer (Lymnaea stagnalis) to an increased average temperature differ when the thermal regime is either constant or fluctuates diurnally. Using thermal response curves for several life‐history and immune defense traits, we first identified the optimum and near‐critically high temperatures that Lymnaea potentially experience during summer heat waves. We then exposed individuals that originated from three different populations to these two temperatures under constant or fluctuating thermal conditions. After 7 days, we assessed growth, reproduction, and two immune parameters (phenoloxidase‐like activity and antibacterial activity of hemolymph) from each individual. Exposure to the near‐critically high temperature led to increased growth rates and decreased antibacterial activity of hemolymph compared to the optimum temperature, whilst temperature fluctuations had no effect on these traits. The results indicate that the temperature level per se, rather than the variability in temperature was the main driver altering trait responses in our study species. Forecasting responses in temperature‐related responses remains challenging, due to system‐specific properties that can include intraspecific variation. However, our study indicates that experiments examining the effects of warming using constant temperatures can give similar predictions as studies with fluctuating thermal dynamics, and may thus be useful indicators of responses in nature.

When traits affecting species interactions evolve rapidly, ecological dynamics can be altered while they occur. These eco-evolutionary dynamics have been documented repeatedly in laboratory and mesocosm experiments. We show here that they are also important for understanding community functioning in a natural ecosystem. Daphnia is a major planktonic consumer influencing seasonal plankton dynamics in many lakes. It is also sensitive to succession in its phytoplankton food, from edible algae in spring to relatively inedible cyanobacteria in summer. We show for Daphnia mendotae in Oneida Lake, New York, United States, that within-year ecological change in phytoplankton (from spring diatoms, cryptophytes and greens to summer cyanobacteria) resulted in consumers evolving increasing tolerance to cyanobacteria over time. This evolution fed back on ecological seasonal changes in population abundance of this major phytoplankton consumer. Oneida Lake is typical of mesotrophic lakes broadly, suggesting that eco-evolutionary consumer-resource dynamics is probably common.

Identifying traits that underlie variation in individual performance of consumers (i.e., trait utility) can help reveal the ecological causes of population divergence and the subsequent consequences for species interactions and community structure. Here, we document a case of rapid divergence (over the past 100 generations, or ∼150 years) in foraging traits and feeding efficiency between a lake and stream population pair of threespine stickleback. Building on predictions from functional trait models of fish feeding, we analyzed foraging experiments with a Bayesian path analysis and elucidated the traits explaining variation in foraging performance and the species composition of ingested prey. Despite extensive previous research on the divergence of foraging traits among populations and ecotypes of stickleback, our results provide novel experimental evidence of trait utility for jaw protrusion, gill raker length, and gill raker spacing when foraging on a natural zooplankton assemblage. Furthermore, we discuss how these traits might contribute to the differential effects of lake and stream stickleback on their prey communities, observed in both laboratory and mesocosm conditions. More generally, our results illustrate how the rapid divergence of functional foraging traits of consumers can impact the biomass, species composition, and trophic structure of prey communities.Keywords: trait utility, jaw protrusion, foraging performance, prey preference, rapid population divergence, Gasterosteus aculeatus.

Divergence in phenotypic traits is facilitated by a combination of natural selection, phenotypic plasticity, gene flow, and genetic drift, whereby the role of drift is expected to be particularly important in small and isolated populations. Separating the components of phenotypic divergence is notoriously difficult, particularly for multivariate phenotypes. Here, we assessed phenotypic divergence of threespine stickleback (Gasterosteus aculeatus) across 19 semi‐interconnected ponds within a small geographic region (~7.5 km²) using comparisons of multivariate phenotypic divergence (PST), neutral genetic (FST), and environmental (EST) variation. We found phenotypic divergence across the ponds in a suite of functionally relevant phenotypic traits, including feeding, defense, and swimming traits, and body shape (geometric morphometric). Comparisons of PSTs with FSTs suggest that phenotypic divergence is predominantly driven by neutral processes or stabilizing selection, whereas phenotypic divergence in defensive traits is in accordance with divergent selection. Comparisons of population pairwise PSTs with ESTs suggest that phenotypic divergence in swimming traits is correlated with prey availability, whereas there were no clear associations between phenotypic divergence and environmental difference in the other phenotypic groups. Overall, our results suggest that phenotypic divergence of these small populations at small geographic scales is largely driven by neutral processes (gene flow, drift), although environmental determinants (natural selection or phenotypic plasticity) may play a role.

Climate change and human pressures are changing the global distribution and the extent of intermittent rivers and ephemeral streams (IRES), which comprise half of the global river network area. IRES are characterized by periods of flow cessation, during which channel substrates accumulate and undergo physico-chemical changes (preconditioning), and periods of flow resumption, when these substrates are rewetted and release pulses of dissolved nutrients and organic matter (OM). However, there are no estimates of the amounts and quality of leached substances, nor is there information on the underlying environmental constraints operating at the global scale. We experimentally simulated, under standard laboratory conditions, rewetting of leaves, riverbed sediments, and epilithic biofilms collected during the dry phase across 205 IRES from five major climate zones. We determined the amounts and qualitative characteristics of the leached nutrients and OM, and estimated their areal fluxes from riverbeds. In addition, we evaluated the variance in leachate characteristics in relation to selected environmental variables and substrate characteristics. We found that sediments, due to their large quantities within riverbeds, contribute most to the overall flux of dissolved substances during rewetting events (56%–98%), and that flux rates distinctly differ among climate zones. Dissolved organic carbon, phenolics, and nitrate contributed most to the areal fluxes. The largest amounts of leached substances were found in the continental climate zone, coinciding with the lowest potential bioavailability of the leached OM. The opposite pattern was found in the arid zone. Environmental variables expected to be modified under climate change (i.e. potential evapotranspiration, aridity, dry period duration, land use) were correlated with the amount of leached substances, with the strongest relationship found for sediments. These results show that the role of IRES should be accounted for in global biogeochemical cycles, especially because prevalence of IRES will increase due to increasing severity of drying events.

Alpine streams can exhibit naturally high levels of flow intermittency. However, how flow intermittency in alpine streams affects ecosystem functions such as food web trophic structure is virtually unknown. Here, we characterized the trophic diversity of aquatic food webs in 28 headwater streams of the Val Roseg, a glacierized alpine catchment. We compared stable isotope (δ¹³C and δ¹⁵N) trophic indices to high temporal resolution data on flow intermittency. Overall trophic diversity, food chain length, and diversity of basal resource use did not differ to a large extent across streams. In contrast, gradient and mixing model analysis indicated that primary consumers assimilated proportionally more periphyton and less allochthonous organic matter in more intermittent streams. Higher coarse particulate organic matter (CPOM) C:N ratios were an additional driver of changes in macroinvertebrate diets. These results indicate that the trophic base of stream food webs shifts away from terrestrial organic matter to autochthonous organic matter as flow intermittency increases, most likely due to reduced CPOM conditioning in dry streams. This study highlights the significant, yet gradual shifts in ecosystem function that occur as streamflow becomes more intermittent in alpine streams. As alpine streams become more intermittent, identifying which functional changes occur via gradual as opposed to threshold responses is likely to be vitally important to their management and conservation.

More than 60% of the spionid polychaetes recorded in South Africa to date have type localities from outside the region. One of these is Rhynchospio glutaea (Ehlers, 1897), originally described from Argentina, which was suggested to have arrived in Table Bay via shipping. Recently specimens conforming to the description of R. glutaea were collected on the south coast of South Africa from within the effluent outflow pipes from an on-shore abalone farm. The species, here named Rhynchospio mzansi n. sp., belongs to the Rhynchospio glutaea complex, and has tridentate hooded hooks that usually start on chaetiger 15–18 and up to four pairs of dorsal anal cirri. Four molecular markers confirm that the South African material is a previously undescribed species that is the most basal of the other species within the R. glutaea complex and genetically closest to R. glutaea and R. arenincola Hartmann, 1936, from the west coast of North America. This is the first species in this genus described for South Africa.

A major goal of evolutionary science is to understand how biological diversity is generated and altered. Despite considerable advances, we still have limited insight into how phenotypic variation arises and is sorted by natural selection. Here we argue that an integrated view, which merges ecology, evolution and developmental biology (eco evo devo) on an equal footing, is needed to understand the multifaceted role of the environment in simultaneously determining the development of the phenotype and the nature of the selective environment, and how organisms in turn affect the environment through eco evo and eco devo feedbacks. To illustrate the usefulness of an integrated eco evo devo perspective, we connect it with the theory of resource polymorphism (i.e. the phenotypic and genetic diversification that occurs in response to variation in available resources). In so doing, we highlight fishes from recently glaciated freshwater systems as exceptionally well‐suited model systems for testing predictions of an eco evo devo framework in studies of diversification. Studies on these fishes show that intraspecific diversity can evolve rapidly, and that this process is jointly facilitated by (i) the availability of diverse environments promoting divergent natural selection; (ii) dynamic developmental processes sensitive to environmental and genetic signals; and (iii) eco evo and eco devo feedbacks influencing the selective and developmental environments of the phenotype. We highlight empirical examples and present a conceptual model for the generation of resource polymorphism - emphasizing eco evo devo, and identify current gaps in knowledge.

Understanding the effects of parasites on host behaviour, of host behaviour on parasite infection, and the reciprocal interactions between these processes is vital to improving our understanding of animal behaviour and disease dynamics. However, behaviour and parasite infection are both highly variable within and between individual hosts, and how this variation affects behaviour–parasite feedbacks is poorly understood. For example, it is unclear how an individual's behaviour before infection might change once it becomes infected, or as the infection progresses, and how these changes depend on the host's parasite susceptibility. Here, using the guppy, Poecilia reticulata, and a directly transmitted ectoparasite, Gyrodactylus turnbulli, I show that parasite-induced behavioural plasticity depends on host sex and susceptibility. Among females, time spent shoaling (sociality), a behaviour that increases parasite transmission, did not depend on infection status (infected/not) or susceptibility. By contrast, male sociality in the absence of infection was negatively correlated with susceptibility, suggesting that the most susceptible males use behaviour to avoid infection. However, in late infection, when parasite transmission is most likely, male sociality and susceptibility became positively correlated, suggesting that susceptible males modify their behaviour upon infection potentially to increase transmission and mating opportunities. I discuss the implications of these patterns for disease dynamics.

Biotransformation of chemical pollutants is an ecological process requiring multifunctionality (multiple metabolic pathways) and, potentially, high biodiversity. Phytoplankton communities are highly diverse functionally and taxonomically and co-occur with complex mixtures of organic pollutants in aquatic environments. Here, we investigated how phytoplankton species richness (SR) and class richness (CR) determine the biotransformation of a mixture of 37 structurally diverse pollutants using laboratory experiments and analysis of high-resolution mass spectrometry data. Laboratory phytoplankton communities were assembled from pure cultures by creating a gradient from one to five taxonomic groups, and 5 to 11 total species, in defined medium. The biotransformation of pollutants over 6 days and the total number of transformed chemicals increased with CR for 13 considerably transformed compounds. The total number of transformation products (TPs, up to 42) was positively affected by both CR and SR: CR had a positive effect on stable TPs found, and SR led to more transient TPs. Our data indicate that both taxonomic and functional diversity are important for biotransformation of anthropogenic chemicals in phytoplankton and suggest that plankton biodiversity could play a role in the remediation of pollutant loads in aquatic ecosystems.

Intermittent rivers and ephemeral streams (IRES) are dynamic ecosystems that shift between aquatic and terrestrial states. IRES are widespread, abundant and increasing in extent, but developing biomonitoring programmes to determine their ecological quality is challenging. To date, quality assessments have focused on the aquatic organisms present during wet phases, whereas dry-phase communities remain poorly characterized. We examined multiple biotic groups present in dry IRES channels, to compare assemblages at sites impacted and unimpacted by human activity and to evaluate the potential of each group as an ecological quality indicator. We explored existing, unpublished data for three biotic groups: an aquatic microflora (diatoms), an aquatic fauna (the invertebrate 'seedbank'), and a mixed flora (aquatic and terrestrial plants); notably, we did not source data for terrestrial assemblages with high potential to act as indicators. Diatom and plant assemblage composition differed between impacted and unimpacted sites, and the latter assemblages were more diverse and included more indicator taxa. Invertebrate seedbank taxa richness was higher at unimpacted sites but compositional differences were not detected, probably due to the coarse taxonomic resolution to which abundant taxa were identified. Performance of standard indices of ecological quality was variable, but differences were identified between impacted and unimpacted conditions for all biotic groups. Our results can inform the enhancement of biomonitoring programmes designed to characterize IRES ecological quality in relation to legislative targets. We highlight the need to integrate wet- and dry-phase survey data in holistic quality assessments. Although we suggest diatoms, aquatic plants and the aquatic invertebrate seedbank as having the potential to inform assessment of dry-phase ecological quality, we highlight the need for research to further characterize these aquatic groups and, crucially, to explore terrestrial assemblages with high potential to act as dry-phase quality indicators.

River reaches downstream dams where a constant residual flow discharge is imposed, often lack sediment supply and periodic inundation due to the absence of natural flood events. In this study, a two-year return flood was released from an upstream reservoir and combined with sediment replenishment to enhance instream habitat conditions downstream of Rossens hydropower dam on the Sarine River in western Switzerland. Sediment replenishment consisted of four sediment deposits distributed as alternate bars along the river banks, a solution which was previously tested in laboratory. The morphological evolution of the replenishment and of the downstream riverbed were surveyed including pre- and post-flood topography. A hydro-morphological index to evaluate the quality of riverine habitats, based on the variability of flow depth and flow velocity in the analyzed reach, was investigated. The combination of the artificial flood with sediment replenishment proved to be a robust measure to supply a river with sediment and to enhance hydraulic habitat suitability.

Global change influences biogeochemical cycles within and between environmental compartments (i.e., the cryosphere, terrestrial and aquatic ecosystems, and the atmosphere). A major effect of global change on carbon cycling is altered exposure of natural organic matter (NOM) to solar radiation, particularly solar UV radiation. In terrestrial and aquatic ecosystems, NOM is degraded by UV and visible radiation, resulting in the emission of carbon dioxide (CO₂) and carbon monoxide, as well as a range of products that can be more easily degraded by microbes (photofacilitation). On land, droughts and land-use change can reduce plant cover causing an increase in exposure of plant litter to solar radiation. The altered transport of soil organic matter from terrestrial to aquatic ecosystems also can enhance exposure of NOM to solar radiation. An increase in emission of CO₂ from terrestrial and aquatic ecosystems due to the effects of global warming, such as droughts and thawing of permafrost soils, fuels a positive feedback on global warming. This is also the case for greenhouse gases other than CO₂, including methane and nitrous oxide, that are emitted from terrestrial and aquatic ecosystems. These trace gases also have indirect or direct impacts on stratospheric ozone concentrations. The interactive effects of UV radiation and climate change greatly alter the fate of synthetic and biological contaminants. Contaminants are degraded or inactivated by direct and indirect photochemical reactions. The balance between direct and indirect photodegradation or photoinactivation of contaminants is likely to change with future changes in stratospheric ozone, and with changes in runoff of coloured dissolved organic matter due to climate and land-use changes.

Aim: Plant functional groups are widely used in community ecology and earth system modelling to describe trait variation within and across plant communities. However, this approach rests on the assumption that functional groups explain a large proportion of trait variation among species. We test whether four commonly used plant functional groups represent variation in six ecologically important plant traits.
Location: Tundra biome.
Time period: Data collected between 1964 and 2016.
Major taxa studied: 295 tundra vascular plant species.
Methods: We compiled a database of six plant traits (plant height, leaf area, specific leaf area, leaf dry matter content, leaf nitrogen, seed mass) for tundra species. We examined the variation in species-level trait expression explained by four traditional functional groups (evergreen shrubs, deciduous shrubs, graminoids, forbs), and whether variation explained was dependent upon the traits included in analysis. We further compared the explanatory power and species composition of functional groups to alternative classifications generated using post hoc clustering of species-level traits.
Results: Traditional functional groups explained significant differences in trait expression, particularly amongst traits associated with resource economics, which were consistent across sites and at the biome scale. However, functional groups explained 19% of overall trait variation and poorly represented differences in traits associated with plant size. Post hoc classification of species did not correspond well with traditional functional groups, and explained twice as much variation in species-level trait expression.
Main conclusions: Traditional functional groups only coarsely represent variation in well-measured traits within tundra plant communities, and better explain resource economic traits than size-related traits. We recommend caution when using functional group approaches to predict tundra ecosystem change, or ecosystem functions relating to plant size, such as albedo or carbon storage. We argue that alternative classifications or direct use of specific plant traits could provide new insight into ecological prediction and modelling.

Purpose: To understand the relationship between baseline ischemic index (IsI) values on ultra-widefield fluorescein angiography and classification as ischemic central retinal vein occlusion (CRVO).
Methods: Single-center retrospective cohort study of CRVO patients imaged using ultra-widefield fluorescein angiography from which IsI values were calculated. An ischemic CRVO was defined as those eyes with an afferent pupillary defect and counting fingers acuity or worse or neovascularization during the first year of follow-up. Logistic regression was performed to characterize the relation between the IsI and clinical outcomes.
Results: Sixty eyes of 60 treatment-naive CRVO patients with baseline ultra-widefield fluorescein angiography and ≥1 year of follow-up were identified. Those with an IsI ≥35% were significantly more likely to have an ischemic CRVO during the first year of follow-up than those with an IsI <35% (83.3 vs. 13.9%, odds ratio 111, P < 0.0001). Baseline and final logarithm of the minimum angle of resolution acuity were worse in eyes with an IsI ≥35% (1.18 vs. 0.46, P < 0.001 and 1.26 vs. 0.45, P < 0.001, respectively) despite similar baseline and final central subfield thickness (P = 0.1–0.23).
Conclusion: A baseline IsI of ≥35% on ultra-widefield fluorescein angiography in eyes with treatment-naive CRVO was sensitive (90%) and specific (92.5%) for classification as an ischemic CRVO during the first year of follow-up.

River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which dependsstrongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized atthe global scale. In response, we used a peer-sourced research network and a highly standardized carbon processingassay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth’sbiomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid ratesare restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperatureconstraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward theequator. These results and data set the stage for unprecedented “next-generation biomonitoring” by establishingbaselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.

Temperature and photoperiod regulate key fitness traits in plants and animals. However, with temperature increase due to global warming, temperature cue thresholds are experienced at shorter photoperiods, disrupting the optimal seasonal timing of physiological, developmental and reproductive events in many species. Understanding the mechanisms of adaptation to the asynchrony between temperature and photoperiod is key to inform our understanding of how species will respond to global warming. Here, we studied the transgenerational mechanisms of responses of the cyclical parthenogen Daphnia magna to different photoperiod lengths co-occurring with warm temperature thereby assessing the impact of earlier spring warming on its fitness. Daphnia uses temperature and photoperiod cues to time dormancy, and to switch between sexual and asexual reproduction. Daphnia life cycle offers the opportunity to measure the relative contribution of plastic and genetic responses to environmental change across generations and over evolutionary time. We use transgenerational common garden experiments on three populations 'resurrected' from a biological archive experiencing temperature increase over five decades. Our results suggest that response to early spring warming evolved underpinned by a complex interaction between plastic and genetic mechanisms while a positive maternal contribution at matching environments between parental and offspring generation was also observed.

Understanding whether populations and communities can evolve fast enough to keep up with ongoing climate change is one of the most pressing issues in biology today. A growing number of studies have documented rapid evolutionary responses to warming, suggesting that populations may be able to persist despite temperature increases. The challenge now is to better understand how species interactions, which are ubiquitous in nature, mediate these population responses to warming. Here, we use laboratory natural selection experiments in a freshwater community to test hypotheses related to how thermal evolution of Daphnia pulex to two selection temperatures (12 and 18°C) is mediated by rapid thermal evolution of its algal resource (Scenedesmus obliquus) or by the presence of the zooplankton predator Chaoborus americanus. We found that cold‐evolved algae (a high‐quality resource) facilitated the evolution of increased thermal plasticity in Daphnia populations selected at 12°C, for both body size and per capita growth rates (r). Conversely, warm‐evolved algae facilitated the evolution of increased r thermal plasticity for Daphnia selected at 18°C. Lastly, we found that the effect of selection temperature on evolved Daphnia body size was more pronounced when Daphnia were also reared with predators. These data demonstrate that trait evolution of a focal population to the thermal environment can be affected by both bottom‐up and top‐down species interactions and that rapid temperature evolution of a resource can have cascading effects on consumer thermal evolution. Our study highlights the importance of incorporating species interactions when estimating ecological and evolutionary responses of populations and communities to ongoing temperature warming.

We compared taxon composition of the Daphnia longispina hybrid community, as reconstructed from dormant eggs (retrieved from sediment samples) and the pelagic population (retrieved from formaldehyde-preserved zooplankton samples), from the same lake and of the same time period. As microsatellite markers do not work on largely fragmented DNA, such as of formaldehyde-preserved samples, both types of samples (dormant eggs and pelagic Daphnia) were screened with single-nucleotide polymorphism (SNP) markers. Here, we designed a genotyping panel of short SNP-bearing amplicons and, to facilitate screening, we developed a multiplex genotyping protocol. The results of this comparison confirmed differences between dormant and pelagic samples. Specifically, D. galeata was overrepresented in the sedimentary egg bank in comparison to the pelagic population, indicating that this taxon is more involved in sexual reproduction than other taxa. In addition to being successfully applied on formaldehyde-preserved samples, SNP-genotyping was more efficient than microsatellites on sedimentary eggs, and was more sensitive for hybrid detection. In conclusion, the SNP-based genotyping panel presented here enables to study the genetic structure of past populations from common formaldehyde-preserved collections. It is also promising for genotyping old dormant eggs, which can extend the temporal range of Daphnia community reconstructions.
 

The metapopulation concept initiated a paradigm shift in ecology and conservation biology, recognizing the eminent role of dispersal and colonization as fundamental processes contributing to species’ long‐term persistence. Early models made ad hoc assumptions about a positive area dependency of dispersal (i.e., total number of emigrants), which persisted in the theoretical literature; however, numerous empirical examples of negative area dependencies of dispersal have been reported. Here, we first give a qualitative overview for different area dependencies of dispersal in empirical systems. Then, using a spatially realistic Levins model, we show that extending assumptions on the area dependence of dispersal (ADD) to include all empirically supported parameter space, specifically also negative ADD, alters predictions on several conservation‐relevant patterns. Importantly, we find that small patches could be of similar importance as large ones if dispersal decreases inversely with patch area, a result contrasting with previous findings based on a positive ADD. This leads to context‐dependent strategies to preserve metapopulations. If dispersal is positively correlated with patch area, efforts should be devoted to preserving large patches and the total habitat area. If dispersal is negatively correlated with patch area, the most efficient strategy is to preserve a high number of patches, including small ones. Our results have direct implications for management decisions in the context of destruction, deterioration, and protection of habitat patches.

In life histories with generation overlap, selection that acts differently on different life-stages can produce reservoirs of genetic variation, for example, in long-lived iteroparous adults or long-lived dormant propagules. Such reservoirs provide "migration from the past" to the current population, and depending on the trend of environmental change, they have the potential either to slow adaptive evolution or accelerate it by re-introducing genotypes not affected by recent selection (e.g., through storage effect in a fluctuating environment). That is, the effect of generation overlap is a "double-edged sword," with each edge cutting in a different direction. Here, we use sexual (quantitative trait) and asexual (clonal) models to explore the effects of generation overlap on adaptive evolution in a fluctuating environment, either with or without a trend in the mean environment state. Our analyses show that when environmental stochasticity scaled by strength of selection is intermediate and when the trend in mean environment is slow, intermediate values of generation overlap can maximize the rate of response to selection and minimize the adaptation lag between the trait mean and the environmental trend. Otherwise, increased generation overlap results in smaller selection response and larger adaptation lag. In the former case, low generation overlap results in low heritable trait variance, while high generation overlap increases the "migration load" from the past. Therefore, to understand the importance of rapid evolution and eco-evolutionary dynamics in the wild for organisms with overlapping generations, we need to understand the interaction of generation overlap, environmental stochasticity, and strength of selection.

Intermittent rivers and ephemeral streams (IRES) may represent over half the global stream network, but their contribution to respiration and carbon dioxide (CO₂) emissions is largely undetermined. In particular, little is known about the variability and drivers of respiration in IRES sediments upon rewetting, which could result in large pulses of CO₂. We present a global study examining sediments from 200 dry IRES reaches spanning multiple biomes. Results from standardized assays show that mean respiration increased 32‐fold to 66‐fold upon sediment rewetting. Structural equation modeling indicates that this response was driven by sediment texture and organic matter quantity and quality, which, in turn, were influenced by climate, land use, and riparian plant cover. Our estimates suggest that respiration pulses resulting from rewetting of IRES sediments could contribute significantly to annual CO₂ emissions from the global stream network, with a single respiration pulse potentially increasing emission by 0.2–0.7%. As the spatial and temporal extent of IRES increases globally, our results highlight the importance of recognizing the influence of wetting‐drying cycles on respiration and CO₂ emissions in stream networks.

1. Understanding the consequences of spatial structure on ecological dynamics is a central theme in ecology. Recently, research has recognised the relevance of river and river-analogue network structures, because these systems are not only highly diverse but also rapidly changing due to habitat modifications or species invasions.
2. Much of the previous work on ecological and evolutionary dynamics in metapopulations and metacommunities in dendritic river networks has been either using comparative approaches or was purely theoretical. However, the use of microcosm experiments provides the unique opportunity to study large-scale questions in a causal and experimental framework.
3. We conducted replicated microcosm experiments, in which we manipulated the spatially explicit network configuration of a landscape and addressed how linear versus dendritic connectivity affects population dynamics, specifically the spatial distribution of population densities, and movement behaviour of the protist model organism Tetrahymena pyriformis. We tracked population densities and individual-level movement behaviour of thousands of individuals over time.
4. At the end of the experiment, we found more variable population densities between patches in dendritic networks compared to linear networks, as predicted by theory. Specifically, in dendritic networks, population densities were higher at nodes that connected to headwaters compared to the headwaters themselves and to more central nodes in the network. These differences follow theoretical predictions and emerged from the different network topologies per se. These differences in population densities emerged despite weakly density-dependent movement.
5. We show that differences in network structure alone can cause characteristic spatial variation in population densities. While such differences have been postulated by theoretical work and are the underlying precondition for differential dispersal evolution in heterogeneous networks, our results may be the first experimental demonstration thereof. Furthermore, these population-level dynamics may affect extinction risks and can upscale to previously shown metacommunity level diversity dynamics. Given that many species in natural river systems exhibit strong spatiotemporal patterns in population densities, our work suggests that abundance patterns should not only be addressed from a local environmental perspective, but may be the outcome of processes that are inherently driven by the respective habitat network structure.

Schmetterlinge bilden mit über 150 000 Arten eine der grössten Insektenordnungen der Welt. In der Schweiz kommen rund 3700 Arten vor, davon sind 182 Arten echte Tagfalter. Wir konnten auf der Furka in kurzer Zeit 27 Tagfalterarten (15%) und 77 nachtaktive Arten feststellen. Zudem wurden 22 Kleinschmetterlingsarten beobachtet.

The present thesis investigated the diversity and distribution of amphipods (Crustacea, Amphipoda) in Switzerland, based on an extensive collection and analysis of faunistic and ecological data. The thesis aimed to provide an updated and substantiated foundation for future ecological, faunistic and taxonomic research on these important crustaceans, with a particular focus on Switzerland. The thesis was conducted as integral part of the project Amphipod.CH that was initiated to intensify the study of amphipods in Switzerland.

Amphipods are an order of crustaceans that represent keystone species in a wide variety of both marine and freshwater ecosystems. As such they contribute considerably to the biodiversity and functioning of these ecosystems, for example by linking different trophic levels or as major decomposers. In many temperate freshwater ecosystems (including groundwater, caves, lakes and stream ecosystems), amphipods are among the most abundant macroinvertebrates. However, their communities are also rapidly changing due to their high sensitivity to environmental change and pollution as well as a high proportion of non-native amphipod species reaching new habitats, particularly in Europe and Switzerland. It is therefore crucial to understand their ecology and systematics in order to detect and understand such changes and take appropriate conservation measures.

In my thesis I focused on improving the knowledge and data on amphipods in Switzerland. Before the onset of the project, only limited information on amphipods had been available for the European Alps and Switzerland in particular. With several major European drainage areas originating in Switzerland, the region represents a biogeographically interesting area . In a first step, I reviewed for the thesis all previously published literature on amphipods and summarized this ecological and faunistic information for a general introduction to amphipods of Switzerland. This includes publications from the 19th century up to the most recent findings from 2017. I then described several new species for Switzerland or even new to science based on molecular methods and morphological features, some of these species are even endemic to Switzerland. Based on this work, I developed a fully illustrated species identification key. It covers all 44 species of amphipods known from Switzerland, is fully compliant with recent systematics and covers all drainage areas of Switzerland. Thereby, it is the first ever key to all amphipods of Switzerland. Finally, I analyzed amphipod communities using diversity analyses covering a large spatial extent to get a deeper insight into the importance of dispersal and habitat connectivity for community formation and biological invasions in dendritic networks. Overall, my thesis improves and synthesizes the knowledge on amphipods of Switzerland and will hopefully ease all future work on this important taxonomic group of freshwater macroinvertebrates.

Habitat connectivity crucially influences dispersal of organisms. It is especially seen as an important driver of the spatial structuring of biological communities in ecosystems that have intrinsic and general connectivity patterns, such as the universal dendritic structure of fluvial networks. These networks not only define dispersal of native species, but also represent corridors of biological invasions, making understanding network topology effects on invasion dynamics and subsequent diversity patterns of high interest. We studied amphipod community diversity and structure in the upper 27,882-km² drainage basin of the river Rhine in Central Europe, focusing on differences between native and non-native species. Overall, species richness increased along the network from headwaters to the outlet nodes. We found, however, contrasting patterns of native and non-native amphipod richness along the network, with headwater nodes representing refugia for native species and more downstream nodes being hotspots of biological invasions. Importantly, while species turnover (b-diversity) of native species increased with distance between nodes in the network, this was not the case for non-native species, indicating a much lower dispersal limitation of the latter. Finally, the overall amphipod community structure closely mirrored the topological modularity of the network, highlighting the network’s imprint on community structure. Our results underpin the importance of connectivity for community formation and the significance of rivers for biological invasions and suggest that empirically observed matches of diversity patterns in rivers predicted by null models are the long-term outcome of species invasions and species sorting.

The Environmental Effects Assessment Panel (EEAP) is one of three Panels of experts that inform theParties to the Montreal Protocol. The EEAP focuses on the effects of UV radiation on human health, terrestrialand aquatic ecosystems, air quality, and materials, as well as on the interactive effects of UV radiationand global climate change. When considering the effects of climate change, it has become clearthat processes resulting in changes in stratospheric ozone are more complex than previously held.Because of the Montreal Protocol, there are now indications of the beginnings of a recovery of stratosphericozone, although the time required to reach levels like those before the 1960s is still uncertain,particularly as the effects of stratospheric ozone on climate change and vice versa, are not yet fully understood.Some regions will likely receive enhanced levels of UV radiation, while other areas will likely experiencea reduction in UV radiation as ozone- and climate-driven changes affect the amounts of UV radiationreaching the Earth’s surface. Like the other Panels, the EEAP produces detailed Quadrennial Reportsevery four years; the most recent was published as a series of seven papers in 2015 (Photochem.Photobiol. Sci., 2015, 14, 1–184). In the years in between, the EEAP produces less detailed and shorterUpdate Reports of recent and relevant scientific findings. The most recent of these was for 2016(Photochem. Photobiol. Sci., 2017, 16, 107–145). The present 2017 Update Report assesses some of thehighlights and new insights about the interactive nature of the direct and indirect effects of UV radiation,atmospheric processes, and climate change. A full 2018 Quadrennial Assessment, will be made availablein 2018/2019.

The research of a generation of ecologists was catalysed by the recognition that the number and identity of species in communities influences the functioning of ecosystems. The relationship between biodiversity and ecosystem functioning (BEF) is most often examined by controlling species richness and randomising community composition. In natural systems, biodiversity changes are often part of a bigger community assembly dynamic. Therefore, focusing on community assembly and the functioning of ecosystems (CAFE), by integrating both species richness and composition through species gains, losses and changes in abundance, will better reveal how community changes affect ecosystem function. We synthesise the BEF and CAFE perspectives using an ecological application of the Price equation, which partitions the contributions of richness and composition to function. Using empirical examples, we show how the CAFE approach reveals important contributions of composition to function. These examples show how changes in species richness and composition driven by environmental perturbations can work in concert or antagonistically to influence ecosystem function. Considering how communities change in an integrative fashion, rather than focusing on one axis of community structure at a time, will improve our ability to anticipate and predict changes in ecosystem function.

The Morphological Quality Index (MQI) and the Morphological Quality Index for monitoring (MQIm) have been applied to eight case studies across Europe with the objective of analyzing the hydromorphological response to various restoration measures and of comparing the results of the MQI and MQIm as a morphological assessment applied at the reach scale, with a conventional site scale physical-habitat assessment method. For each restored reach, the two indices were applied to the pre-restoration and post-restoration conditions. The restored reach was also compared to an adjacent, degraded reach. Results show that in all cases the restoration measures improved the morphological quality of the reach, but that the degree of improvement depends on many factors, including the initial morphological conditions, the length of the restored portion in relation to the reach length, and on the type of intervention. The comparison with a conventional site scale physical-habitat assessment method shows that the MQI and MQIm are best suited for the evaluation of restoration effects on river hydromorphology at the geomorphologically-relevant scale of the river reach.

The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature–trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming.

Motivation: The Tundra Trait Team (TTT) database includes field‐based measurements of key traits related to plant form and function at multiple sites across the tundra biome. This dataset can be used to address theoretical questions about plant strategy and trade‐offs, trait–environment relationships and environmental filtering, and trait variation across spatial scales, to validate satellite data, and to inform Earth system model parameters.
Main types of variable contained: The database contains 91,970 measurements of 18 plant traits. The most frequently measured traits (> 1,000 observations each) include plant height, leaf area, specific leaf area, leaf fresh and dry mass, leaf dry matter content, leaf nitrogen, carbon and phosphorus content, leaf C:N and N:P, seed mass, and stem specific density.
Spatial location and grain: Measurements were collected in tundra habitats in both the Northern and Southern Hemispheres, including Arctic sites in Alaska, Canada, Greenland, Fennoscandia and Siberia, alpine sites in the European Alps, Colorado Rockies, Caucasus, Ural Mountains, Pyrenees, Australian Alps, and Central Otago Mountains (New Zealand), and sub‐Antarctic Marion Island. More than 99% of observations are georeferenced.
Time period and grain: All data were collected between 1964 and 2018. A small number of sites have repeated trait measurements at two or more time periods.
Major taxa and level of measurement: Trait measurements were made on 978 terrestrial vascular plant species growing in tundra habitats. Most observations are on individuals (86%), while the remainder represent plot or site means or maximums per species.
Software format: csv file and GitHub repository with data cleaning scripts in R; contribution to TRY plant trait database (www.try-db.org) to be included in the next version release.

Global change threatens invertebrate biodiversity and its central role in numerous ecosystem functions and services. Functional trait analyses have been advocated to uncover global mechanisms behind biodiversity responses to environmental change, but the application of this approach for invertebrates is underdeveloped relative to other organism groups. From an evaluation of 363 records comprising >1.23 million invertebrates collected from rivers across nine biogeographic regions on three continents, consistent responses of community trait composition and diversity to replicated gradients of reduced glacier cover are demonstrated. After accounting for a systematic regional effect of latitude, the processes shaping river invertebrate functional diversity are globally consistent. Analyses nested within individual regions identified an increase in functional diversity as glacier cover decreases. Community assembly models demonstrated that dispersal limitation was the dominant process underlying these patterns, although environmental filtering was also evident in highly glacierized basins. These findings indicate that predictable mechanisms govern river invertebrate community responses to decreasing glacier cover globally.

Low concentrations of antibiotics have numerous effects on bacteria. However, it is unknown whether ecological factors such as trophic interactions and spatial structuring influence the effects of low concentrations of antibiotics on multispecies microbial communities. Here, we address this question by investigating the effects of low antibiotic concentration on community composition and horizontal transfer of an antibiotic resistance plasmid in a 62-strain bacterial community in response to manipulation of the spatial environment and presence of predation. The strong effects of antibiotic treatment on community composition depend on the presence of predation and spatial structuring that have strong community effects on their own. Overall, we find plasmid transfer to diverse recipient taxa. Plasmid transfer is likely to occur to abundant strains, occurs to a higher number of strains in the presence of antibiotic, and also occurs to low-abundance strains in the presence of spatial structures. These results fill knowledge gaps concerning the effects of low antibiotic concentrations in complex ecological settings.

All organisms leave traces of DNA in their environment. This environmental DNA (eDNA) is often used to track occurrence patterns of target species. Applications are especially promising in rivers, where eDNA can integrate information about populations upstream. The dispersion of eDNA in rivers is modulated by complex processes of transport and decay through the dendritic river network, and we currently lack a method to extract quantitative information about the location and density of populations contributing to the eDNA signal. Here, we present a general framework to reconstruct the upstream distribution and abundance of a target species across a river network, based on observed eDNA concentrations and hydro-geomorphological features of the network. The model captures well the catchment-wide spatial biomass distribution of two target species: a sessile invertebrate (the bryozoan Fredericella sultana) and its parasite (the myxozoan Tetracapsuloides bryosalmonae). Our method is designed to easily integrate general biological and hydrological data and to enable spatially explicit estimates of the distribution of sessile and mobile species in fluvial ecosystems based on eDNA sampling.

Large variability in dissolved organic carbon (DOC) uptake rates has been reported for headwater streams, but the causes of this variability are still not well understood. Here we assessed acetate uptake rates across 11 European streams comprising different ecoregions by using whole-reach pulse acetate additions. We evaluated the main climatic and biogeochemical drivers of acetate uptake during two seasonal periods. Our results show a minor influence of sampling periods but a strong effect of climate and dissolved organic matter (DOM) composition on acetate uptake. In particular, mean annual precipitation explained half of the variability of the acetate uptake velocities (Vf_Acetate) across streams. Temperate streams presented the lowest Vf_Acetate, together with humic-like DOM and the highest stream respiration rates. In contrast, higher Vf_Acetate were found in semiarid streams, with protein-like DOM, indicating a dominance of reactive, labile compounds. This, together with lower stream respiration rates and molar ratios of DOC to nitrate, suggests a strong C limitation in semiarid streams, likely due to reduced inputs from the catchment. Overall, this study highlights the interplay of climate and DOM composition and its relevance to understand the biogeochemical mechanisms controlling DOC uptake in streams.

Perennial rivers and streams make a disproportionate contribution to global carbon (C) cycling. However, the contribution of intermittent rivers and ephemeral streams (IRES), which sometimes cease to flow and can dry completely, is largely ignored although they represent over half the global river network. Substantial amounts of terrestrial plant litter (TPL) accumulate in dry riverbeds and, upon rewetting, this material can undergo rapid microbial processing. We present the results of a global research collaboration that collected and analysed TPL from 212 dry riverbeds across major environmental gradients and climate zones. We assessed litter decomposability by quantifying the litter carbon-to-nitrogen ratio and oxygen (O₂) consumption in standardized assays and estimated the potential short-term CO₂ emissions during rewetting events. Aridity, cover of riparian vegetation, channel width and dry-phase duration explained most variability in the quantity and decomposability of plant litter in IRES. Our estimates indicate that a single pulse of CO₂ emission upon litter rewetting contributes up to 10% of the daily CO₂ emission from perennial rivers and stream, particularly in temperate climates. This indicates that the contributions of IRES should be included in global C-cycling assessments.

Regulations designed to prevent global inequalities in the use of genetic resources apply to both commercial and non-commercial research. Conflating the two may have unintended consequences for collaboration between the Global North and biodiverse countries in the Global South, which may promote global injustice rather than mitigate it.

Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.

Main types of variables included: The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.


Spatial location and grain: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).

Time period and grain: BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.
Major taxa and level of measurement: BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.

Software format: .csv and .SQL.

Durch Wasserkraft genutzte Flüsse und Auenlandschaften sind in ihrem Abfluss- und Geschieberegime und damit in ihrer Morphologie und Ökologie oft stark beeinträchtigt. In der Saane unterhalb der Staumauer Rossens führten eine jahrzehntelange Restwasserbewirtschaftung und eine starke Reduktion der Geschiebefracht zu einer mangelnden Abfluss- und Geschiebedynamik und damit zu einer Reihe von Defiziten wie einer fehlenden, für Auen typischen Habitatdynamik oder einer an stabile Verhältnisse angepasste Makrozoobenthosgemeinschaft. Künstliche Hochwasser und Geschiebeschüttungen sind mögliche Massnahmen zur Verbesserung solcher morphologischen und ökologischen Defizite. Ein solches künstliches Hochwasser in Verbindung mit einer Geschiebeschüttung im September 2016 führte in der Restwasserstrecke der Saane zu einer Reihe von ökologischen und morphologischen Veränderungen. Dazu gehörten unter anderem Habitat- und Geschiebeumlagerungen, Entfernung von Kolmation und Kiesbank überwuchernder Vegetation oder auch die Reduktion von sehr hohen Individuendichten in der Makrozoobenthosgemeinschaft. Allerdings konnte auch gezeigt werden, dass die positiven Auswirkungen, insbesondere auf das Makrozoobenthos, nur kurzfristig anhielten, was eine regelmässige Durchführung solcher Massnahmen nahelegt, um dauerhaft und nachhaltig wirksam zu sein. Das ist insbesondere für komplexe Auenlandschaften von Bedeutung, die unter natürlichen Bedingungen eine hohe Dynamik aufweisen. Insgesamt konnten mit dieser Studie die Auswirkungen dieses künstlichen Hochwassers umfassend quantifiziert, bewertet sowie der praktische Nutzen gezeigt werden. Die Resultate können dazu beitragen, solche Massnahmen aus ökologischer und ökonomischer Sicht (Wasserverlust zur Energieproduktion) in Zukunft angemessen zu dimensionieren und Modellvorhersagen als Planungsgrundlagen zu verbessern, um somit zur verbesserten ökologischen Verträglichkeit der Grosswasserkraft als wichtiger Energieträger beizutragen.

Rivers and floodplains used for hydropower are often severely affected by altered discharge and sediment regimes, thus influencing their morphology and ecology. In the Saane River below the Rossens dam, decades of residual flow management and reduction in sediment load reduced flow and sediment dynamics and thus led to ecological deficits, including the loss of habitat heterogeneity typical of floodplains and a macrozoobenthos community adapted to more constant environmental conditions. Artificial flooding and sediment replenishment are potential measures to improve such morphological and ecological deficits. An artificial flooding in conjunction with sediment replenishment in September 2016 led to various ecological and morphological changes in the residual flow section of the Saane such as habitat and sediment remodeling, reduction in colmation and gravel bank overgrowth vegetation, and a reduction in the high densities of macrozoobenthos. However, it also was shown that the effects on macrozoobenthos, in particular, were shortterm, which suggests regular implementation of such measures are required to be effective and sustainable over the longterm. This is especially important for complex floodplains showing a high dynamic under natural conditions. Overall, this study comprehensively quantified, assessed, and generally demonstrated the practical benefits of artificial floods. The results can help to adequately dimension such measures from an ecological and economic point of view (water loss for energy production) in the future and improve model predictions as a planning tool towards contributing to the ecological compatibility of large hydropower as an important energy source.

Species richness and spatial variation in community composition (i.e., beta diversity) are key measures of biodiversity. They are largely determined by natural factors, but also increasingly affected by anthropogenic factors. Thus, there is a need for a clear understanding of the human impact on species richness and beta diversity, the underlying mechanisms, and whether human-induced changes can override natural patterns. Here, we dissect the patterns of species richness, community composition and beta diversity in relation to different environmental factors as well as human impact in one framework: aquatic macrophytes in 66 boreal lakes in Eastern Finland. The lakes had been classified as having high, good or moderate status (according to ecological classification of surface waters in Finland) reflecting multifaceted human impact. We used generalized least square models to study the association between different environmental variables (Secchi depth, irregularity of the shoreline, total phosphorus, pH, alkalinity, conductivity) and species richness. We tested the null hypothesis that the observed community composition can be explained by random distribution of species. We used multivariate distance matrix regression to test the effect of each environmental variable on community composition, and distance-based test for homogeneity of multivariate dispersion to test whether lakes classified as high, good or moderate status have different beta diversity. We showed that environmental drivers of species richness and community composition were largely similar, although dependent on the particular life-form group studied. The most important ones were characteristics of water quality (pH, alkalinity, conductivity) and irregularity of the shoreline. Differences in community composition were related to environmental variables independently of species richness. Species richness was higher in lakes with higher levels of human impact. Lakes with different levels of human impact had different community composition. Between-lake beta diversity did not differ in high, good or moderate status groups. However, the variation in environmental variables shaping community composition was larger in lakes with moderate status compared to other lakes. Hence, beta diversity in lakes with moderate status was smaller than what could be expected on the basis of these environmental characteristics. This could be interpreted as homogenization.

Mycorrhizal symbiosis between soil fungi and land plants is one of the most widespread and ecologically important mutualisms on earth. It has long been hypothesized that the Glomeromycotina, the mycorrhizal symbionts of the majority of plants, facilitated colonization of land by plants in the Ordovician. This view was recently challenged by the discovery of mycorrhiza-like associations with Mucoromycotina in several early diverging lineages of land plants. Utilizing a large, species-level database of plants' mycorrhiza-like associations and a Bayesian approach to state transition dynamics we here show that the recruitment of Mucoromycotina is the best supported transition from a non-mycorrhizal state. We further found that transitions between different combinations of either or both of Mucoromycotina and Glomeromycotina occur at high rates, and found similar promiscuity among combinations that include either or both of Glomeromycotina and Ascomycota with a nearly fixed association with Basidiomycota. Our results portray an evolutionary scenario of evolution of mycorrhizal symbiosis with a prominent role for Mucoromycotina in the early stages of land plant diversification.

The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new "species" paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category – which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a "process" counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.

The amphipod genus Niphargus (Amphipoda: Niphargidae Bousfield, 1977) is the most species-rich genus of freshwater amphipods in the World. Species of this genus, which live almost exclusively in subterranean water, offer an interesting model system for basic and applied biodiversity science. Their use, however, is often limited due to the hitherto unresolved taxonomy within the whole genus. As a comprehensive taxonomic revision of the currently >425 Niphargus species is too demanding, it has been suggested that the taxonomy of the genus could be advanced in smaller steps, by reviewing regional faunas, that would eventually integrate into a global revision. In this study, we provide such a revision of Niphargus in Switzerland. First, we molecularly delimited, morphologically diagnosed, and formally described two new species, namely Niphargus luchoffmanni sp. n. and Niphargus tonywhitteni sp. n. Second, we updated and revised a checklist of Niphargus in Switzerland with new findings, and prepared a list of reference sequences for routine molecular identification, available at BOLD and GenBank. All available specimens of 22 known species from the area were morphologically examined, and their morphological variation was compiled in a data file of DEscription Language for TAxonomy, which can be used for automated generation of dichotomous or interactive keys. The data file is freely available at the World Amphipoda Database. Together, the checklist, the library of reference sequences, the DELTA file, but also a list of hitherto unresolved aspects are an important step towards a complete revision of the genus within a well-defined and biogeographically interesting area in Central Europe.

Understanding how microbial diversity influences ecosystem properties is of paramount importance. Cellular traits – which determine responses to the abiotic and biotic environment – may help us rigorously link them. However, our capacity to measure traits in natural communities has thus far been limited. Here we compared the predictive power of trait richness (trait space coverage), evenness (regularity in trait distribution) and divergence (prevalence of extreme phenotypes) derived from individual-based measurements with two species-level metrics (taxonomic richness and evenness) when modelling the productivity of natural phytoplankton communities. Using phytoplankton data obtained from 28 lakes sampled at different spatial and temporal scales, we found that the diversity in individual-level morphophysiological traits strongly improved our ability to predict community resource-use and biomass yield. Trait evenness – the regularity in distribution of individual cells/colonies within the trait space – was the strongest predictor, exhibiting a robust negative relationship across scales. Our study suggests that quantifying individual microbial phenotypes in trait space may help us understand how to link physiology to ecosystem-scale processes. Elucidating the mechanisms scaling individual-level trait variation to microbial community dynamics could there improve our ability to forecast changes in ecosystem properties across environmental gradients.

Ecology and evolution unfold in spatially structured communities, where dispersal links dynamics across scales. Because dispersal is multicausal, identifying general drivers remains challenging. In a coordinated distributed experiment spanning organisms from protozoa to vertebrates, we tested whether two fundamental determinants of local dynamics, top-down and bottom-up control, generally explain active dispersal. We show that both factors consistently increased emigration rates and use metacommunity modelling to highlight consequences on local and regional dynamics.

Explaining the evolution and maintenance of animal groups remains a challenge. Surprisingly, fundamental ecological factors, such as resource variance and competition for limited resources, tend to be ignored in models of cooperation. We use a mathematical model previously developed to quantify the influence of different group sizes on resource use efficiency in egalitarian groups and extend its scope to groups with severe reproductive skew (eusocial groups). Accounting for resource limitation, the model allows calculation of optimal group sizes (highest resource use efficiency) and equilibrium population sizes in egalitarian as well as eusocial groups for a broad spectrum of environmental conditions (variance of resource supply). We show that, in contrast to egalitarian groups, eusocial groups may not only reduce variance in resource supply for survival, thus reducing the risk of starvation, they may also increase variance in resource supply for reproduction. The latter effect allows reproduction even in situations when resources are scarce. These two facets of eusocial groups, resource sharing for survival and resource pooling for reproduction, constitute two beneficial mechanisms of group formation. In a majority of environmental situations, these two benefits of eusociality increase resource use efficiency and lead to supersaturation – a strong increase in carrying capacity. The increase in resource use efficiency provides indirect benefits to group members even for low intra-group relatedness and may represent one potential explanation for the evolution and especially the maintenance of eusociality and cooperative breeding.

Ecosystems are widely interconnected by spatial flows of material, but the overall importance of these flows relative to local ecosystem functioning remains unclear. Here we provide a quantitative synthesis on spatial flows of carbon connecting ecosystems worldwide. Cross-ecosystem flows range over eight orders of magnitude, bringing between 10⁻³ and 10⁵ gC m⁻² year⁻¹ to recipient ecosystems. Magnitudes are similar to local fluxes in freshwater and benthic ecosystems, but two to three orders of magnitude lower in terrestrial systems, demonstrating different dependencies on spatial flows among ecosystem types. The strong spatial couplings also indicate that ecosystems are vulnerable to alterations of cross-ecosystem flows. Thus, a reconsideration of ecosystem functioning, including a spatial perspective, is urgently needed.

The meta-ecosystem framework demonstrates the significance of among-ecosystem spatial flows for ecosystem dynamics and has fostered a rich body of theory. The high level of abstraction of the models, however, impedes applications to empirical systems. We argue that further understanding of spatial dynamics in natural systems strongly depends on dense exchanges between field and theory. From empiricists, more and specific quantifications of spatial flows are needed, defined by the major categories of organismal movement (dispersal, foraging, life-cycle, and migration). In parallel, the theoretical framework must account for the distinct spatial scales at which these naturally common spatial flows occur. Integrating all levels of spatial connections among landscape elements will upgrade and unify landscape and meta-ecosystem ecology into a single framework for spatial ecology.

It is well-known that ecological and evolutionary processes can occur on similar time scales resulting in eco-evolutionary dynamics. One of the main questions in eco-evolutionary dynamics involves the assessment of the relative contribution of evolution, ecology and their interaction in the eco-evolutionary change under study. This has led to the development of several methods aimed to quantify the contributions of ecology and evolution to observed trait change, here referred to as eco-evolutionary partitioning metrics. This study provides an overview on currently-used partitioning metrics with a focus on methods that can quantify evolutionary and non-evolutionary contributions to population and community trait change. I highlight key differences between these metrics found in previous studies. Additionally, I also provide a detailed comparison between the 'Geber' method and the reaction norm approach. Next, I provide a guideline for researchers to assess which metrics are best suited for their data, give an overview on the type of data needed for these metrics, and how this data can be collected with a focus on community data.

The measurement and assessment of life history traits, such as fecundity and survival, typically rely on life tables generated from individual-based assays, where growth, maturation and reproductive rates are measured in isolated individuals. In reality, individuals often live in populations, which together form communities. For many species, it is possible to distinguish single individuals and measure their individual life history traits acting in populations, in wolves for example. However, for other species individuals are indistinguishable, for example in zooplankton, so it is impossible to mark and track a single animal. In these indistinguishable and non-markable animals, the problem with traditional life history assessment is that it is based on traits measured in individuals and these trait values are then extrapolated to population level without measuring life history traits of individuals in the populations. To overcome the limitations of individual life history trait assessments, other parameters are necessary to describe populations, for example the rate of change of population size using population growth rate or Edmondson egg ratio. Extrapolating from individuals to populations is suitable for estimating population level effects as long as individuals in the population do not interact. However, if individuals do interact, which is common, then effects of those interactions between individuals, must also be considered.
The main aim of my research was to determine life history trait parameters of individuals and simultaneously assess population growth rate variation directly in Daphnia populations grown at different population densities. By using several genotypes potentially adapted to different environmental conditions, I was also able to test whether life history traits and population growth rates differed between single and mixed genotype populations.
For this I conducted two life history assays using 10 resurrected Daphnia galeata clones ineither different initial densities or populations starting with 2 individuals of mixed or singlegenotypes. Both experiments were conducted without food limitation, to disentangle the effect of density from competition for food.
In all clones, population growth rate decreased with higher initial density, even though food availability was increased too. Of all life history traits I examined, only one, investment in reproduction, changed with increasing initial density, while neither age nor size at maturity, nor Edmondson egg ratio differed between initial densities. Instead Edmonson egg ratio decreased with rising ephippia production. In every life history trait, there were large differences between clones. Additionally, populations grown in single genotype populations showed no difference in population growth rate compared to mixed genotype populations.
It appears that initial population density depresses population growth rate most likely through fecundity reduction in populations, even when food is not limiting, and is independent of genotypic diversity. I could point that in D. galeata decreasing investment in current reproduction is linked to increasing investment in future reproduction. This study shows that in Daphnia experiments considering life history traits, it is important to regard density-dependence. Furthermore because genotypes differed greatly in the strength of the association with density, and in individual life history parameters, this study highlights that experiments using Daphnia, or any other clonal organism need to be based on multiple genotypes to allow more generalizable results.

The crucian carp (Carassius carassius) is one of few fish species associated with small ponds in the UK. These populations contain genetic diversity not found in Europe and are important to conservation efforts for the species which has declined across its range in Europe. Detection and monitoring of extant crucian carp populations are crucial for conservation success. Environmental DNA (eDNA) analysis could be very useful in this respect as a rapid, cost-efficient monitoring tool.
We developed a species-specific quantitative polymerase chain reaction (qPCR) assay for eDNA surveillance of crucian carp to enable non-invasive, large-scale distribution monitoring. We compared fyke netting and eDNA analysis at ponds with (n = 10) and without (n = 10) crucian carp for presence–absence detection. We examined biotic (crucian carp density represented by catch-per-unit-effort [CPUE] estimate) and abiotic influences on eDNA detection probability using a hierarchical occupancy model, and eDNA quantification using a mixed-effects model.
eDNA analysis achieved 90% detection for crucian carp (n = 10), failing in only one pond where presence was known. CPUE estimate and conductivity had positive and negative influences on eDNA detection probability in qPCR replicates respectively. Similarly, conductivity had a negative effect on DNA copy number, whereas copy number increased with CPUE estimate.
Our results demonstrate that eDNA analysis could enable detection of crucian carp populations in ponds and benefit ongoing conservation efforts, but imperfect species detection in relation to biotic and abiotic factors and eDNA workflow requires further investigation. Nonetheless, we have established an eDNA framework for the crucian carp as well as sources of imperfect detection which future investigations can build upon.

Global analyses of biodiversity consistently reveal recurrent patterns of species distributions worldwide. However, unveiling the specific mechanisms behind those patterns remains logistically challenging, yet necessary for reliable biodiversity forecasts. Here, we combine theory and experiments to investigate the processes underlying spatial biodiversity patterns in dendritic, river-like landscapes, iconic examples of highly threatened ecosystems. We used geometric scaling properties, common to all rivers, to show that the distribution of biodiversity in these landscapes fundamentally depends on how ecological selection is modulated across space: while uniform ecological selection across the network leads to higher diversity in downstream confluences, this pattern can be inverted by disturbances when population turnover (i.e. local mortality) is higher upstream than downstream. Higher turnover in small headwater patches can slow down ecological selection, increasing local diversity in comparison to large downstream confluences. Our results show that disturbance-mediated slowing down of competitive exclusion can generate a specific transient signature in terms of biodiversity distribution when applied over a spatial gradient of disturbance, which is a common feature of many river landscapes.

1. Competition of two species for the same resource is expected to result in competitive exclusion of the inferior competitor. In natural communities, however, other antagonists and symbionts moderate competition. Thus, we have to go beyond studying pairwise interactions.
2. Natural enemies may facilitate coexistence if they affect the superior competitor more strongly, or they can hinder coexistence via apparent competition. Less well studied is the role of symbionts, which may influence species coexistence in conjunction with enemies.
3. Eukaryotes commonly harbour microbial endosymbionts that provide protection against natural enemies, but are costly in their absence. Such defensive symbionts could thus mediate coexistence of species competing for the same resource, both in the presence and in the absence of enemies, but as yet there is little evidence for this claim.
4. We addressed this proposed role of defensive symbionts in replicated simple communities consisting of two aphid species sharing the same host plant and the same natural enemy, a parasitoid wasp. Both, one, or neither species were infected with a resistance-conferring symbiont, and they competed in the absence as well as the presence of parasitoids.
5. The symbiont had significant effects in the absence of parasitoids by lowering competitive ability especially in one species, but the effects were more dramatic in the presence of parasitoids. With both species protected by the symbiont, parasitoid densities remained low and both aphid species persisted. When neither species was protected, parasitoids drove both species to extinction. Surprisingly, the same outcome was observed when only one species was protected. The susceptible species supported high densities of parasitoids that also killed the resistant aphids via mechanisms other than parasitism, presumably by disturbing them to the point of starvation. This is an intriguing form of apparent competition.
6. Our results demonstrate an important role of defensive symbionts in insect communities through modifying species interactions. This highlights the need for experimental data when studying species coexistence in competitive networks. Furthermore, the observation that a susceptible host can negatively affect a resistant host via a shared parasitoid is an instructive insight for biological control. A plain language summary is available for this article.

Biological invasions, such as commonly observed in dendritic riverine networks can change biodiversity, leading to global species loss and consequently alter ecosystem functioning. Key invariant regional scale properties such as habitat size, connectivity and dispersal properties, have recently been identified as drivers of community structures in river ecosystems. Those network properties are thus likely important to understand the success of invading species. Using protist microcosm experiments, I disentangled how patch size and patch connectivity affect the establishment success of invading species in dendritic river-like networks. I showed that invasion success and invader densities depend on the invading species and community composition. Further, I showed that a larger patch size as well as a high biodiversity in a patch immediately preceding an invasion reduced invasion success. Even more, the effect of diversity on invasion success changed across an increasing patch size gradient from a negative to a positive correlation, while overall increasing patch size reduced invasion success. Contrarily, connectivity did not have a direct effect on invasion success but indirectly affected invasions by shaping diversity patterns in the whole network. My results emphasize that it is essential to manage invasions of species on a landscape level to protect vulnerable ecosystems.

Occurrence and fate of glyphosate, a widely used herbicide, and its main metabolite AMPA was investigated in Lake Greifensee, Switzerland. Monthly vertical concentration profiles in the lake showed an increase of glyphosate concentrations in the epilimnion from 15 ng/L in March to 145 ng/L in July, followed by a sharp decline to <5 ng/L in August. A similar pattern was observed for AMPA. Concentrations of glyphosate and AMPA in the two main tributaries generally were much higher than in the lake. Simulations using a numerical lake model indicated that a substantial amount of glyphosate and AMPA dissipated in the epilimnion, mainly in July and August, with half-lives of only ≈2–4 days which is ≫100 times faster than in the preceding months. Fast dissipation coincided with high water temperatures and phytoplankton densities, and low phosphate concentrations. This indicates that glyphosate might have been used as an alternative phosphorus source by bacterio- and phytoplankton. Metagenomic analysis of lake water revealed the presence of organisms known to be capable of degrading glyphosate and AMPA.

Algal biofuels have the potential to curb emissions of greenhouse gases from fossil fuels, but current growing methods fail to produce fuels that meet the multiple standards necessary for economical industrial use. For example, algae grown as monocultures for biofuel production have not simultaneously and economically achieved high yields of the high-quality, lipid-rich biomass desired for the industrial-scale production of bio-oil. Decades of study in the field of ecology have demonstrated that simultaneous increases in multiple functions, such as the quantity and quality of biomass, can occur in natural ecosystems by increasing biological diversity. Here we show that species consortia of algae can improve the production of bio-oil, which benefits from both high biomass yield and high quality of biomass rich in fatty acids. We explain the underlying causes of increased quantity and quality of algal biomass among species consortia by showing that, relative to monocultures, species consortia can differentially regulate lipid metabolism genes while growing to higher levels of biomass, in part due to greater utilization of nutrient resources. We identify multiple genes involved in lipid biosynthesis that are frequently upregulated in bicultures, and further show that these elevated levels of gene expression are highly predictive of the elevated levels in biculture relative to monoculture of multiple quality metrics of algal biomass. These results show that interactions between species can alter the expression of lipid metabolism genes, and further demonstrate that our understanding of diversity-function relationships from natural ecosystems can be harnessed to improve production of bio-oil.

Importance section: Algal biofuels are one of the more promising forms of renewable energy. In our study, we investigate whether ecological interactions between species of microalgae regulate two important factors in cultivation-the biomass of the crop produced and the quality of the biomass that is produced. We found that species interactions often improved production yields, especially the fatty acid content of the algal biomass, and that differentially expressed genes involved in fatty acid metabolism are predictive of improved quality metrics of bio-oil. Other studies have found that diversity often improves productivity and stability in agricultural and natural ecosystems. Our results provide further evidence that growing multispecies crops of microalgae may improve the production of high-quality biomass for bio-oil.

Environmental high flows are being implemented in many flow-regulated rivers globally. The questions arise as to whether different rivers respond similarly to artificial floods, and what are the long-term ecological consequences of such flood programs? This study evaluated abiotic/biotic dynamics during experimental floods in two rivers with contrasting valley morphologies (canyon-confined vs open-valley) as well as long-term response patterns of macroinvertebrates in both rivers to 16 years of experimental floods. Both systems showed an increase in measured parameters (turbidity, total phosphorus, drift, seston) during the rising limb of the flood with subsequent decreases being observed before the falling limb of the flood (all parameters displayed typical hysteresis patterns with discharge). Contrasting differences existed in respect to immediate effects of these two floods on macroinvertebrates and benthic periphyton (decreases or no change). Over the long term, major channel changes occurred from initial floods with less change observed from later floods in both systems. Macroinvertebrate densities fluctuated seasonally, but showed no long-term response to the flood program, whereas taxa richness increased in both systems. The rivers differed in macroinvertebrate community structure and this was reflected in shifts in community assembly over the study period in both systems (being substantially greater in the system flowing through a confined valley). The results suggest that immediate flood effects are quite similar among rivers, even over multiple years, but long-term trajectories in community assembly reflect changes in local habitat conditions in respect to external drivers such as landscape geomorphology.

There is growing interest in biological control as a sustainable and environmentally friendly way to control pest insects. Aphids are among the most detrimental agricultural pests worldwide, and parasitoid wasps are frequently employed for their control. The use of asexual parasitoids may improve the effectiveness of biological control because only females kill hosts and because asexual populations have a higher growth rate than sexuals. However, asexuals may have a reduced capacity to track evolutionary change in their host populations. We used a factorial experiment to compare the ability of sexual and asexual populations of the parasitoid Lysiphlebus fabarum to control caged populations of black bean aphids (Aphis fabae) of high and low clonal diversity. The aphids came from a natural population, and one-third of the aphid clones harbored Hamiltonella defensa, a heritable bacterial endosymbiont that increases resistance to parasitoids. We followed aphid and parasitoid population dynamics for 3 months but found no evidence that the reproductive mode of parasitoids affected their effectiveness as biocontrol agents, independent of host clonal diversity. Parasitoids failed to control aphids in most cases, because their introduction resulted in strong selection for clones protected by H. defensa. The increasingly resistant aphid populations escaped control by parasitoids, and we even observed parasitoid extinctions in many cages. The rapid evolution of symbiont-conferred resistance in turn imposed selection on parasitoids. In cages where asexual parasitoids persisted until the end of the experiment, they became dominated by a single genotype able to overcome the protection provided by H. defensa. Thus, there was evidence for parasitoid counteradaptation, but it was generally too slow for parasitoids to regain control over aphid populations. It appears that when pest aphids possess defensive symbionts, the presence of parasitoid genotypes able to overcome symbiont-conferred resistance is more important for biocontrol success than their reproductive mode.

Die Gewässer zwischen Gletschereis und Bergbächen sind zwar meist eisig kalt, die Lebensbedingungen sind aber für Gewässerbewohner gleichförmiger als für Landorganismen. Während der vier Feldtage fanden wir rund 90 Kleintierarten und 215 Arten von Kieselalgen. Diese widerspiegeln die kleinräumige Vielfalt der unterschiedlichen Gewässertypen. Bei den artenreichen Köcherfliegen wurde die Larve einer Art gefunden, die bisher nur als erwachsenes Tier bekannt war. Bei den Kieselalgen gelangen zwei Erstnachweise für die Schweiz.

Construction of small hydropower plants (<10 megawatts) is booming worldwide, exacerbating ongoing habitatfragmentation and degradation, and further fueling biodiversity loss. A systematic approach for selectinghydropower sites within river networks may help to minimize the detrimental effects of small hydropower onbiodiversity. In addition, a better understanding of reach-and basin-scale impacts is key for designing planning tools. We synthesize the available information about (1) reach-scale and (2) basin-scale impacts of small hydropower plants on biodiversity and ecosystem function, and (3) interactions with other anthropogenic stressors.We then discuss state-of-the-art, spatially explicit planning tools and suggest how improved knowledge of theecological and evolutionary impacts of hydropower can be incorporated into project development. Such toolscan be used to balance the benefits of hydropower production with the maintenance of ecosystem services andbiodiversity conservation. Adequate planning tools that consider basin-scale effects and interactions with other stressors, such as climate change, can maximize long-term conservation.

While the host immune system is often considered the most important physiological mechanism against parasites, precontact mechanisms determining exposure to parasites may also affect infection dynamics. For instance, chemical cues released by hosts can attract parasite transmission stages. We used the freshwater snail Lymnaea stagnalis and its trematode parasite Echinoparyphium aconiatum to examine the role of host chemical attractiveness, physiological condition, and immune function in determining its susceptibility to infection. We assessed host attractiveness through parasite chemo-orientation behavior; physiological condition through host body size, food consumption, and respiration rate; and immune function through two immune parameters (phenoloxidase-like and antibacterial activity of hemolymph) at an individual level. We found that, although snails showed high variation in chemical attractiveness to E. aconiatum cercariae, this did not determine their overall susceptibility to infection. This was because large body size increased attractiveness, but also increased metabolic activity that reduced overall susceptibility. High metabolic rate indicates fast physiological processes, including immune activity. The examined immune traits, however, showed no association with susceptibility to infection. Our results indicate that postcontact mechanisms were more likely to determine snail susceptibility to infection than variation in attractiveness to parasites. These may include localized immune responses in the target tissue of the parasite. The lack of a relationship between food consumption and attractiveness to parasites contradicts earlier findings that show food deprivation reducing snail attractiveness. This suggests that, although variation in resource level over space and time can alter infection dynamics, variation in chemical attractiveness may not contribute to parasite-induced fitness variation within populations when individuals experience similar environmental conditions.

Aquatic biomonitoring has become an essential task in Europe and many other regionsas a consequence of strong anthropogenic pressures affecting the health of lakes, rivers,oceans and groundwater. A typical assessment of the environmental quality status, suchas it is required by European but also North American and other legislation, relies onmatching the composition of assemblages of organisms identified using morphologicalcriteria present in aquatic ecosystems to those expected in the absence of anthropogenicpressures. Through decade-long and difficult intercalibration exercises amongnetworks of regulators and scientists in European countries, a pragmatic biomonitoringapproach was developed and adopted, which now produces invaluable information.Nonetheless, this approach is based on several hundred different protocols, making it susceptible to issues with comparability, scale and resolution. Furthermore, dataacquisition is often slow due to a lack of taxonomic experts for many taxa and regionsand time-consuming morphological identification of organisms. High-throughputgenetic screening methods such as (e)DNA metabarcoding have been proposed asa possible solution to these shortcomings. Such “next-generation biomonitoring”, alsotermed “biomonitoring 2.0”, has many advantages over the traditional approach interms of speed, comparability and costs. It also creates the potential to include new bioindicatorsand thereby further improves the assessment of aquatic ecosystem health.However, several major conceptual and technological challenges still hinder its implementationinto legal and regulatory frameworks. Academic scientists sometimes tend tooverlook legal or socioeconomic constraints, which regulators have to consider on aregular basis. Moreover, quantification of species abundance or biomass remains a significantbottleneck to releasing the full potential of these approaches. Here, we highlightthe main challenges for next-generation aquatic biomonitoring and outline principlesand good practices to address these with an emphasis on bridging traditional disciplinaryboundaries between academics, regulators, stakeholders and industry.

Rivers are among the most threatened freshwater ecosystems, and anthropogenic activities are affecting both river structures and water quality. While assessing the organisms can provide a comprehensive measure of a river's ecological status, it is limited by the traditional morphotaxonomy-based biomonitoring. Recent advances in environmental DNA (eDNA) metabarcoding allow to identify prokaryotes and eukaryotes in one sequencing run, and could thus allow unprecedented resolution. Whether such eDNA-based data can be used directly to predict the pollution status of rivers as a complementation of environmental data remains unknown. Here we used eDNA metabarcoding to explore the main stressors of rivers along which community structure changes, and to identify the method's potential for predicting pollution status based on eDNA data. We showed that a broad range of taxa in bacterial, protistan, and metazoan communities could be profiled with eDNA. Nutrients were the main driving stressor affecting communities' structure, alpha diversity, and the ecological network. We specifically observed that the relative abundance of indicative OTUs was significantly correlated with nutrient levels. These OTUs data could be used to predict the nutrient status up to 79% accuracy on testing data sets. Thus, our study gives a novel approach to predicting the pollution status of rivers by eDNA data.

Abiotic conditions have long been considered essential in structuring freshwater macroinvertebrate communities. Ecological drift, dispersal and biotic interactions also structure communities, and although these mechanisms are more difficult to detect, they may be of equal importance in natural communities. Here, we hypothesized that in 10 naturally replicated headwater streams in eastern Switzerland, locally dominant amphipod species would be associated with differences in environmental conditions. We conducted repeated surveys of amphipods and used a hierarchical joint species distribution model to assess the influence of different drivers on species co-occurrences. The species had unique environmental requirements, but a distinct spatial structure in their distributions was unrelated to habitat. Species co-occurred much less frequently than predicted by the model, which was surprising because laboratory and field evidence suggests they are capable of coexisting in equal densities. We suggest that niche preemption may limit their distribution and that a blocking effect related to the specific linear configuration of streams determines which species colonizes and dominates a given stream catchment, thus suggesting a new solution a long-standing conundrum in freshwater ecology.

Context: Freshwater ecosystems depend on surrounding terrestrial landscape for resources. Most important are terrestrial leaf litter subsidies, which differ depending on land use. We lack a good understanding of the variation of these inputs across spatial scales.
Objectives: We sought to determine: (1) the relative importance of local versus catchment-level forestation for benthic leaf litter biomass in streams, (2) how landscape configuration alters these relationships, and (3) how land use affects the quality and diversity of leaf litter subsidies.
Methods: We measured biomass and identity of benthic leaf litter in 121 reaches in 10 independent catchments seasonally over the course of a year. We assessed direct and indirect effects of forestation, reach position, and seasonality on leaf litter biomass using structural equation models, and assessed how leaf litter diversity varied with land use.
Results: In catchments with forested headwaters, the degree of forestation and reach position in the catchment influenced benthic leaf litter biomass indirectly through local reach-scale forestation. In catchments where forest was only located downstream, or with minimal forest, none of these factors influenced reach-level benthic leaf litter. Leaf litter diversity peaked in fall in all land use types, but was generally lowest in forested reaches.
Conclusions: Not only habitat amount, but its location relative to other habitats is important for ecosystem function in the context of cross-ecosystem material flows. Here, lack of upstream forest altered spatial patterns of leaf litter storage. Studies with high spatiotemporal resolution may further reveal effects of landscape configuration on other ecosystems.

Freshwater ecosystems rely on allochthonous resources. Integration of these subsidies depends on diversity of both terrestrial resources and aquatic shredder and decomposer communities, but the diversity effects on leaf litter breakdown and decomposition are less clear in aquatic than terrestrial ecosystems. We need a better understanding of this relationship because aquatic communities are rapidly changing with species invasions and anthropogenic impacts. Here, we experimentally disentangled the effects of leaf and shredder richness on leaf litter breakdown by macroinvertebrates in mesocosm experiments using three species of amphipods, a dominant guild of crustaceans in European freshwater ecosystems. Increased leaf richness led to lower-than-predicted leaf consumption by native shredders, with mixed evidence of resource-switching or prioritization of preferred food items within a leaf mix. Higher shredder species richness never promoted leaf consumption rates compared to predictions from relevant single-species experiments, and instead sometimes substantially decreased leaf consumption. We then conducted a meta-analysis of leaf litter consumption rates by seven widely distributed amphipod species (the three used in the experiments and four additional species). As expected based on our own experiments, nonnative amphipod species generally had lower biomass-adjusted leaf litter consumption rates, although their larger body size led to higher per-individual leaf consumption rates. Contamination of the water by metals, pesticides, and other chemicals additionally significantly decreased leaf litter consumption by multiple native and nonnative species compared to unpolluted systems. While the meta-analysis suggested that litter consumption, and thus breakdown, would decline if native shredders are replaced by nonnative heterospecifics, complete species replacement is not the only outcome following immigration in a meta-community context. Our experiments suggest that breakdown rates could remain reasonably high where native species coexist with nonnative arrivals. Experiments that neglect the ecological realism of species coexistence will necessarily mischaracterize effects on ecosystem functioning.

Background: Regulatory circuits of infection in the emerging experimental model system, water flea Daphnia and their microparasites, remain largely unknown. Here we provide the first molecular insights into the response of Daphnia galeata to its highly virulent and common parasite Caullerya mesnili, an ichthyosporean that infects the gut epithelium. We generated a transcriptomic dataset using RNAseq from parasite-exposed (vs. control) Daphnia, at two time points (4 and 48 h) after parasite exposure.
Results: We found a down-regulation of metabolism and immunity-related genes, at 48 h (but not 4 h) after parasite exposure. These genes are involved in lipid metabolism and fatty acid biosynthesis, as well as microbe recognition (e.g. c-type lectins) and pathogen attack (e.g. gut chitin).
Conclusions: General metabolic suppression implies host energy shift from reproduction to survival, which is in agreement with the known drastic reduction in Daphnia fecundity after Caullerya infection. The down-regulation of gut chitin indicates a possible interaction between the peritrophic matrix and the evading host immune system. Our study provides the first description of host transcriptional responses in this very promising host-parasite experimental system.

Seagrass roots host a diverse microbiome that is critical for plant growth and health. Composition of microbial communities can be regulated in part by root exudates, but the specifics of these interactions in seagrass rhizospheres are still largely unknown. As light availability controls primary productivity, reduced light may impact root exudation and consequently the composition of the root microbiome. Hence, we analyzed the influence of light availability on root exudation and community structure of the root microbiome of three co-occurring seagrass species, Halophila ovalis, Halodule uninervis and Cymodocea serrulata. Plants were grown under four light treatments in mesocosms for 2 weeks; control (100% surface irradiance (SI), medium (40% SI), low (20% SI) and fluctuating light (10 days 20% and 4 days 100%). 16S rDNA amplicon sequencing revealed that microbial diversity, composition and predicted function were strongly influenced by the presence of seagrass roots, such that root microbiomes were unique to each seagrass species. Reduced light availability altered seagrass root exudation, as characterized using fluorescence spectroscopy, and altered the composition of seagrass root microbiomes with a reduction in abundance of potentially beneficial microorganisms. Overall, this study highlights the potential for above-ground light reduction to invoke a cascade of changes from alterations in root exudation to a reduction in putative beneficial microorganisms and, ultimately, confirms the importance of the seagrass root environment - a critical, but often overlooked space.

Removal of lateral constraints to restore rivers has become increasingly common in river resource management, but little is known how the interaction of de-channelization with flow influences ecosystem structure and function. We evaluated the ecosystem effects of river widening to improve sediment relations in the Thur River, Switzerland, 12 years after implementation. We tested if restored and non-restored reaches differed in water physico-chemistry, hyporheic function, primary production, and macroinvertebrate density and composition in relation to the flow regime. Our results showed that (i) spatio-temporal variation in sediment respiration and macroinvertebrate taxonomic richness were driven by interactions between restoration and flow; (ii) riverbed conditions including substrate size, organic matter content, and groundwater–surface water exchange changed due to restoration, but (iii) physico-chemistry, hydraulic conditions, and primary production were not altered by restoration. Importantly, our study revealed that abiotic conditions, except channel morphology, changed only marginally, whereas other ecosystem attributes responded markedly to changes in flow-restoration interactions. These results highlight integrating a more holistic ecosystem perspective in the design and monitoring of restoration projects such as river widening in resource management, preferably in relation to flow-sediment regimes and interactions with the biotic components of the ecosystem.

Evolution is a fundamental ecosystem process. The study of genomic variation of organisms can not only improve our understanding of evolutionary processes, but also of contemporary and future ecosystem dynamics. We argue that integrative research between the fields of genomics and ecosystem ecology could generate new insights. Specifically, studies of biodiversity and ecosystem functioning, evolutionary rescue, and eco-evolutionary dynamics could all benefit from information about variation in genome structure and the genetic architecture of traits, whereas genomic studies could benefit from information about the ecological context of evolutionary dynamics. We propose new ways to help link research on functional genomic diversity with (reciprocal) interactions between phenotypic evolution and ecosystem change. Despite numerous challenges, we anticipate that the wealth of genomic data being collected on natural populations will improve our understanding of ecosystems.

Biological systems consist of elements that interact within and across hierarchical levels. For example, interactions among genes determine traits of individuals, competitive and cooperative interactions among individuals influence population dynamics, and interactions among species affect the dynamics of communities and ecosystem processes. Such systems can be represented as hierarchical networks, but can have complex dynamics when interdependencies among levels of the hierarchy occur. We propose integrating ecological and evolutionary processes in hierarchical networks to explore interdependencies in biological systems. We connect gene networks underlying predator–prey trait distributions to food webs. Our approach addresses longstanding questions about how complex traits and intraspecific trait variation affect the interdependencies among biological levels and the stability of meta-ecosystems.

Floodplain areas belong to the most diverse, dynamic and complex ecological habitats of the terrestrial portion of the Earth. Spatial and temporal quantification of floodplain dynamics is needed for assessing the impacts of hydromorphological controls on river ecosystems. However, estimation of land cover dynamics in a post-classification setting is hindered by a high contribution of classification errors. A possible solution relies on the selection of specific information of the change map, instead of increasing the overall classification accuracy. In this study, we analyze the capabilities of Unmanned Aerial Systems (UAS), the associated classification processes and their respective accuracies to extract a robust estimate of floodplain dynamics. We show that an estimation of dynamics should be built on specific land cover interfaces to be robust against classification errors and should include specific features depending on the season-sensor coupling. We use five different sets of features and determine the optimal combination to use information largely based on blue and infrared bands with the support of texture and point cloud metrics at leaf-off conditions. In this post-classification setting, the best observation of dynamics can be achieved by focusing on the gravel-water interface. The semi-supervised approach generated error of 10% of observed changes along highly dynamic reaches using these two land cover classes. The results show that a robust quantification of floodplain land cover dynamics can be achieved by high-resolution remote sensing.

Human impacts on biodiversity are well recognized, but uncertainties remain regarding patterns of diversity change at different spatial and temporal scales. Changes in microbial assemblages are, in particular, not well understood, partly due to the lack of community composition data over relevant scales of space and time. Here, we investigate biodiversity patterns in cyanobacterial assemblages over one century of eutrophication and climate change by sequencing DNA preserved in the sediments of ten European peri-Alpine lakes. We found species losses and gains at the lake scale, while species richness increased at the regional scale over approximately the past 100 years. Our data show a clear signal for beta diversity loss, with the composition and phylogenetic structure of assemblages becoming more similar across sites in the most recent decades, as have the general environmental conditions in and around the lakes. We attribute patterns of change in community composition to raised temperatures affecting the strength of the thermal stratification and, as a consequence, nutrient fluctuations, which favoured cyanobacterial taxa able to regulate buoyancy. Our results reinforce previous reports of human-induced homogenization of natural communities and reveal how potentially toxic and bloom-forming cyanobacteria have widened their geographic distribution in the European temperate region.

The use of environmental DNA (eDNA) as a species detection tool is attracting attention from both scientific and applied fields, especially for detecting invasive or rare species. In order to use eDNA as an efficient and reliable tool, however, we need to understand its origin and state as well as factors affecting its degradation. Various biotic and abiotic environmental factors have been proposed to affect degradation of eDNA in aquatic environments and thus to influence detection rates of species. Here, we were interested in two of them, namely UV light, which can break down DNA, and the presence of filter feeders, which can remove DNA and DNA-bound particles. A few, mostly laboratory-based studies have found minor effects of UVB on the degradation of eDNA. Ultraviolet A radiation (UVA), however, has been neglected although it also causes DNA lesions and is 10- to 100-fold more prevalent than UVB when reaching the earth’s surface. Filter feeders are common in aquatic ecosystem, but their effects on eDNA has hitherto been ignored. We conducted a full-factorial aquatic mesocosm experiment under near-natural outdoor conditions manipulating UV radiation as well as the presence of Dreissena polymorpha, a strong filter feeder capable of filtering cells or organelles containing DNA. Surprisingly, we found that neither UV radiation nor the presence of the filter feeder affected eDNA-based detection rates of macroinvertebrates, even though the experiment took place in summer when UV radiation intensity and filtration activity is high for the chosen experimental site and conditions. These results, in combination with studies from marine or laboratory settings finding no effect of sunlight and its UV components on the detectability of eDNA, suggest that eDNA based species assessments could be relatively robust with respect to our two factors studied.

The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.

Losses and gains in species diversity affect ecological stability^1–7 and the sustainability of ecosystem functions and services^8–13. Experiments and models have revealed positive, negative and no effects of diversity on individual components of stability, such as temporal variability, resistance and resilience^{2,3,6,11,12,14}. How these stability components covary remains poorly understood¹⁵. Similarly, the effects of diversity on overall ecosystem stability¹⁶, which is conceptually akin to ecosystem multifunctionality^17,18, remain unknown. Here we studied communities of aquatic ciliates to understand how temporal variability, resistance and overall ecosystem stability responded to diversity (that is, species richness) in a large experiment involving 690 micro-ecosystems sampled 19 times over 40 days, resulting in 12,939 samplings. Species richness increased temporal stability but decreased resistance to warming. Thus, two stability components covaried negatively along the diversity gradient. Previous biodiversity manipulation studies rarely reported such negative covariation despite general predictions of the negative effects of diversity on individual stability components³. Integrating our findings with the ecosystem multifunctionality concept revealed hump- and U-shaped effects of diversity on overall ecosystem stability. That is, biodiversity can increase overall ecosystem stability when biodiversity is low, and decrease it when biodiversity is high, or the opposite with a U-shaped relationship. The effects of diversity on ecosystem multifunctionality would also be hump- or U-shaped if diversity had positive effects on some functions and negative effects on others. Linking the ecosystem multifunctionality concept and ecosystem stability can transform the perceived effects of diversity on ecological stability and may help to translate this science into policy-relevant information.

Most of the existing literature on river water temperature focuseds on river thermal sensitivity to long-term trends of climate variables, whereas how river water temperature responds to extreme weather events, such as heatwaves, still requires in-depth analysis. Research in this direction is particularly relevant in that heatwaves are expected to increase in intensity, frequency, and duration in the coming decades, with likely consequences on river thermal regimes and ecology. In this study we analyzed the long-term temperature and streamflow series of 19 Swiss rivers with different hydrological regime (regulated, low-land, and snow-fed), and characterized how concurrent changes in air temperature and streamflow concurred to affect their thermal dynamics. We focused on quantifying the thermal response to the three most significant heatwave events that occurred in Central Europe since 1950 (July-August 2003, July 2006, and July 2015). We found that the thermal response of the analyzed rivers contrasted strongly depending on the river hydrological regime, confirming the behavior observed under typical weather conditions. Low-land rivers were extremely sensitive to heatwaves. In sharp contrast, high-altitude snow-fed rivers and regulated rivers receiving cold water from higher altitude hydropower reservoirs or diversions showed a damped thermal response. The results presented in this study suggest that water resource managers should be aware of the multiple consequences of heatwave events on river water temperature and incorporate expected thermal responses in adaptive management policy. In this respect, additional efforts and dedicated studies are required to deepen our knowledge on how extreme heatwave events can affect river ecosystems.

The river Spöl flows from Livigno reservoir on the Swiss–Italian border in the central Alps. Flow regulationsince 1970 has decreased and stabilized the mean annual discharge of 8.6 to 1.0 m³/s (winter: 0.55 m³/s, summer:2.5m³/s). Thirty experimental floods were released between 2000 and 2016 to improve the ecology of the river.A 100-m reach ~2.3 km downstream of the dam was used to monitor changes in water physicochemistry, periphyton,transported and benthic organic matter, and macroinvertebrates. Fish redds (native Brown Trout) were countedeach autumn along the same stretch (~2.6 km) of river. Most physicochemical variables displayed strong seasonalcycles unrelated to the flow program, but N, P, and water temperature increased significantly over the 18-ystudy. Seston decreased after each high flow, but was seasonal and increased over the study. Periphyton biomass decreasedafter each high flow to low levels and increased between high flows. Benthic organic matter decreased 2x over thestudy but increased between floods.Macroinvertebrate densities decreased over the study.High flows reducedmacroinvertebratedensities to <10,000 individuals (ind)/m², with densities usually increasing to ~10,000 to 20,000 ind/m² between floods. Floods reduced taxonomic richness with increases between floods. Ordination showed temporalshifts in macroinvertebrate assemblages over the study. Mayflies and stoneflies responded positively and chironomidsand gammarids negatively to the floods over the study. Fish redds increased from 58 in 1999 to >200 by 2003. Reddcounts decreased to <30 after an accidental sediment spill in 2013 but rebounded to 153 redds in 2016. Macroinvertebrateassemblages recovered within months after the spill. Long-term monitoring was essential for elucidatingecosystemdynamics and evaluating biological responses to pulse disturbances, such as the sediment spill, duringthe study.

Recognition that evolution operates on the same timescale as ecological processes has motivated growing interest in eco-evolutionary dynamics. Nonetheless, generating sufficient data to test predictions about eco-evolutionary dynamics has proved challenging, particularly in natural contexts. Here we argue that genomic data can be integrated into the study of eco-evolutionary dynamics in ways that deepen our understanding of the interplay between ecology and evolution. Specifically, we outline five major questions in the study of eco-evolutionary dynamics for which genomic data may provide answers. Although genomic data alone will not be sufficient to resolve these challenges, integrating genomic data can provide a more mechanistic understanding of the causes of phenotypic change, help elucidate the mechanisms driving eco-evolutionary dynamics, and lead to more accurate evolutionary predictions of eco-evolutionary dynamics in nature.

Although species distributions can change in an unexpectedly short period of time, most species distribution models (SDMs) use only long-term averaged environmental conditions to explain species distributions. We aimed to demonstrate the importance of incorporating antecedent environmental conditions into SDMs in comparison to long-term averaged environmental conditions. We modeled the presence/absence of 18 fish species captured across 108 sampling events along a 50-km length of the Sagami River in Japan throughout the 1990s (one to four times per site at 45 sites). We constructed and compared the two types of SDMs: 1) a conventional model that uses only long-term averaged (10-yr) environmental conditions; and 2) a proposed model that incorporates environmental conditions 2 yr prior to a sampling event (antecedent conditions) together with long-term averages linked to life-history stages. These models both included geomorphological, hydrological, and sampling conditions as predictors. A random forest algorithm was applied for modeling and quantifying the relative importance of the predictors. For seven species, antecedent hydrological conditions were more important than the long-term averaged hydrological conditions. Furthermore, the distributions of two species with low prevalence could not be predicted using long-term averaged hydrological conditions but only using antecedent hydrological conditions. In conclusion, incorporating antecedent environmental factors linked with life-history stages at appropriate time scales can better explain changes in species distribution through time.

Aim: theory and experiments strongly support the importance of interactive effects of multiple factors shaping biodiversity, although their importance rarely has been investigated at biogeographically relevant scales. In particular, the importance of higher order interactions among environmental factors at such scales is largely unknown. We investigated higher order interactions of environmental factors to explain diversity patterns in a metacommunity of aquatic invertebrates at a biogeographically relevant scale and discuss the findings in an environmental management context.
Location: all major drainage basins in Switzerland (Rhine, Rhone, Ticino and Inn; 41,285 km²).
Methods: riverine α-diversity patterns at two taxonomic levels (family richness of all benthic macroinvertebrates and species richness of Ephemeroptera, Plecoptera and Trichoptera) were examined at 518 sites across the basins. We applied a novel machine learning technique to detect key three-way interactions of explanatory variables by comparing the relative importance of 1,140 three-way combinations for family richness and 680 three-way combinations for species richness.
Results: relatively few but important three-way interactions were meaningful for predicting biodiversity patterns among the numerous possible combinations. Specifically, we found that interactions among elevational gradient, prevalence of forest coverage in the upstream basin and biogeoclimatic regional classification were distinctly important.
Main conclusion: our results indicated that a high prevalence of terrestrial forest generally sustains riverine benthic macroinvertebrate diversity, but this relationship varies considerably with biogeoclimatic and elevational conditions likely due to community composition of forests and macroinvertebrates changing along climatic and geographical gradients. An adequate management of riverine ecosystems at relevant biogeographical scales requires the identification of such interactions and a context-dependent implementation.

Dispersal is a process of central importance for the ecological and evolutionary dynamics of populations and communities, because of its diverse consequences for gene flow and demography. It is subject to evolutionary change, which begs the question, what is the genetic basis of this potentially complex trait? To address this question, we (i) review the empirical literature on the genetic basis of dispersal, (ii) explore how theoretical investigations of the evolution of dispersal have represented the genetics of dispersal, and (iii) discuss how the genetic basis of dispersal influences theoretical predictions of the evolution of dispersal and potential consequences.
Dispersal has a detectable genetic basis in many organisms, from bacteria to plants and animals. Generally, there is evidence for significant genetic variation for dispersal or dispersal-related phenotypes or evidence for the micro-evolution of dispersal in natural populations. Dispersal is typically the outcome of several interacting traits, and this complexity is reflected in its genetic architecture: while some genes of moderate to large effect can influence certain aspects of dispersal, dispersal traits are typically polygenic. Correlations among dispersal traits as well as between dispersal traits and other traits under selection are common, and the genetic basis of dispersal can be highly environment-dependent.
By contrast, models have historically considered a highly simplified genetic architecture of dispersal. It is only recently that models have started to consider multiple loci influencing dispersal, as well as non-additive effects such as dominance and epistasis, showing that the genetic basis of dispersal can influence evolutionary rates and outcomes, especially under non-equilibrium conditions. For example, the number of loci controlling dispersal can influence projected rates of dispersal evolution during range shifts and corresponding demographic impacts. Incorporating more realism in the genetic architecture of dispersal is thus necessary to enable models to move beyond the purely theoretical towards making more useful predictions of evolutionary and ecological dynamics under current and future environmental conditions. To inform these advances, empirical studies need to answer outstanding questions concerning whether specific genes underlie dispersal variation, the genetic architecture of context-dependent dispersal phenotypes and behaviours, and correlations among dispersal and other traits.

Ecosystems face multiple anthropogenic threats globally, and the effects of these environmental stressors range from individual‐level organismal responses to altered system functioning. Understanding the combined effects of stressors on process rates mediated by individuals in ecosystems would greatly improve our ability to predict organismal multifunctionality (e.g. multiple consumer‐mediated functions). We conducted a laboratory experiment to test direct and indirect, as well as immediate and delayed effects of a heat wave (pulsed stress) and micropollutants (MPs) (prolonged stress) on individual consumers (the great pond snail Lymnaea stagnalis) and their multifunctionality (i.e. consumption of basal resources, growth, reproduction, nutrient excretion and organic‐matter cycling). We found that stressful conditions increased the process rates of multiple functions mediated by individual consumers. Specifically, the artificial heat wave increased process rates in the majority of the quantified functions (either directly or indirectly), whereas exposure to MPs increased consumption of basal resources which led to increases in the release of nutrients and fine particulate organic matter. Moreover, snails exposed to a heat wave showed decreased reproduction and nutrient excretion after the heat‐wave, indicating the potential for ecologically relevant delayed effects. Our study indicates that the immediate and delayed effects of stressors on individual organisms may directly and indirectly impact multiple ecosystem functions. In particular, delayed effects of environmental stress on individual consumers may cumulatively impede recovery due to decreased functioning following a perturbation. Reconciling these results with studies incorporating responses at higher levels of biological complexity will enhance our ability to forecast how individual responses upscale to ecosystem multifunctionality.

1. Leaf litter decomposition is a major ecosystem process that can link aquatic to terrestrial ecosystems by flows of nutrients. Biodiversity and ecosystem functioning research hypothesizes that the global loss of species leads to impaired decomposition rates and thus to slower recycling of nutrients. Especially in aquatic systems, an understanding of diversity effects on litter decomposition is still incomplete.
2. Here we conducted an experiment to test two main factors associated with global species loss that might influence leaf litter decomposition. First, we tested whether mixing different leaf species alters litter decomposition rates compared to decomposition of these species in monoculture. Second, we tested the effect of the size structure of a lotic decomposer community on decomposition rates.
3. Overall, leaf litter identity strongly affected decomposition rates, and the observed decomposition rates matched measures of metabolic activity and microbial abundances. While we found some evidence of a positive leaf litter diversity effect on decomposition, this effect was not coherent across all litter combinations and the effect was generally additive and not synergistic.
4. Microbial communities, with a reduced functional and trophic complexity, showed a small but significant overall reduction in decomposition rates compared to communities with the naturally complete functional and trophic complexity, highlighting the importance of a complete microbial community on ecosystem functioning.
5. Our results suggest that top-down diversity effects of the decomposer community on litter decomposition in aquatic systems are of comparable importance as bottom-up diversity effects of primary producers. A plain language summary is available for this article.

Sediment bypass tunnels (SBTs) are guiding structures used to reduce sediment accumulation in reservoirs during high flows by transporting sediments to downstream reaches during operation. Previous studies monitoring the ecological effects of SBT operations on downstream reaches suggest a positive influence of SBTs on riverbed sediment conditions and macroinvertebrate communities based on traditional morphology-based surveys. Morphology-based macroinvertebrate assessments are costly and time-consuming, and the large number of morphologically cryptic, small-sized and undescribed species usually results in coarse taxonomic identification. Here, we used DNA metabarcoding analysis to assess the influence of SBT operations on macroinvertebrates downstream of SBT outlets by estimating species diversity and pairwise community dissimilarity between upstream and downstream locations in dam-fragmented rivers with operational SBTs in comparison to dam-fragmented (i.e., no SBTs) and free-flowing rivers (i.e., no dam). We found that macroinvertebrate community dissimilarity decreases with increasing operation time and frequency of SBTs. These factors of SBT operation influence changes in riverbed features, e.g. sediment relations, that subsequently effect the recovery of downstream macroinvertebrate communities to their respective upstream communities. Macroinvertebrate abundance using morphologically-identified specimens was positively correlated to read abundance using metabarcoding. This supports and reinforces the use of quantitative estimates for diversity analysis with metabarcoding data.

Maternal effects can substantially affect ecological and evolutionary processesin natural populations. However, as they often are environmentally induced,establishing their genetic basis is challenging. One important, but largely neglected,source of maternal effects are egg coats (i.e., the maternally derived extracellularmatrix that surrounds the embryo). In the moor frog, the gelatinous egg coats (i.e.,egg jelly) are produced in the mother’s oviduct and consist primarily of highlyglycosylated mucin type O-glycans. These O-glycans affect jelly water balance and,subsequently, contribute to adaptive divergence in embryonic acid tolerance.To identify candidate genes for maternal effects, we conducted RNAseqtranscriptomics on oviduct samples from seven R. arvalis females, representing thefull range of within and among population variation in embryonic acid stresstolerance across our study populations. De novo sequencing of these oviducttranscriptomes detected 124,071 unigenes and functional annotation analysesidentified a total of 57,839 unigenes, of which several identified genes likely code forvariation in egg jelly coats. These belonged to two main groups: mucin type coreprotein genes and five different types of glycosylation genes. We further predict26,711 gene-linked microsatellite (simple sequence repeats) and 231,274 singlenucleotide polymorphisms. Our study provides the first set of genomic resourcesfor R. arvalis, an emerging model system for the study of ecology and evolution innatural populations, and gives insight into the genetic architecture of egg coatmediated maternal effects.

The State of Mato Grosso in Brazil has undergone intensive land use changes over the past decades. Native ecosystems have been converted into agrosystems for the production of cash crops and cattle. The Brazilian Forest Code advocates full protection of specifically sensitive habitats, and it also safeguards a fixed percentage of native vegetation known as "Legal Reserves" (LRs) inside private rural properties. As part of Brazilian Legal Amazonia region, in Mato Grosso, these percentages account for 35 % of savannas and 80 % of forests found inside each rural property. Here we analyze at the scale of the three biomes: Cerrado, Amazonia and Pantanal, the changes in native vegetation cover (NVC) from 1992 to 2007 and the representativeness of NVC types within the LRs, as well as the role of LRs for general landscape configuration and conservation. In Mato Grosso, 90 % of all studied NVC types are represented inside LR patches. Legal Reserves also accounted for 37 % of the total protected areas and for 37.8 % of all remnant NVCs found in Mato Grosso in 2007. The importance of LRs for landscape structure varied greatly according to biome, but it is noteworthy that LRs were generally missing in highly deforested zones. The relative small size of LRs in all biomes (55 to 64 % of them are ≤12 ha) makes them specifically vulnerable to further changes in land use. Considering the current tendency of ongoing fragmentation, the importance of LRs for landscape connectivity should be increased, specifically by improving the network of corridors between these remnant native vegetation areas.

1. Competition can be fully hierarchical or intransitive, and this degree of hierarchy is driven by multiple factors, including environmental conditions, the functional traits of the species involved or the topology of competition networks. Studies simultaneously analysing these drivers of competition hierarchy are rare. Additionally, organisms compete either directly or via interference competition for resources or space, within a local neighbourhood or across the habitat. Therefore, the drivers of competition could change accordingly and depend on the taxa studied.
2. We performed the first multi‐taxon study on pairwise competition across major taxonomic groups, including experiments with vascular plants, mosses, saprobic fungi, aquatic protists and soil bacteria. We evaluated how general is competition intransitivity from the pairwise competition matrix including all species and also for each possible three‐species combination (triplets). We then examined which species were likely to engage in competitive loops and the effects of environmental conditions, competitive rank and functional traits on intransitive competition.
3. We found some degree of competition intransitivity in all taxa studied, with 38% to 5% of triplets being intransitive. Variance in competitive rank between species and more fertile conditions strongly reduced intransitivity, with triplets composed of species differing widely in their competitive ranks much less likely to be intransitive.
4. Including functional traits of the species involved more than doubled the variation explained compared to models including competitive rank only. Both trait means and variance within triplets affected the odds of them being intransitive. However, the traits responsible and the direction of trait effects varied widely between taxa, suggesting that traits can have a wide variety of effects on competition.
5. Synthesis. We evaluated the drivers of competition across multiple taxa and showed that productivity and competitive rank are fundamental drivers of intransitivity. We also showed that not only the functional traits of each species, but also those of the accompanying species, determine competition intransitivity. Intransitive competition is common across multiple taxa but can dampen under fertile conditions or for those species with large variance in their competitive abilities. This provides a first step towards predicting the prevalence of intransitive competition in natural communities.

Historical contingency broadly refers to the proposition that even random historical events can constrain the ecological and evolutionary pathways of organisms and that of entire communities. Focusing on communities, these pathways can be reflected into specific structural changes within and across trophic levels – how species interact with and affect each other – which has important consequences for species coexistence. Using the registry of the last 2000 years of plant introductions and their novel herbivores encountered in Central Europe, we find that the order of arrival of closely related (but not of distantly related) plant species constrained the structural changes within the trophic level formed by herbivore species across the observation period. Because it is difficult for field and lab experiments to be conducted over hundreds of years to record and replay the assembly history of a community, our study provides an alternative to understand how structural changes have occurred across extensive periods of time.

1. Associating with conspecifics afflicted with infectious diseases increases the risk of becoming infected, but engaging in avoidance behaviour incurs the cost of lost social benefits. Across systems, infected individuals vary in the transmission risk they pose, so natural selection should favour risk-sensitive avoidance behaviour that optimally balances the costs and benefits of sociality.
2. Here, we use the guppy Poecilia reticulata–Gyrodactylus turnbulli host–parasite system to test the prediction that individuals avoid infected conspecifics in proportion to the transmission risk they pose.
3. In dichotomous choice tests, uninfected fish avoided both the chemical and visual cues, presented separately, of infected conspecifics only in the later stages of infection.
4. A transmission experiment indicated that this avoidance behaviour accurately tracked transmission risk (quantified as both the speed at which transmission occurs and the number of parasites transmitting) through the course of infection.
5. Together, these findings reveal that uninfected hosts can use redundant cues across sensory systems to inform dynamic risk-sensitive avoidance behaviour. This correlation between the transmission risk posed by infected individuals and the avoidance response they elicit has implications for the evolutionary ecology of infectious disease, and its explicit inclusion may improve the ability of epidemic models to predict disease spread.

Climate change, in particular rising temperature, is suspected to be a major driver for the emergence of many wildlife diseases. Proliferative kidney disease of salmonids, caused by the myxozoan Tetracapsuloides bryosalmonae, was used to evaluate how temperature dependence of host-parasite interactions modulates disease emergence. Brown trout (Salmo trutta fario) kept at 12 and 15 °C, were experimentally infected with T. bryosalmonae. Parasite development in the fish host and release of spores were quantified simultaneously to unravel parasite transmission potential from the vertebrate to the invertebrate host. A change to a stable plateau in infection intensity of the kidney coincided with a threshold at which spore shedding commenced. This onset of parasite release was delayed at the low temperature in accordance with reaching this infection intensity threshold, but the amount of spores released was irrespective of temperature. The production of parasite transmission stages declined with time. In conclusion, elevated temperature modifies the parasite transmission opportunities by increasing the duration of transmission stage production, which may affect the spread and establishment of the parasite in a wider range of rivers.

Hydropower is an important pillar of the electricity productionin Switzerland and its extension is planned in the next decades. Therefore, amore sustainable management of hydropower plants is needed. Sedimentreplenishment combined with artificially-triggered flood pulses are gainingincreasing interest to restore residual flow reaches. In the Sarine river inSwitzerland, such a measure was conducted. Mimicking laboratoryexperiments for the first time, four deposits, totaling 1000 m³ of sediment,were added to the river downstream of Rossens dam. Some 489 pebbles wereequipped with RFID PIT tags and distributed among them. After the floodpulse passed, 57% of the tags were re-located. The maximum detected traveldistance of a pebble was 284 m. Some deposits were eroded, while othersresisted. Due to a limited submergence, mainly lateral erosion was observed.Nevertheless, erosion of deposits as well as deposition of eroded material inclusters resulted in the same scheme as observed in laboratory experimentswhich could be validated with this field experiment.

The geometry and hydrodynamics of river reaches are key ecohydraulic descriptors. Statistics of water depth and velocity measurements are usually taken as proxies for habitat suitability in rivers. However, little is known about the sufficiency of data to produce effective and representative results. In this research, 19 reaches with differences in terms of discharge, river width, substrate, reach length, cross-section spacing and geomorphology are investigated. Measurements of flow depth and velocity were taken at multiple, equally spaced cross-sections along each reach. Data were sub-sampled using different methodologies and analysed each time. The sets of sub-sampled data were then compared with those calculated with the full data set from a reach. The focus was put towards the hydro-morphological index of diversity (HMID), a combination of the classical ecohydraulic variables flow depth and velocity. It represents the spatial variability of hydraulic habitats in a reach. The results point out that, with a well-defined sampling strategy, 100 measurement points lead to a good estimation of the HMID value in a reach, if more than eight measurement points are taken per cross-section. For geomorphologies with small complexity or when the analysis only includes the estimation of mean flow depth or mean flow velocity, this number can be decreased according to the results presented here. These findings help both, aquatic ecologists and engineers to estimate their data reliability for hydraulic field measurements in a river reach and are herein discussed taking into account the different studied morphologies.

Resource limitation is a major driver of the ecological and evolutionary dynamics of organisms. Short-term responses to resource limitation include plastic changes in molecular phenotypes including protein expression. Yet little is known about the evolution of the molecular phenotype under longer-term resource limitation. Here, we combine experimental evolution of the green alga Chlamydomonas reinhardtii under multiple different nonsubstitutable resource limitation regimes with proteomic measurements to investigate evolutionary adaptation of the molecular phenotype. We demonstrate convergent proteomic evolution of core metabolic functions, including the Calvin-Benson cycle and gluconeogenesis, across different resource limitation environments. We do not observe proteomic changes consistent with optimized uptake of particular limiting resources. Instead, we report that adaptation proceeds in similar directions under different types of non-substitutable resource limitation. This largely convergent evolution of the expression of core metabolic proteins is associated with an improvement in the resource assimilation efficiency of nitrogen and phosphorus into biomass.

Scanning flow cytometry (SFCM) is characterized by the measurement of time-resolved pulses of fluorescence and scattering, enabling the high-throughput quantification of phytoplankton morphology and pigmentation. Quantifying variation at the single cell and colony level improves our ability to understand dynamics in natural communities. Automated highfrequency monitoring of these communities is presently limited by the absence of repeatable, rapid protocols to analyse SFCM datasets, where images of individual particles are not available. Here we demonstrate a repeatable, semi-automated method to (1) rapidly clean SFCM data from a phytoplankton community by removing signals that do not belong to live phytoplankton cells, (2) classify individual cells into trait clusters that correspond to functional groups, and (3) quantify the biovolumes of individual cells, the total biovolume of the whole community and the total biovolumes of the major functional groups. Our method involves the development of training datasets using lab cultures, the use of an unsupervisedclustering algorithm to identify trait clusters, and machine learning tools (random forests) to (1) evaluate variable importance, (2) classify data points, and (3) estimate biovolumes of individual cells. We provide example datasets and R code for our analytical approach that can be adapted for analysis of datasets from other flow cytometers or scanning flow cytometers.

Forecasting changes to ecological communities is one of the central challenges in ecology. However, nonlinear dependencies, biotic interactions and data limitations have limited our ability to assess how predictable communities are. Here, we used a machine learning approach and environmental monitoring data (biological, physical and chemical) to assess the predictability of phytoplankton cell density in one lake across an unprecedented range of time‐scales. Communities were highly predictable over hours to months: model R² decreased from 0.89 at 4 hours to 0.74 at 1 month, and in a long‐term dataset lacking fine spatial resolution, from 0.46 at 1 month to 0.32 at 10 years. When cyanobacterial and eukaryotic algal cell densities were examined separately, model‐inferred environmental growth dependencies matched laboratory studies, and suggested novel trade‐offs governing their competition. High‐frequency monitoring and machine learning can set prediction targets for process‐based models and help elucidate the mechanisms underlying ecological dynamics.

Members of the genus Lysiphlebus Foerster are medium-sized endoparasitoid aphidiine wasps with over 30 species distributed worldwide. They attack numerous aphid hosts, and some species are important biological control agents. All European Lysiphlebus species are revised based on sequence information from the mitochondrial COI barcoding gene and the nuclear 28SD2 gene, morphological traits, and on information about their host specificity. The taxonomic status of 13 European Lysiphlebus species is confirmed, while 11 are redescribed and illustrated. The following four Lysiphlebus species are synonymized: L. melandriicola Starý, 1961 [= L. fabarum (Marshall, 1896)], L. hirtus Starý, 1985 (= L. confusus Tremblay & Eady, 1978), L. hispanus Starý, 1973 (= L. desertorum Starý, 1965), and L. safavii Starý, 1985 (= L. hirticornis Mackauer, 1960). Two new Lysiphlebus species are described: L. volkli sp.n. and L. brachycaudi sp.n. Our results, based on both COI and 28SD2, confirm the existence of three monophyletic species groups within the genus: (1) the ‘fabarum’ group, which includes L. fabarum, L. cardui (Marshall, 1896), L. confusus, L. hirticornis, L. brachycaudi sp.n., and L. volkli sp.n.; (2) the ‘testaceipes’ group, which includes L. testaceipes (Cresson, 1880), L. orientalis Starý & Rakhshani, 2010, L. fritzmuelleri Mackauer, 1960, L. balcanicus Starý, 1998, L. desertorum, [and probably L. dissolutus (Nees, 1811)]; and (3) the ‘alpinus’ group, consisting solely of L. alpinus Starý, 1971. Geometric morphometrics of fore wing shape proved to be a powerful tool to delineate sibling species within the ‘fabarum’ group. We were able to confirm for the first time sexual lines of L. cardui and L. confusus. Furthermore, an additional potentially asexual Lysiphlebus taxon in Europe is revealed based on the discovery of an asexual line of L. volkli sp.n. in Iran. An illustrated key for identification of the European Lysiphlebus species is provided.

1. Rivers are spatially organised into hierarchic dendritic networks. This unique physical structure and the associated directionality of physical flows set them apart from most other environments by regulating the dispersal of resident biota and therefore the distribution of biodiversity.
2. The aim of this special issue is to highlight the importance of the river network on structuring biodiversity, particularly through metacommunity dynamics and associated dispersal processes.
3. The issue covers a wide range of topics, including disease spread, nutrient uptake, trophic dynamics, effects of anthropogenic stressors and the joint roles of dispersal and environmental filtering. Contributions employ a broad range of approaches, including field and laboratory experiments, modelling, population genetics and conceptual synthesis.
4. Although these studies represent just a sample of the research that is being performed on biodiversity and metacommunity dynamics in river networks, several important findings have emerged; a common theme being that the structure of the network and spatial dynamics clearly influence the dynamics of populations and communities, and their functions. By taking a broad taxonomic focus (from diatoms and protists to fish), and spanning a large geographic gradient (from the tropics to the subarctic), this special issue provides a broad look at the dynamics that occur in river networks relating to their unique makeup. We hope that this selection of studies spurs additional research on these interesting, globally important, yet severely threatened ecological systems.

1. River networks are hierarchical dendritic habitats embedded within the terrestrial landscape, with varying connectivity between sites depending on their positions along the network. This physical organisation influences the dispersal of organisms, which ultimately affects metacommunity dynamics and biodiversity patterns.
2. We provide a conceptual synthesis of the role of river networks in structuring metacommunities in relation to dispersal processes in riverine ecosystems. We explore where the river network best explains observed metacommunity structure compared to other measurements of physical connectivity. We mostly focus on invertebrates, but also consider other taxonomic groups, including microbes, fishes, plants, and amphibians.
3. Synthesising studies that compared multiple spatial distance metrics, we found that the importance of the river network itself in explaining metacommunity patterns depended on a variety of factors, including dispersal mode (aquatic versus aerial versus terrestrial) and landscape type (arid versus mesic), as well as location-specific factors, such as network connectivity, land use, topographic heterogeneity, and biotic interactions. The river network appears to be less important for strong aerial dispersers and insects in arid systems than for other groups and biomes, but there is considerable variability. Borrowing from other literature, particularly landscape genetics, we developed a conceptual model that predicts that the explanatory power of the river network peaks in mesic systems for obligate aquatic dispersers.
4. We propose directions of future avenues of research, including the use of manipulative field and laboratory experiments that test metacommunity theory in river networks. While field and laboratory experiments have their own benefits and drawbacks (e.g. reality, control, cost), both are powerful approaches for understanding the mechanisms structuring metacommunities, by teasing apart dispersal and niche-related factors.
5. Finally, improving our knowledge of dispersal in river networks will benefit from expanding the breadth of cost-distance modelling to better infer dispersal from observational data; an improved understanding of life-history strategies rather than relying on independent traits; exploring individual-level variation in dispersal through detailed genetic studies; detailed studies on fine-scale environmental (e.g. daily hydrology) and organismal spatiotemporal variability; and synthesising comparative, experimental, and theoretical work. Expanding in these areas will help to push the current state of the science from a largely pattern-detection mode into a new phase of more mechanistically driven research.

According to the Red Queen hypothesis, clonal diversity in asexual populations could be maintained by negative frequency-dependant selection by coevolving parasites. If common clones are selected against and rare clones gain a concomitant advantage, we expect that clonal turnover should be faster during parasite epidemics than between them. We tested this hypothesis exploring field data of the Daphnia–Caullerya host–parasite system. The clonal make-up and turnover of the Daphnia host population was tracked with high temporal resolution from 1998 until 2013, using first allozyme and later microsatellite markers. Significant differences in the clonal composition between random and infected subsamples of Daphnia populations were detected on six of seven tested occasions, confirming genetic specificity of the host–parasite interaction in this system. We used time series analysis to compare the rates of host clonal turnover to the incidence of parasitism, and found that Caullerya prevalence was significantly associated with microsatellite-based clonal turnover. As alternate hypotheses, we further tested whether turnover was related to a variety of biotic, abiotic, and host demographic parameters. Other significant correlates of turnover were cyanobacterial biomass and (weakly) temperature. Overall, parasitism seems to be a strong driver of host clonal turnover, in support of the Red Queen hypothesis.

With ongoing global change, life is continuously forced to move to novel areas, which leads to dynamically changing species ranges. As dispersal is central to range dynamics, factors promoting fast and distant dispersal are key to understanding and predicting species ranges. During range expansions, genetic variation is depleted at the expanding front. Such conditions should reduce evolutionary potential, while increasing kin competition. Organisms able to recognise relatives may be able to assess increased levels of relatedness at expanding range margins and to increase their dispersal in a plastic manner. Using individual-based simulations and experimental range expansions of a spider mite, we demonstrate that plastic responses to kin structure can be at least as important as evolution in driving range expansion speed. Because recognition of kin or kind is increasingly documented across the tree of life, we anticipate it to be a highly important but neglected driver of range expansions.

Nach erfolgreichem Abschluss der interdisziplinären Vorgängerprojekte «Rhone-Thur», «Integrales Flussgebietsmanagement» und «Geschiebeund Habitatsdynamik» wurde im Rahmen des durch das Bundesamt für Umwelt (BAFU) unterstützten Forschungsprogramms «Wasserbau und Ökologie» ein neues Projekt gestartet, welches sich auf die Sedimentdynamik und Vernetzung in Fliessgewässern konzentriert. Das Ziel des Projekts ist es, das im Rahmen der Vorgängerprojekte erarbeitete Wissen weiter zu vertiefen und auszubauen. Dabei stehen wiederum konkrete Fragen und Antworten zu Hochwasserschutz- und Revitalisierungsprojekten im Vordergrund. Im vorliegenden Beitrag werden die Zielsetzung sowie die Projektschwerpunkte mit den daraus resultierenden einzelnen Teilprojekten vorgestellt.

High alpine catchments are affected by climate change, but have not been studied as intensely as other ecosystems. This Master's thesis aims at the detection of long-term trends in the ecohydrology of the Macun lake system. This catchment is located in the Swiss National Park and consists of two basins with different water sources. The data analysed consists of three major parts: yearly sampling of 10 sites since 2002 and sampling over the snow-free period of 2002 and 2017 of 31 sites. During each sampling campaign, a water sample was collected for later lab analysis and temperature, conductivity, and turbidity were measured in the field. Additionally, there are data available from an Exosonde located near the outlet of Lai d'Immez, which recorded data from summer 2016 till early spring 2017 and summer 2017 until present. Over the past 17 years, DN and TIC showed the strongest changes. DN decreased while TIC increased, which corresponds to atmospheric concentrations. Further, pH dropped and is now below 6, which seems to affect diatom communities. Both years, 2002 and 2017, showed spatial differences, but a decrease in those differences was not detectable. During the snow-free period in 2017, both spatial and temporal differences were present. The southern, glacialy influenced basin, showed higher variation than the north basin. Conductivity and nitrogen had higher concentrations in the south basin, which is due to the glacial input. The north basin on the other hand had higher concentrations of organic carbon, which indicates a higher productivity of this basin. This thesis has identified various trends and patterns, and offers a basis for further research in the same catchment as well as for comparison with other catchments.

Parasitoid wasps are frequently employed to control pest aphids in greenhouse crops. However, aphids can be infected with heritable bacterial endosymbionts that strongly increase their resistance to parasitoid wasps. These defensive symbionts have the potential to compromise the effectiveness of biological control. Unfortunately, we still lack the necessary studies to assess their effects at the scale of greenhouses, but laboratory experiments indicate clearly that defensive symbionts represent a problem. Selection by parasitoids results in the rapid evolution of symbiont-conferred resistance, to the point that symbiont-protected aphid populations can escape control by parasitoids. The limited evidence available from field experiments is slightly less disquieting, suggesting that even though it is operational under natural conditions, protection by defensive symbionts does not always provide a net fitness benefit to the aphid hosts. Factors that can limit the success of symbiont-protected aphids are physiological and ecological costs of harboring defensive symbionts, as well as counteradaptations by parasitoids. Based on a review of the pertinent literature, I derive recommendations for mitigating the challenges resulting from the presence of defensive symbionts for the biological control of pest aphids. These include selective breeding of parasitoids as well as clever release strategies, potentially in combination with other biocontrol agents.

Understanding the coevolution of hosts and parasites is a long‐standing goal of evolutionary biology. There is a well‐developed theoretical framework to describe the evolution of host–parasite interactions under the assumption of direct, two‐species interactions, which can result in arms race dynamics or sustained genotype fluctuations driven by negative frequency dependence (Red Queen dynamics). However, many hosts rely on symbionts for defence against parasites. Whilst the ubiquity of defensive symbionts and their potential importance for disease control are increasingly recognized, there is still a gap in our understanding of how symbionts mediate or possibly take part in host–parasite coevolution. Herein we address this question by synthesizing information already available from theoretical and empirical studies. First, we briefly introduce current hypotheses on how defensive mutualisms evolved from more parasitic relationships and highlight exciting new experimental evidence showing that this can occur very rapidly. We go on to show that defensive symbionts influence virtually all important determinants of coevolutionary dynamics, namely the variation in host resistance available to selection by parasites, the specificity of host resistance, and the trade‐off structure between host resistance and other components of fitness. In light of these findings, we turn to the limited theory and experiments available for such three‐species interactions to assess the role of defensive symbionts in host–parasite coevolution. Specifically, we discuss under which conditions the defensive symbiont may take over from the host the reciprocal adaptation with parasites and undergo its own selection dynamics, thereby altering or relaxing selection on the hosts' own immune defences. Finally, we address potential effects of defensive symbionts on the evolution of parasite virulence. This is an important problem for which there is no single, clear‐cut prediction. The selection on parasite virulence resulting from the presence of defensive symbionts in their hosts will depend on the underlying mechanism of defence. We identify the evolutionary predictions for different functional categories of symbiont‐conferred resistance and we evaluate the empirical literature for supporting evidence. We end this review with outstanding questions and promising avenues for future research to improve our understanding of symbiont‐mediated coevolution between hosts and parasites.

Spatial dynamics and local environmental processes shape ecological communities and affect diversity in dendritic riverine networks. Understanding the contributions of individual and interacting parameters on diversity and community composition is a contentious topic. Recent theoretical work suggests that diversity in dendritic networks is to a large extent explained by dispersal and network connectivity. Empirical studies identified similar diversity patterns depending on network position but also found that contribution of relevant processes differed depending on scale. In this study I explored α-, true β-, and functional diversity within aquatic invertebrate communities and identified variables that explained diversity patterns at two levels of taxonomic resolution (species/complex-level and family-level). The studied area encompasses the dendritic network of the pre-alpine river Thur drainage basin that spans over seven Strahler orders. Macroinvertebrate samples and chemico-physical parameters were taken at 60 sites selected to represent the Thur’s inherent network structure, from 2^nd-order headwaters to 7^th-order rivers. Using regression analysis, linear, and general linear models, I related diversity patterns to network connectivity, network distance, and a set of local environmental variables. On both levels of taxonomic resolution, I found that local diversity showed a unimodal distribution that peaked in mid-sized stream reaches. Low α-diversity contrasted with high true β-diversity in headwaters. Local diversity was best explained by distance from outlet and by a set of chemical variables that indicate anthropogenic impact on water quality. Using model selection, it was not possible to reduce the explanatory variables and interactions to a straightforward set that best explained true β-diversity. My results highlight the importance of local factors such as chemical content of stream water and spatial position within the river network on local macroinvertebrate diversity. Furthermore, constraints of partially treated waste water on the composition and structure of aquatic invertebrate communities were indicated.

Background
Transfusion practice might significantly influence patient morbidity and mortality. BetweenEuropean countries, transfusion practice of red blood cells (RBC) greatly differs. Onlysparse data are available on transfusion practice of general internal medicine physicians inSwitzerland.

Methods
In this cross-sectional survey, physicians working in general medicine teaching hospitals inSwitzerland were investigated regarding their self-reported transfusion practice in anemicpatients without acute bleeding. The definition of anemia, transfusion triggers, knowledgeon RBC transfusion, and implementation of guidelines were assessed.

Results
560 physicians of 71 hospitals (64%) responded to the survey. Anemia was defined at verydiverging hemoglobin values (by 38% at a hemoglobin <130 g/L for men and by 57% at<120 g/L in non-pregnant women). 62% and 43% respectively, did not define anemia in menand in women according to the World Health Organization. Fifty percent reported not totransfuse RBC according to international guidelines. Following factors were indicated toinfluence the decision to transfuse: educational background of the physicians, geographicalregion of employment, severity of anemia, and presence of known coronary artery disease.60% indicated that their knowledge on Transfusion-related Acute Lung Injury (TRALI) didnot influence transfusion practice. 50% of physicians stated that no local transfusion guidelines exist and 84% supported the development of national recommendations ontransfusion in non-acutely bleeding, anemic patients.

Conclusion
This study highlights the lack of adherence to current transfusion guidelines in Switzerland.Identifying and subsequently correcting this deficit in knowledge translation may have a significantimpact on patient care.

Global environmental change and biodiversity loss are closely linked through different feedback mechanisms. The University of Zurich Research Priority Programme on 'Global Change and Biodiversity' approach is to work with interdisciplinarity and transdisciplinarity to integrate mechanisms of interactions, feedback and scale and improve our understanding of the feedbacks between global change and biodiversity effects. Such work across research disciplines is not without its challenges. Here we share some of the questions that arose from our research approach over the last five years and how we addressed these challenges. First, our transdisciplinary approach allows combining different disciplines into a more holistic perspective towards integrative research, but demands collaborative work to establish common terminology, concepts, and metrics. Second, the research theme's common perspective (biodiversity is desirable, global change is not) may also induce a confirmation bias from preconceived ideas. Third, new challenges emerge from scaling mechanisms and feedbacks at different spatial and temporal scales. Fourth, we investigate how to relate biodiversity, global change, ecosystem services and functions using interdisciplinary approaches. Fifth, we identify gaps between existing experiments and data requirements, and propose the definition of new experimental setups by linking processes and performing experiments at typical experimental scales as well as at larger scales. We conclude by emphasising the necessity to integrate theory, experiments, modelling and simulation, high performance computing and big data to understand feedbacks between biodiversity loss and processes of global change.

Amphipods are keystone species in many freshwater ecosystems. Understanding their distribution and diversity is crucial to ensure and preserve freshwater ecosystem functioning, particularly in the northern hemisphere. For the European Alps information on amphipods has been relatively limited until recently. We describe a new, widely distributed amphipod species, Gammarus alpinus sp. nov., found across the Alps and analyse its distribution, biogeography as well as genetic and morphological differentiation. Until now, this species has been reported as Gammarus lacustris. Based on genetic and morphometric measurements, we show that G. alpinus is highly divergent from G. lacustris. The latter has a circumpolar distribution, but may be absent from the Alps. The observed occurrence pattern of G. alpinus might be explained by a Pliocene range expansion and vicariance due to climate warming following the Quaternary glaciation. Historical drainage divides suggest a single recolonization route from a distinct southern refugium. While G. lacustris is widely distributed and not endangered at a global scale, G. alpinus is endemic to the Alps and its habitat is negatively affected by eutrophication, non-native species and possibly climate change.

Species establish different interactions (e.g. antagonistic, mutualistic) with multiple species, forming multilayer ecological networks. Disentangling network co-structure in multilayer networks is crucial to predict how biodiversity loss may affect the persistence of multispecies assemblages. Existing methods to analyse multilayer networks often fail to consider network co-structure. We present a new method to evaluate the modular co-structure of multilayer networks through the assessment of species degree co-distribution and network module composition. We focus on modular structure because of its high prevalence among ecological networks. We apply our method to two Lepidoptera-plant networks, one describing caterpillar-plant herbivory interactions and one representing adult Lepidoptera nectaring on flowers, thereby possibly pollinating them. More than 50% of the species established either herbivory or visitation interactions, but not both. These species were over-represented among plants and lepidopterans, and were present in most modules in both networks. Similarity in module composition between networks was high but not different from random expectations. Our method clearly delineates the importance of interpreting multilayer module composition similarity in the light of the constraints imposed by network structure to predict the potential indirect effects of species loss through interconnected modular networks.

Running waters are among the most threatened ecosystems globally, having altered hydrological regimes, homogenized habitat, and impaired water quality. These multiple stressors impact aquatic biodiversity and ecosystem function across space and time, although a clear mechanistic understanding is still lacking. Here, we examined the trophic response of macroinvertebrates among streams in a Swiss lowland catchment encompassing a gradient of land uses. Clear compositional changes were observed as anthropogenic impacts increased from least-impacted to agricultural and urbanized sites. Taxonomic diversity was lowest at sites with morphological and water quality impairment (agricultural sites), whereas taxonomic identity (susceptible vs. generalist species) mainly changed due to water quality degradation (agricultural and urban sites) based on the SPEAR (pesticides) index. Using stable isotopes (δ¹³C, δ¹⁵N), a simplification in macroinvertebrate trophic structure was evident along the land use gradient. At a site receiving wastewater treatment effluent, stable isotopes also revealed trophic shifts in primary consumers that corresponded to changes in available food resources. Results further showed that some taxa losses, e.g., the mayfly Ecdyonurus, to land- use effects may be due to low trophic plasticity. The combination of analyses, including stable isotopes, provided an improved mechanistic understanding of community and population responses to land-use changes along river networks.

Macroinvertebrate colonization of restored rivers is a function of dispersal into the restored reach and its suitability for population establishment. To maximize potential for colonization success, spatial considerations such as distance to colonizer source pools and dispersal pathways must be included in restoration planning. Unfortunately, the dispersal abilities of macroinvertebrates and ecological importance of different dispersal modes for colonization are still poorly understood. We used a field experiment that controlled colonization by passive drift and allowed distinction between active upstream aquatic and active/passive aerial dispersal, thus testing their differential importance during colonization of experimentally restored stream reaches. Two agricultural streams emanating below culverts were longitudinally separated along the first 30 m and one stream side each was covered with a fine-mesh net to limit aerial dispersal. Colonization of manually disturbed background and experimentally introduced cobble substrate was investigated over 6 months. We found that upstream in-stream dispersal, especially in these agricultural streams, can be rapid (days) and play an important role in the short-term colonization of restored streams. We conclude that a landscape perspective, in addition to in-stream measures, must be considered when attempting to restore streams dominated by agricultural and urban land use that constrains available species pools and limits dispersal pathways.

Dynamic interactions between ecological conditions and the phenotypic composition of populations likely play an important role in evolution, but the direction and strength of these feedbacks remain difficult to characterize. We investigated these dynamics across two generations of threespine sticklebacks from two evolutionary lineages undergoing secondary contact and hybridization. Independently manipulating the density and lineage of adults in experimental mesocosms led to contrasting ecosystem conditions with strong effects on total survival in a subsequent generation of juveniles. Ecosystem modifications by adults also varied the strength of selection on competing hybrid and non-hybrid juveniles. This variation in selection indicated (1) a negative eco-evolutionary feedback driven by lineage-specific resource depletion and dependence and (2) a large performance advantage of hybrid juveniles in depleted environments. This work illustrates the importance of interactions between phenotype, population density and the environment in shaping selection and evolutionary trajectories, especially in the context of range expansion with secondary contact and hybridization.

Ecological stoichiometry is a powerful concept. Rarely, however, has it been applied to fungi, despite their pivotal role in ecosystems. In view of the paucity of stoichiometric data, we grew 16 fungal isolates from streams in liquid culture (C:N:P = 160:16:1) and analysed them for nitrogen (N), phosphorus (P) and ergosterol as a fungal biomass marker. Interspecific differences explained up to 60% of the variation in N, P and ergosterol concentrations, and variation between strains of the same species accounted for up to another 16%. We found an average C:N:P of 136:10:1 in mycelia, while N:ergosterol and P:ergosterol ratios were 9.5 and 2.5, respectively. These ratios are an important step towards establishing reliable conversion factors to estimate the contribution of fungi to litter nutrient contents in complex field samples. Estimates could be further improved by applying the species-specific conversion factors we obtained. Additional analyses of fungal strains in conditions reflecting field situations are needed to strengthen the basis of such estimates of fungal nutrient pools in ecosystems; however, inherent variation within species limits the accuracy and precision that can be achieved.

Host resistance to parasites is a rapidly evolving trait that can influence how hosts modify ecosystems. Eco-evolutionary feedbacks may develop if the ecosystem effects of host resistance influence selection on subsequent host generations. In a mesocosm experiment, using a recently diverged (<100 generations) pair of lake and stream three-spined sticklebacks, we tested how experimental exposure to a common fish parasite (Gyrodactylus spp.) affects interactions between hosts and their ecosystems in two environmental conditions (low and high nutrients). In both environments, we found that stream sticklebacks were more resistant to Gyrodactylus and had different gene expression profiles than lake sticklebacks. This differential infection led to contrasting effects of sticklebacks on a broad range of ecosystem properties, including zooplankton community structure and nutrient cycling. These ecosystem modifications affected the survival, body condition, and gene expression profiles of a subsequent fish generation. In particular, lake juvenile fish suffered increased mortality in ecosystems previously modified by lake adults, whereas stream fish showed decreased body condition in stream fish-modified ecosystems. Parasites reinforced selection against lake juveniles in lake fish-modified ecosystems, but only under oligotrophic conditions. Overall, our results highlight the overlapping timescales and the interplay of host-parasite and host-ecosystem interactions. We provide experimental evidence that parasites influence host-mediated effects on ecosystems and, thereby, change the likelihood and strength of eco-evolutionary feedbacks.

The rate of self-fertilization (that is, selfing) is a key evolutionary parameter in hermaphroditic species, yet obtaining accurate estimates of selfing rates in natural populations can be technically challenging. Most published estimates are derived from population-level heterozygote deficiency (that is, F_IS) or identity disequilibria (for example, the software RMES (robust multilocus estimate of selfing)). These indirect methods can be applied to population genetic survey data, whereas direct methods using progeny arrays require much larger data sets that are often difficult to collect in natural populations or even require captive breeding. Unfortunately, indirect methods rely on assumptions that can be problematic, such as negating biparental inbreeding, inbreeding disequilibrium and (for F_IS) the presence of null alleles. The performance of indirect estimates against progeny-array estimates is still largely unknown. Here we used both direct progeny-array and indirect population-level methods to estimate the selfing rate in a single natural population of the simultaneously hermaphroditic freshwater snail Radix balthica throughout its reproductive lifespan using 10 highly polymorphic microsatellites. We found that even though progeny arrays (n=1034 field-collected embryos from 60 families) did not reveal a single selfed embryo, F_IS^-based selfing rates (n=316 adults) were significantly positive in all 6 sequential population samples. Including a locus with a high frequency of null alleles further biased F_IS^-based estimates. Conversely, RMES-based estimates were very similar to progeny-array estimates and proved insensitive to null alleles. The assumptions made by RMES were thus either met or irrelevant in this particular population, making RMES a valid, cost-efficient alternative to progeny arrays.

Molluscan benthic assemblages provide unique opportunities for understanding both spatial and temporal patterns of biodiversity. Species richness in the shell remains found at a site (i.e. the death assemblage) is typically several times higher than in the counterpart living assemblage, reflecting a complex history of settlement, dissemination and decomposition post-mortem. We used high-density temporal and spatial sampling (> 37000 individuals representing 196 taxa) of a shallow (5–8 m) nearshore sandy habitat off the coast of south-east Sardinia (Italy, Mediterranean Sea) to study the factors responsible for differences in the relative diversity of living and death assemblages. We found that death assemblages at all sites were considerably more diverse than living communities (1.5–3.5x more dead than living taxa after sample-size standardization), with 78% of all taxa solely recovered as empty shells, resulting in low live-dead agreement. By carefully filtering the raw data and combining them with habitat information extracted from the literature, we disentangled the major causes of this discordance and quantified their individual effects. Increased dead diversities could not be attributed to undersampling of the living community, but instead resulted from three phenomena of decreasing importance: the post-mortem, out-of-habitat transport of non-indigenous taxa (57% of dead-only taxa were allochthonous), the time-averaged presence of rare indigenous taxa (40% of dead-only taxa), and the likely local extirpation of a small number of species (3% of dead-only taxa). Our approach demonstrates how ecological inferences based on death assemblages can be improved by restricting analyses to demonstrably indigenous taxa, and highlights how mollusc shell remains can be used to provide information over both ecological and evolutionary timescales.

Polyandry is a common phenomenon and challenges the traditional view of stronger sexual selection in males than in females. In simultaneous hermaphrodites, the physical proximity of both sex functions was long thought to preclude the operation of sexual selection. Laboratory studies suggest that multiple mating and polyandry in hermaphrodites may actually be common, but data from natural populations are sparse. We therefore estimated the rate of multiple paternity and its seasonal variability in the annual, sperm-storing, simultaneously hermaphroditic freshwater snail Radix balthica for the entire duration of the reproductive lifespan. We also tested whether multiple paternity was associated with clutch size or embryonic development. To obtain these data, we measured and genotyped 60 field-collected egg clutches using nine highly polymorphic microsatellite markers. Overall, 50% of the clutches had multiple fathers, and both the frequency (20-93% of clutches) and magnitude of multiple paternity (mean 1.3-3.8 fathers per clutch) substantially increased over time, probably because of extensive sperm storage. Most multiply sired clutches (83%) had a dominant father, but neither clutch size nor the proportion of developed embryos per clutch was associated with levels of multiple paternity. Both the evident promiscuity and the frequent skew of paternity shares suggest that sexual selection may be an important evolutionary force in the study population.

Proliferative kidney disease (PKD) is a major threat to wild and farmed salmonid populations because of its lethal effect at high water temperatures. Its causative agent, the myxozoan Tetracapsuloides bryosalmonae, has a complex lifecycle exploiting freshwater bryozoans as primary hosts and salmonids as secondary hosts. We carried out an integrated study of PKD in a prealpine Swiss river (the Wigger). During a 3-year period, data on fish abundance, disease prevalence, concentration of primary hosts’ DNA in environmental samples [environmental DNA (eDNA)], hydrological variables, and water temperatures gathered at various locations within the catchment were integrated into a newly developed metacommunity model, which includes ecological and epidemiological dynamics of fish and bryozoans, connectivity effects, and hydrothermal drivers. Infection dynamics were captured well by the epidemiological model, especially with regard to the spatial prevalence patterns. PKD prevalence in the sampled sites for both young-of-the-year (YOY) and adult brown trout attained 100% at the end of summer, while seasonal population decay was higher in YOY than in adults. We introduce a method based on decay distance of eDNA signal predicting local species’ density, accounting for variation in environmental drivers (such as morphology and geology). The model provides a whole-network overview of the disease prevalence. In this study, we show how spatial and environmental characteristics of river networks can be used to study epidemiology and disease dynamics of waterborne diseases.

Inducible, anti-predator traits are a classic example of phenotypic plasticity. Their evolutionary dynamics depend on their genetic basis, the historical pattern of predation risk that populations have experienced and current selection gradients. When populations experience predators with contrasting hunting strategies and size preferences, theory suggests contrasting micro-evolutionary responses to selection. Daphnia pulex is an ideal species to explore the microevolutionary response of anti-predator traits because they face heterogeneous predation regimes, sometimes experiencing only invertebrate midge predators and other times experiencing vertebrate fish and invertebrate midge predators. We explored plausible patterns of adaptive evolution of a predator-induced morphological reaction norm. We combined estimates of selection gradients that characterize the various habitats that D. pulex experiences with detail on the quantitative genetic architecture of inducible morphological defences. Our data reveal a fine scale description of daphnid defensive reaction norms, and a strong covariance between the sensitivity to cues and the maximum response to cues. By analysing the response of the reaction norm to plausible, predator-specific selection gradients,we showhowin the context of this covariance, micro-evolution may be more uniform than predicted from size-selective predation theory. Our results show how covariance between the sensitivity to cues and the maximum response to cues for morphological defence can shape the evolutionary trajectory of predator-induced defences in D. pulex.

Phenotypes can both evolve in response to, and affect, ecosystem change, but few examples of diverging ecosystem-effect traits have been investigated. Bony armor traits of fish are good candidates for this because they evolve rapidly in some freshwater fish populations, and bone is phosphorus rich and likely to affect nutrient recycling in aquatic ecosystems. Here, we explore how ontogeny, rearing environment, and bone allocation among body parts affect the stoichiometric phenotype (i.e., stoichiometric composition of bodies and excretion) of threespine stickleback. We use two populations from distinct freshwater lineages with contrasting lateral plating phenotypes (full vs. low plating) and their hybrids, which are mostly fully plated. We found that ontogeny, rearing environment, and body condition were the most important predictors of organismal stoichiometry. Although elemental composition was similar between both populations and their hybrids, we found significant divergence in phosphorus allocation among body parts and in phosphorus excretion rates. Overall, body armor differences did not explain variation in whole body phosphorus, phosphorus allocation, or phosphorus excretion. Evolutionary divergence between these lineages in both allocation and excretion is likely to have important direct consequences for ecosystems, but may be mediated by evolution of multiple morphological or physiological traits beyond plating phenotype.

Overland transport of recreational boats is among the most important distribution vectors for aquatic invasive zebra and quagga mussels between inland waters. Simple measures such as instructing boat owners how to prepare their boat for transport so that the boat does not carry invasive species are considered to be important prevention measures. Nevertheless, the net effects of such measures are poorly understood and the boat cleaning behavior of boat owners has never been studied in detail before the implementation of such preventive measures. Using a "self-report" questionnaire, we investigated the boat cleaning behavior of boat owners in Switzerland where almost no preventive measures have been taken yet. We found that the self-reported boat cleaning rates are high, with 92% of boaters cleaning their boat upon finding mussels attached to their boat and 84% of them cleaning their boat before a transport. Nevertheless, only half of the boat owners report using high pressure washing to clean their boat before overland transport and many use ineffective cleaning methods.
We show the importance of informing boat owners on the appropriate methods to remove invasive species from their boat and suggest that high pressure washing facilities should be made available at all potentially infested water bodies. Furthermore, our analysis shows that the boat cleaning behavior could be significantly improved by changing how boat owners value the perceived costs and benefits of cleaning, as well as by increasing their awareness of the potential negative impacts on aquatic ecosystems caused by non-native species. With regard to a possible spread of zebra mussels to uninfested alpine lakes and the imminent spread of quagga mussels in Switzerland, we conclude that the Swiss boating community would be open to accepting implementation of prevention measures.

Early detection and monitoring of invasive species is important for the development of effective measures directed at minimising the negative effects of invaders. In the early stages of invasion, aquatic invasive species are typically rare and their detection using costly and time-consuming field surveys is often challenging. Environmental DNA (eDNA) methods are increasingly applied in freshwater systems to detect and quantify target species with relative ease over large geographic scales and across the invasion fronts. In this study we test eDNA detection and quantification methods for invasive zebra and quagga mussels. Both mussel species have invaded widely in North America and Europe and show strong negative ecosystem-wide impacts. We extracted DNA from filtered water samples which we collected along the Rhine catchment in Switzerland, Germany and The Netherlands, including the known invasion area of the zebra mussel and the invasion front of the quagga mussel. Standard PCR and quantitative PCR (qPCR) methods were compared for detection and qPCR was used to quantify the eDNA signal for each species. Our results show that the invasion front of the quagga mussel has moved southwards, including areas where this species had not been detected previously with traditional benthic invertebrate sampling methods. Standard PCR and qPCR showed a similar performance in detecting both mussel species. Moreover, the eDNA quantification of the two species showed low variance within sampling site and matched with expected densities of zebra and quagga mussels based on previous field survey studies. The tested eDNA methods are cost effective and have the potential to be widely applied for the surveillance of zebra and quagga mussels in the future.

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called "eDNA metabarcoding" and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.

Reciprocal selection between aphids, their protective endosymbionts, and the parasitoid wasps that prey upon them offers an opportunity to study the basis of their coevolution. We investigated adaptation to symbiont-conferred defense by rearing the parasitoid wasp Lysiphlebus fabarum on aphids (Aphis fabae) possessing different defensive symbiont strains (Hamiltonella defensa). After ten generations of experimental evolution, wasps showed increased abilities to parasitize aphids possessing the H. defensa strain they evolved with, but not aphids possessing the other strain. We show that the two symbiont strains encode different toxins, potentially creating different targets for counter-adaptation. Phenotypic and behavioral comparisons suggest that neither life-history traits nor oviposition behavior differed among evolved parasitoid lineages. In contrast, comparative transcriptomics of adult female wasps identified a suite of differentially expressed genes among lineages, even when reared in a common, symbiont-free, aphid host. In concurrence with the specificity of each parasitoid lineages' infectivity, most differentially expressed parasitoid transcripts were also lineage-specific. These transcripts are enriched with putative venom toxins and contain highly expressed, potentially defensive viral particles. Together, these results suggest that wild populations of L. fabarum employ a complicated offensive arsenal with sufficient genetic variation for wasps to adapt rapidly and specifically to their hosts' microbial defenses.

Alpine landscapes are changing rapidly due to environmental change, ultimately affecting the structure and function of running water ecosystems. This study examined the trophic structure, using stable isotopes of carbon and nitrogen, of macroinvertebrate assemblages in 32 non-glacial headwaters in 4 glacierized alpine catchments in Switzerland in summer and autumn. We predicted a simple trophic structure (primary and secondary consumers) in streams with consumer isotopic signatures reflecting predominant primary producers (autochthonous versus allochthonous sources) in each season. Principal components analysis revealed seasonal shifts in water physico-chemistry in each catchment, mostly due to changes in phosphorous constituents. Catchment differences in stream physico-chemistry reflected differences in local geologies; i.e., gneiss versus dolomite geologies. Trophic structures, based on nitrogen isotope ratios (δ¹⁵N), were indeed simple, comprising primary consumers (mean δ¹⁵N = –2.2 ± 0.4 SE) of basal resources and secondary consumers (predators; mean δ¹⁵N = 1.4 ± 0.6 SE). All streams were fishless. Carbon ratios (δ¹³C) of primary resources ranged on average from –27.2 ± 1.4 SE (riparian plants) to –24.6 ± 0.6 SE (periphyton), with only riparian plants showing a significant difference between summer and autumn. Carbon ratios (δ¹³C) of macroinvertebrates ranged from –22.2 to –27.9 with higher values found in autumn than summer for Limnephiliidae and Perlodidae. The results indicated that allochthonous resources provided a significant energy base to these headwater streams, in contrast to glacial-fed alpine streams having a dominant autochthonous resource base. The results showed that primary consumers in these alpine streams were mostly generalists (omnivores), adjusting diets to capitalize on changes in available resources. Omnivory may buffer macroinvertebrate assemblages in alpine streams to shifts in basal resources due to landscape transformation resulting from ongoing environmental change.

I metodi impiegati nel mondo intero per misurare la dinamica dei sedimenti e i suoi effetti sulle condizioni ambientali, sui processi ecologici e sugli esseri viventi sono svariati. Si fa ricorso tanto ai metodi classici quanto alle nuove tecnologie, come il telerilevamento mediante droni, la misurazione del consumo di ossigeno nel fondo ghiaioso o le analisi genetiche. La scheda 2 offre una visione generale dei metodi in uso e spiega il loro utilizzo nell’ambito del progetto di ricerca «Dinamica dei sedimenti e degli habitat».

Différentes méthodes servent à mesurer la dynamique des sédiments et ses effets sur l’environnement, les processus écologiques et les organismes vivants. Les scientifiques recourent aussi bien à des systèmes classiques qu’à des technologies récentes comme la télédétection à l’aide de drones, la mesure de la consommation d’oxygène dans les couches de gravier qui garnissent le fond des cours d’eau ou des analyses génétiques. La présente fiche passe en revue les méthodes utilisées et présente leur application dans le cadre du projet de recherche « Dynamique du charriage et des habitats ».

Weltweit werden verschiedene Methoden verwendet, um die Sedimentdynamik und ihre Auswirkungen auf Umweltbedingungen, ökologische Prozesse und Lebewesen zu messen. Im Einsatz sind sowohl klassische Methoden als auch neu entwickelte Technologien wie Fernerkundung mittels Drohnen, Messungen des Sauerstoffverbrauchs in der Kiessohle oder genetische Untersuchungen. Das vorliegende Merkblatt gibt einen Überblick über die verwendeten Methoden und zeigt Anwendungen im Rahmen des Forschungsprojekts «Geschiebe- und Habitatsdynamik».

Les lacs de retenue bloquent le passage des matériaux charriés. Cela conduit à des déficits de charriage en aval, qui se répercutent négativement sur l’état écologique et morphologique des cours d’eau. Il est possible d’accroître la disponibilité des sédiments et d’atténuer ces déficits en construisant des galeries de déviation et en déclenchant des crues artificielles. Exemples à l’appui, la fiche 6 explique en quoi consistent ces deux mesures et décrit leurs effets sur l’écologie et la morphologie des eaux.

La continuità del trasporto di sedimenti è interrotta dalla presenza di laghi artificiali. Nei tratti a valle dei corsi d’acqua si crea così un deficit di sedimenti che ha conseguenze negative per l’ecologia e la morfologia dei corsi d’acqua. Le gallerie di bypass dei sedimenti e le piene artificiali incrementano la disponibilità di sedimenti e ne riducono la carenza. Questa scheda descrive entrambe le misure spiegandole con esempi concreti. Mostra inoltre gli effetti di tali misure sull’ecologia e sulla morfologia delle acque.

Die Geschiebedurchgängigkeit wird durch Stauseen unterbrochen. Im Unterlauf führt dies zu einem Geschiebedefizit, mit negativen Folgen für die Ökologie und Morphologie der Fliessgewässer. Sedimentumleitstollen und künstliche Hochwasser sind Massnahmen, mit denen sich die Sedimentverfügbarkeit erhöhen und Geschiebedefizite mildern lassen. Das vorliegende Merkblatt beschreibt die beiden Massnahmen und erläutert sie anhand von Fallbeispielen. Zudem zeigt es auf, wie sie sich auf die Ökologie und Morphologie von Gewässern auswirken.

Le zone golenali caratterizzate da una grande varietà di ambienti presentano una maggiore resistenza ecologica rispetto a quelle con minore varietà. La varietà di habitat e specie delle zone golenali dipende principalmente dallo spazio riservato alle acque, dalla dinamica dei deflussi e dei sedimenti nonché dalla connettività degli ambienti. L’adozione di misure specifiche che favoriscono lo sviluppo delle specie tipicamente golenali può aumentare la varietà di specie. La scheda 5 illustra i principali fattori che influenzano gli ambienti golenali, riporta alcuni esempi e offre una visione generale sullo stato attuale delle ricerca nell’ambito delle zone golenali.

Auen mit einer grossen Vielfalt an Lebensräumen sind ökologisch widerstandsfähiger als solche mit geringer Lebensraumvielfalt. In Auen wird die Lebensraumund Artenvielfalt hauptsächlich durch den Gewässerraum, die Abfluss- und Sedimentdynamik sowie die Lebensraumvernetzung bestimmt. Mit spezifischen Massnahmen zur Förderung von auentypischen Arten kann die Artenvielfalt erhöht werden. Das vorliegende Merkblatt erläutert die wichtigsten Einflussfaktoren, führt Beispiele auf und gibt einen Einblick in die aktuelle Forschung zu Auen.

Les zones alluviales sont plus résistantes écologiquement lorsqu’elles comportent de nombreux habitats différents. Leur richesse en habitats et en espèces dépend principalement de l’espace réservé aux eaux, de la dynamique des écoulements et des sédiments et de la connectivité écologique. Des mesures de conservation ciblées sur les espèces typiques des zones alluviales peuvent augmenter la biodiversité. La fiche 5 décrit les principaux facteurs agissant sur la biodiversité des zones alluviales, fournit des exemples concrets et donne un aperçu des recherches en cours.

Groundwater belongs to the spatially most extensive, but least explored freshwater systems. On a global scale, the species richness of several subterranean invertebrate taxa parallels species richness found in surface waters, while on a local scale species richness hardly exceeds 20 species. This results in a high contribution of groundwater ecosystems to regional β- and γ-diversity, and to a smaller degree to α-diversity, and deserves focused attention. In general, more species are to be found in large cave systems. The second largest cave system in Europe is Hölloch in Switzerland. In this paper we revised the taxonomic, phylogenetic and ecological diversity of the amphipod community in the Hölloch cave system. While previous records listed five geographically widespread species of the genus Niphargus for this cave system, we could not confirm the presence of any of those species, but rather found three highly distinct species new to science. In this paper we describe Niphargus styx sp. nov., Niphargus murimali sp. nov., and Niphargus muotae sp. nov., and suggest that previous records from that cave were probably misidentificationsf. Although amphipod species richness in this cave system seems to be lower than previously thought in terms of absolute numbers, the cave retained its regional and international importance in terms of nature conservation for multiple reasons. First, all newly described species are probably endemic to this cave system. Second, they are phylogenetically distantly related and exhibit moderate to high phylogenetic diversity. Third, the species, as inferred from their functional morphology, are also ecologically highly divergent. Based on geographic distribution of their nearest relatives, we hypothesize that the cave system was most likely independently colonized from North, West and South and that the pre-adapted ancestors occupied different ecological niches within the system.

Colonial hosts offer unique opportunities for exploitation by endoparasites resulting from extensive clonal propagation, but these interactions are poorly understood. The freshwater bryozoan, Fredericella sultana, and the myxozoan, Tetracapsuloides bryosalmonae, present an appropriate model system for examining such interactions. F. sultana propagates mainly asexually, through colony fragmentation and dormant propagules (statoblasts). Our study examines how T. bryosalmonae exploits the multiple transmission routes offered by the propagation of F. sultana, evaluates the effects of such transmission on its bryozoan host, and tests the hypothesis that poor host condition provokes T. bryosalmonae to bail out of a resource that may soon be unsustainable, demonstrating terminal investment. We show that infections are present in substantial proportions of colony fragments and statoblasts over space and time and that moderate infection levels promote statoblast hatching and hence effective fecundity. We also found evidence for terminal investment, with host starvation inducing the development of transmission stages. Our results contribute to a growing picture that interactions of T. bryosalmonae and F. sultana are generally characterized by parasite persistence, facilitated by multiple transmission pathways and host condition-dependent developmental cycling, and host tolerance, promoted by effective fecundity effects and an inherent capacity for renewed growth and clonal replication.

Background: Persistent covert infections of the myxozoan, Tetracapsuloides bryosalmonae, in primary invertebrate hosts (the freshwater bryozoan, Fredericella sultana) have been proposed to represent a reservoir for proliferative kidney disease in secondary fish hosts. However, we have limited understanding of how covert infections persist and vary in bryozoan populations over time and space and how they may impact these populations. In addition, previous studies have likely underestimated covert infection prevalence. To improve our understanding of the dynamics, impacts and implications of covert infections we employed a highly sensitive polymerase chain reaction (PCR) assay and undertook the first investigation of covert infections in the field over an annual period by sampling bryozoans every 45 days from three populations within each of three rivers.
Results: Covert infections persisted throughout the year and prevalence varied within and between rivers, but were often > 50%. Variation in temperature and water chemistry were linked with changes in prevalence in a manner consistent with the maintenance of covert infections during periods of low productivity and thus poor growth conditions for both bryozoans and T. bryosalmonae. The presence and increased severity of covert infections reduced host growth but only when bryozoans were also investing in the production of overwintering propagules (statoblasts). However, because statoblast production is transitory, this effect is unlikely to greatly impact the capacity of bryozoan populations to act as persistent sources of infections and hence potential disease outbreaks in farmed and wild fish populations.
Conclusions: We demonstrate that covert infections are widespread and persist over space and time in bryozoan populations. To our knowledge, this is the first long-term study of covert infections in a field setting. Review of the results of this and previous studies enables us to identify key questions related to the ecology and evolution of covert infection strategies and associated host-parasite interactions.

Tetracapsuloides bryosalmonae is a myxozoan parasite of freshwater bryozoans and salmonids, causing proliferative kidney disease in the latter. To date, detection of the parasite has required collection of hosts and subsequent molecular or histological examination. The release of infectious spores from both hosts offers an opportunity to detect the parasite in water samples. We developed a novel SYBR® Green quantitative real-time PCR (qPCR) assay for T. bryosalmonae in water samples which provides an estimation of bryozoan malacospore numbers and tested the assay in 3 rivers in southern England (UK) over a period of 5 wk. The assay proved to be both highly sensitive and specific to the parasite, detecting low levels of spores throughout the study period. Larger-volume samples afforded greater detection likelihood, but did not increase the number of spores detected, possibly as a result of low and patchy spore distributions and lack of within-site replication of large-volume samples. Based on point-measurements, temperature was positively associated with the likelihood of detecting spores, possibly reflecting the temperature dependence of spore shedding from bryozoan hosts. The presence of T. bryosalmonae in water samples was predominantly influenced by spatial (sites within rivers, amongst rivers) and temporal (sampling dates) factors, while the latter also influenced quantification cycle (C_q) values and spore abundance. Environmental monitoring for infectious stages can complement traditional methods, providing faster and easier detection and avoiding potentially prolonged searching, collecting and destructive sampling of invertebrate and vertebrate hosts.

Eco-evolutionary dynamics are now recognized to be highly relevant for population and community dynamics. However, the impact of evolutionary dynamics on spatial patterns, such as the occurrence of classical metapopulation dynamics, is less well appreciated. Here, we analyse the evolutionary consequences of spatial network connectivity and topology for dispersal strategies and quantify the eco-evolutionary feedback in terms of altered classical metapopulation dynamics. We find that network properties, such as topology and connectivity, lead to predictable spatio-temporal correlations in fitness expectations. These spatio-temporally stable fitness patterns heavily impact evolutionarily stable dispersal strategies and lead to eco-evolutionary feedbacks on landscape level metrics, such as the number of occupied patches, the number of extinctions and recolonizations as well as metapopulation extinction risk and genetic structure. Our model predicts that classical metapopulation dynamics are more likely to occur in dendritic networks, and especially in riverine systems, compared to other types of landscape configurations. As it remains debated whether classical metapopulation dynamics are likely to occur in nature at all, our work provides an important conceptual advance for understanding the occurrence of classical metapopulation dynamics which has implications for conservation and management of spatially structured populations.

Range expansions and biological invasions are prime examples of transient processes that are likely impacted by rapid evolutionary changes. As a spatialprocess, range expansions are driven by dispersal and movement behaviour. Although it is widely accepted that dispersal and movement may be context-dependent, for instance density-dependent, and best represented by reaction norms, the evolution of density-dependent movement during range expansions has received little experimental attention. We therefore tested current theory predicting the evolution of increased movement at low densities at range margins using highly replicated and controlled range expansion experiments across multiple genotypes of the protist model system Tetrahymena thermophila. Although rare, we found evolutionary changes during range expansions even in the absence of initial standing genetic variation. Range expansions led to the evolution of negatively density-dependent movement at range margins. In addition, we report the evolution of increased intrastrain competitive ability and concurrently decreased population growth rates in range cores. Our findings highlight the importance of understanding movement and dispersal as evolving reaction norms and plastic life-history traits of central relevance for range expansions, biological invasions and the dynamics of spatially structured systems in general.

Aim: Globally, the geographical distributions of species are dynamic and strongly influenced by dispersal. At the same time, range dynamics feed back and may select for increased dispersal at expanding range fronts. This interplay between macroecological and evolutionary dynamics happens almost universally across environmental gradients and such gradients can have a direct impact on the fitness of organisms due to the match or mismatch between an individual's environmental optimum and the current conditions along the gradient. Importantly, gradients also provide individuals with information on environmental changes because dispersing individuals may sense whether environmental conditions improve or deteriorate. However, the ability of organisms to use this information on the environment and to subsequently adjust dispersal decisions plastically, that is, deciding to further disperse into the gradient or not, has been largely ignored and the macroecological consequences remain unclear. We here aim to demonstrate the impact of informed dispersal on the eco-evolutionary dynamics of ranges.
Location: aboratory and theoretical.
Methods: We used individual-based simulations and controlled experiments in replicated microcosm landscapes. Range expansions of the protist model organism Tetrahymena were tracked using video recording and analysis.
Results: We show that information on environmental gradients had a severe impact on range dynamics and inverted the spatial distribution of population densities in comparison with controls where this information was not provided. Additionally, the use of information on gradients prevented evolutionary changes in dispersal rates and an acceleration of range expansion.
Main conclusions: We demonstrate the strong impact of informed dispersal and subsequent behavioural changes on range dynamics in environmental gradients. More generally, our findings highlight the importance of informed dispersal for spatial ecological and evolutionary dynamics.

Aim. Biological invasions are today the second-largest global threat for biodiversity. Once introduced, exotic plant species can modify ecosystem composition, structure and dynamics, eventually driving native species to local extinction. Among the groups of organisms, most likely to be directly affected by exotic invasive plants are herbivorous insects, such as butterflies, which strongly depend on plants throughout their life cycle. However, it remains unclear whether invasive plants have a negative or a positive effect on butterfly diversity at a landscape scale.
Location. Switzerland.
Methods. Using an extensive inventory (393 sites across Switzerland) of both butterfly and invasive plants, we explore the impact of 31 invasive black listed plant species on local butterfly richness. We further identify each butterfly species’ response to invasive plants (i.e. positive, neutral or negative) and analyse the functional and phylogenetic characteristics of these different groups of species.
Results. Our results indicate that butterfly richness negatively correlates with an increase in invasive plant richness. When studying the individual response of each butterfly species to the number of invasive plants, we found that no single butterfly is profiting from invasive plant species, while 28 butterfly species (24%) suffer from the presence of invasive plants. We further show that the species negatively affected are on average less mobile than the unaffected species and that they are phylogenetically clustered.
Main conclusions. Our results present evidences of the influence of invasive species on other trophic levels and interaction networks. We further highlight that a lack of management efforts for mitigating invasive plant impacts threatens specific sections of the functional and phylogenetic diversity of butterflies.

Mounting theoretical evidence suggests that demographic stochasticity, environmental heterogeneity and biased movement of organisms individually affect the dynamics of biological invasions and range expansions. Studies of species spread in heterogeneous landscapes have traditionally characterized invasion velocities as functions of the mean resource density throughout the landscape, thus neglecting higher-order moments of the spatial resource distribution. Here, we show theoretically that different spatial arrangements of resources lead to different spread velocities even if the mean resource density throughout the landscape is kept constant. Specifically, we find that increasing the resource autocorrelation length causes a reduction in the speed of species spread. The model shows that demographic stochasticity plays a key role in the slowdown, which is strengthened when individuals can actively move towards resources. We then experimentally corroborated the theoretically predicted reduction in propagation speed in microcosm experiments with the protist Euglena gracilis by comparing spread in landscapes with different resource autocorrelation lengths. Our work identifies the resource autocorrelation length as a key modulator and a simple measure of landscape susceptibility to biological invasions, which needs to be considered for predicting invasion dynamics within naturally heterogeneous environmental corridors.

For algal biofuels to be economically sustainable and avoid exacerbating nutrient pollution, algal cultivation and processing must maximize rates of biofuel production while simultaneously minimizing the consumption of nitrogen (N) and phosphorus (P) fertilizers. We experimentally tested whether algal polycultures could be engineered to improve N and P nutrient-use efficiency compared to monocultures by balancing trade-offs in nutrient-use efficiency and biocrude production. We analyzed the flows of N and P through the processes of cultivation, biocrude production through hydrothermal liquefaction, and nutrient recycling in a laboratory-scale system. None of the six species we examined exhibited high N efficiency, P efficiency, and biocrude production simultaneously; each had poor performance in at least one function (i.e., <25th percentile). Polycultures of two to six species did not outperform the best species in any single function, but some polycultures exhibited more balanced performance and maintained all three functions at higher levels simultaneously than any of the monocultures (i.e., >67th percentile). Moreover, certain polycultures came closer to optimizing all three functions than any of the monocultures. By balancing trade-offs between N and P efficiency and biocrude production, polycultures could be used to simultaneously reduce the demand for both N and P fertilizers by up to 85%.

Most spatial ecology focuses on how species dispersal affects community dynamics and coexistence. Ecosystems, however, are also commonly connected by flows of resources. We experimentally tested how neighbouring communities indirectly influence each other in absence of dispersal, via resource exchanges. Using two-patch microcosm meta-ecosystems, we manipulated community composition and dynamics, by varying separately species key functional traits (autotroph versus heterotroph species and size of consumer species) and trophic structure of aquatic communities (species growing alone or in presence of competitors or predators). We then analysed the effects of species functional traits and trophic structure on communities connected through spatial subsidies in the absence of actual dispersal. Both functional traits and trophic structure strongly affected dynamics across neighbouring communities. Heterotroph communities connected to autotroph neighbours developed better than with heterotroph neighbours, such that coexistence of competitors was determined by the functional traits of the neighbouring community. Densities in autotroph communities were also strikingly higher when receiving subsidies from heterotroph communities compared to their own subsidies when grown in isolated ecosystems. In contrast, communities connected to predator-dominated ecosystems collapsed, without any direct contact with the predators. Our results demonstrate that because community composition and structure modify the distribution of biomass within a community, they may also affect communities connected through subsidies through quantitative and qualitative changes of detritus flows. This stresses that ecosystem management should account for such interdependencies mediated by spatial subsidies, given that local community alterations cascade across space onto other ecosystems even if species dispersal is completely absent.

1. Current approaches to conservation may be inadequate to maintain ecosystem integrity because they are mostly based on rarity status of organisms rather than functional significance. Alternatively, approaches focusing on the protection of ecological networks lead to more appropriate conservation targets to maintain ecosystem integrity.
2. We propose that a shift in focus from species to interaction networks is necessary to achieve pressing conservation management and restoration ecology goals of conserving biodiversity, ecosystem processes and ultimately landscape-scale delivery of ecosystem services.
3. Using topical examples from the literature, we discuss historical and conceptual advances, current challenges, and ways to move forward. We also propose a road map to ecological network conservation, providing a novel ready to use approach to identify clear conservation targets with flexible data requirements.
4. Synthesis and applications. Integration of how environmental and spatial constraints affect the nature and strength of local interaction networks will improve our ability to predict their response to change and to conserve them. This will better protect species, ecosystem processes, and the resulting ecosystem services we depend on.

Angesichts des erheblichen aktuellen Biodiversitätsverlusts und des allmählichen Wegbröckelns der Ökosystemleistungen, das damit einhergeht, scheinen die herkömmlichen Erhaltungsansätze teilweise nicht mehr geeignet, um die Ökosysteme – auf die der Mensch nun einmal angewiesen ist – in ihrer Gesamtheit zu bewahren, da sich die Prioritäten bei der Erhaltung in erster Linie an der Seltenheit einer Art orientieren statt an ihrer funktionellen Bedeutung für das Ökosystem. Vor dem allgemeinen Hintergrund knapper Budgets für die Arterhaltung entsteht ein Missverhältnis zwischen den unternommenen Anstrengungen zur Erhaltung einer bestimmten Art in einem bestimmten Ökosystem und der Erfordernis, die Funktions- und Widerstandsfähigkeit des Ökosystems in seiner Gesamtheit zu erhalten. Die Autoren sind der Auffassung, dass es einer umfassenden Neuausrichtung dieser Anstrengungen im Sinne eines Schutzes der ökologischen Netzwerke bedarf, um sowohl die Biodiversität als auch das sie umgebende Ökosystem als Ganzes zu schützen.

In many natural systems, the physical structure of the landscape dictates the flow of resources. Despite mounting evidence that communities' dynamics can be indirectly coupled by reciprocal among ecosystem resource flows, our understanding of how directional resource flows might indirectly link biological communities is limited. We here propose that differences in community structure upstream should lead to different downstream dynamics, even in the absence of dispersal of organisms. We report an experimental test of the effect of upstream community structure on downstream community dynamics in a simplified but highly controlled setting, using protist microcosms. We implemented directional flows of resources, without dispersal, from a standard resource pool into upstream communities of contrasting interaction structure and then to further downstream communities of either one or two trophic levels. Our results demonstrate that different types of species interactions in upstream habitats may lead to different population sizes and levels of biomass in these upstream habitats. This, in turn, leads to varying levels of detritus transfer (dead biomass) to the downstream communities, thus influencing their population densities and trophic interactions in predictable ways. Our results suggest that the structure of species interactions in directionally structured ecosystems can be a key mediator of alterations to downstream habitats. Alterations to upstream habitats can thus cascade down to downstream communities, even without dispersal.

We compared several measures of quality for biomass and biocrude oil produced via hydrothermal liquefaction for monocultures and polycultures of the freshwater microalgae Ankistrodesmus falcatus, Chlorella sorokiniana, Pediastrum duplex, Scenedesmus acuminatus, Scenedesmus ecornis, and Selenastrum capricornutum. On average, the 2-species cultures provided product quality comparable to that of the monocultures, while that of the average 4- and 6-species polycultures was lower. No single monoculture or polyculture performed the best with respect to all quality metrics considered, including biomass fatty acid content and biocrude elemental content and higher heating value. However, for each measure of quality, some polycultures did outperform or match the performance of the best monoculture for each respective metric. Numerous polycultures performed outside the range of product quality exhibited by their constituent species (transgressive overyielding), and polycultures with P. duplex did so to the greatest extent. Microalgal biochemical composition was correlated with biocrude properties, however including species identity as an additional correlation variable further explained the observed variation. Finally, we highlight several polycultures that offer potentially compelling trade-offs between product quantity and quality compared to the most productive monoculture.

Lakes in the Alps represent a considerable fraction of nutrient-poor lakes in Central Europe, with unique biodiversity and ecosystem properties. Although some individual lakes are well studied, less knowledge is available on large-scale patterns essential to general understanding of their functioning. Here, we aimed to describe crustacean zooplankton communities (Cladocera, Copepoda) and identify their environmental drivers in the pelagic zone of 54 oligotrophic lakes in the montane region of the Alps (400–1200 m) in Austria, Germany, and Switzerland, covering a spatial scale of 650 km. Moreover, we aimed to provide data on the distribution and ecological requirements of the North American invader Bythotrephes longimanus in its Central European native range. Communities were mainly dominated by widespread species typical of lowland habitats, and only a few true specialists of oligotrophic alpine lakes were present. The most frequent taxa were the Daphnia longispina complex and Eudiaptomus gracilis, with 48 and 45 occurrences, respectively. Species richness decreased with altitude and increased with lake area. The main structuring factors of community composition were chlorophyll a concentration and depth, which drove an apparent separation of mesotrophic and oligotrophic communities. Bythotrephes had 13 occurrences, showing a preference for deep oligotrophic lakes. Its presence was not coupled with lower crustacean species richness, as was repeatedly observed in North America. Additionally, it frequently co-occurred with the other large predatory cladoceran, Leptodora kindtii. B. longimanus might be considered a truly montane species in Central Europe, given its absence in lowland and alpine lakes.

In wild populations natural selection is a constant companion and adaptation the only way of surviving, and in the long-term that adaptation must be heritable. Daphnia represent an ideal system to test for heritable adaptation as they are a widespread freshwater zooplankton. Even though different species are found all over the world, individual populations have limited dispersal ability and are mostly confined to their lake and compelled to adapt to that lake’s properties and its fluctuations. Daphnia reproduce mainly asexually, but when presented with adverse environments they produce resting eggs which can be recovered from lake sediments. These eggs can be hatched in the laboratory and provide snapshots of past phenotypes and genotypes.
Switzerland’s lake Greifensee has been intensively studied over the past decades during which time the environment within the lake changed a lot. In the second half of the 20th century human-caused eutrophication of the lake took place, peaking in the 1950-1970s and a subsequent clearing of the lake water when waste water treatment plants were put into operation. By using the resurrection method, it has previously been shown that Daphnia from times of eutrophication are better adapted to pollution in water than their counterparts originating from times of clear water. In this Thesis, I combine whole genome resequencing and population genetic methods to find genetic evidence of this adaptation in 43 Daphnia galeata clones hatched from ephippia taken from dated core samples of Greifensee originating from 1958 to 2012.
The population genomic methods I used revealed genetic differentiation and isolation over time, temporal population structure and evidence of strong diversifying selection. Comparison of allele frequencies with long term environmental data collected from Greifensee, suggests a strong association between allele frequency and environmental parameters particularly phosphorous and temperature. My results identify a number of variable sites in the Daphnia galeata genome that are correlated with changing environments, and these candidates can be used in future studies to test functional significance. In the final section of my thesis I also discuss the many technical advances in Daphnia growing and harvesting that was made during this research.

The Fauna Indicativa characterizes ecological preferences and biological traits of all species ofdragonflies, grasshoppers, ground beetles and butterflies of Switzerland in tables. In most cases,entries for preferences and traits are given as numbers and either specified as scaled values or Yes-No decisions. Other characteristics are specified as letters. The entries are specific to populations inSwitzerland and are based mostly upon literature data and the assessment by experts. The Fauna Indicativa is a tool for the ecological evaluation of faunistic data and may form the base for developingindicators for monitoring. With the help of this tool, arthropod communities can be used in aneasy way for the description of state and change of habitats in Switzerland. Examples for the applicationsof the Fauna Indicativa are given.

Quantifying how environmental factors control the growth of phytoplankton communities is essential for building a mechanistic understanding of global biogeochemical cycles and aquatic food web dynamics. The strong effects of temperature on population growth rate have inspired two frameworks-the Eppley curve and the metabolic theory of ecology-that produce different quantitative relationships and employ distinct statistical approaches. Reconciling these relationships is necessary to ensure the accuracy of ecosystem models. In this paper, we develop ways to compare these frameworks, overcoming their methodological differences. Then, analyzing an extensive dataset (> 4200 growth rate measurements), we find that increases in population growth rate with temperature are consistent with metabolic theory, and weaker than previous estimates of the Eppley curve. A 10°C temperature increase will increase growth rates by a factor of 1.53, rather than 1.88 as in previous studies of the Eppley curve. Size and functional group membership are also critical. Population growth rates decrease with size, but much less strongly that metabolic theory predicts. The growth rates of different functional groups scale similarly with temperature, but some groups grow faster than others, independent of temperature. Our results reconcile the analytical methods of the Eppley curve and metabolic theory, demonstrate that metabolic theory's temperature-scaling predictions are more accurate, and provide new insights into the factors controlling phytoplankton growth. To avoid over-estimating the effects of temperature on primary productivity, the parameterization of ecosystem models should be revised.

Phenotypic variation is vital for microbial populations to survive environmental perturbations. Both genetic and non-genetic factors contribute to an organism’s phenotypic variation and therefore its fitness. To investigate the correlation between genetic diversity and phenotypic variation, we applied our recently developed mass spectrometry method that allows for the simultaneous measurement of more than 25 different lipids and pigments with high throughput in the unicellular microalga Chlamydomonas reinhardtii. We monitored the impact of nitrogen limitation on a genetically diverse wild-type strain CC-1690 and two isoclonal isolates from CC-1690 named ANC3 and ANC5. Measuring molecular composition of thousands of single cells at different time points of the experiment allowed us to capture a dynamic picture of the phenotypic composition and adaptation of the populations over time. Although the genetically diverse population maintained phenotypic variation over the whole time course of the experiment, the isoclonal cultures showed higher synchronicity in their phenotypic response. Furthermore, the genetically diverse population showed equal or greater phenotypic variation over the whole time range in multidimensional trait space compared with isoclonal populations. However, along individual trait axes non-genetic variance was higher in isoclonal populations.

Predicting the evolution of phenotypic traits requires an understanding of natural selection on them. Despite its indispensability in the fight against parasites, selection on host immune defense has remained understudied. Theory predicts immune traits to be under stabilizing selection due to associated trade-offs with other fitness-related traits. Empirical studies, however, report mainly positive directional selection. This discrepancy could be caused by low phenotypic variation in the examined individuals and/or variation in host resource level that confounds trade-offs in empirical studies. In a field experiment where we maintained Lymnaea stagnalis snails individually in cages in a lake, we investigated phenotypic selection on two immune defense traits, phenoloxidase (PO)-like activity and antibacterial activity, in hemolymph. We used a diverse laboratory population and manipulated snail resource level by limiting their food supply. For six weeks, we followed immune activity, growth, and two fitness components, survival and fecundity of snails. We found that PO-like activity and growth were under stabilizing selection, while antibacterial activity was under positive directional selection. Selection on immune traits was mainly driven by variation in survival. The form of selection on immune defense apparently depends on the particular trait, possibly due to its importance for countering the present parasite community.

Ecological stoichiometry has generated new insights into how the balance of elements affects ecological interactions and ecosystem processes, but little is known about the ecological and evolutionary dynamics of stoichiometric traits. Understanding the origins and drivers of stoichiometric trait variation between and within species will improve our understanding about the ecological responses of communities to environmental change and the ecosystem effects of organisms. In addition, studying the plasticity, heritability, and genetic basis of stoichiometric traits might improve predictions about how organisms adapt to changing environmental conditions, and help to identify interactions and feedbacks between phenotypic evolution and ecosystem processes.

It is widely recognized that ecological dynamics influence evolutionary dynamics, and conversely that evolutionary changes alter ecological processes. Because fragmentation impacts all biological levels (from individuals to ecosystems) through isolation and reduced habitat size, it strongly affects the links among evolutionary and ecological processes such as population dynamics, local adaptation, dispersal and speciation. Here, we review our current knowledge of the eco-evolutionary dynamics in fragmented landscapes, focusing on both theory and experimental studies. We then suggest future experimental directions to study eco-evolutionary dynamics and/or feedbacks in fragmented landscapes, especially to bridge the gap between theoretical predictions and experimental validations.

Background: On-going global climate change poses a serious threat for natural populations unless they are able to evolutionarily adapt to changing environmental conditions (e.g. increasing average temperatures, occurrence of extreme weather events). A prerequisite for evolutionary change is within-population heritable genetic variation in traits subject to selection. In relation to climate change, mainly phenological traits as well as heat and desiccation resistance have been examined for such variation. Therefore, it is important to investigate adaptive potential under climate change conditions across a broader range of traits. This is especially true for life-history traits and defences against natural enemies (e.g. parasites) since they influence organisms’ fitness both directly and through species interactions. We examined the adaptive potential of fitness-related traits and their responses to heat waves in a population of a freshwater snail, Lymnaea stagnalis. We estimated family-level variation and covariation in life history (size, reproduction) and constitutive immune defence traits [haemocyte concentration, phenoloxidase (PO)-like activity, antibacterial activity of haemolymph] in snails experimentally exposed to typical (15 °C) and heat wave (25 °C) temperatures. We also assessed variation in the reaction norms of these traits between the treatments.
Results:We found that at the heat wave temperature, snails were larger and reproduced more, while their immune defence was reduced. Snails showed high family-level variation in all examined traits within both temperature treatments. The only negative genetic correlation (between reproduction and antibacterial activity) appeared at the high temperature. However, we found no family-level variation in the responses of most examined traits to the experimental heat wave (i.e. largely parallel reaction norms between the treatments). Only the reduction of PO-like activity when exposed to the high temperature showed family-level variation, suggesting that the cost of heat waves may be lower for some families and could evolve under selection.
Conclusion: Our results suggest that there is genetic potential for adaptation within both thermal environments and that trait evolution may not be strongly affected by trade-offs between them. However, rare differences in thermal reaction norms across families indicate limited evolutionary potential in the responses of snails to changing temperatures during extreme weather events.

Understanding ecological divergence of morphologically similar but genetically distinct species – previously considered as a single morphospecies – is of key importance in evolutionary ecology and conservation biology. Despite their morphological similarity, cryptic species may have evolved distinct adaptations. If such ecological divergence is unaccounted for, any predictions about their responses to environmental change and biodiversity loss may be biased. We used spatio-temporally replicated field surveys of larval cohort structure and population genetic analyses (using nuclear microsatellite markers) to test for life-history divergence between two cryptic lineages of the alpine mayfly Baetis alpinus in the Swiss Alps. We found that the more widespread and abundant cryptic lineage represents a ‘generalist’ with at least two cohorts per year, whereas the less abundant lineage is restricted to higher elevations and represents a ‘specialist’ with a single cohort per year. Importantly, our results indicate partial temporal segregation in reproductive periods between these lineages, potentially facilitating local coexistence and reproductive isolation. Taken together, our findings emphasize the need for a taxonomic revision: widespread and apparently generalist morphospecies can hide cryptic lineages with much narrower ecological niches and distribution ranges.

The fluxes of energy, matter, and organisms are important structuring forces of metaecosystems. Such ecosystem fluxes likely interact with environmental heterogeneity and differentially affect the diversity of multiple communities. In an aquatic mesocosm experiment, we tested how ecosystem flux and patch heterogeneity affected the diversity of bacteria, phytoplankton, and zooplankton metacommunities, and the structure and functioning of metaecosystems. We built metaecosystems consisting of three mesocosms that were either connected by flux of living organisms, organic material, and nutrients (alive ecosystem flux) or only by flux of organic material and nutrients (dead ecosystem flux). The three patches of each metaecosystem were either homogeneous or heterogeneous in nutrient loading. We found that the three groups of organisms responded differently to our treatments: flux of living organisms increased bacterial diversity irrespective of nutrient heterogeneity, while flux effects on phytoplankton diversity depended on nutrient heterogeneity, potentially indicating source-sink effects. Although zooplankton diversity was largely unaffected by our manipulations, subtle changes of community composition in response to ecosystem flux had strong effects on lower trophic levels, highlighting the importance of indirect flux effects via alterations in trophic interactions. Furthermore, differential effects of communities on the mean and spatial variability of local abiotic environments influenced the development of metaecosystem heterogeneity through time. Despite identical nutrient loading at the scale of the metaecosystem, abiotic conditions diverged between homogeneous and heterogeneous metaecosystems. For example, concentrations in dissolved organic carbon (DOC) were higher in homogeneous than heterogeneous metaecosystems, possibly because of differential responses of the algal community to local environmental conditions. Similarly, we found that flux effects on organisms translated into effects on DOC concentrations at the patch level, suggesting that flux-mediated changes in abundances of species can alter abiotic conditions. Our study shows that the dynamics of biotic and abiotic compartments of spatially structured ecosystems are intricately linked, highlighting the importance of integrating metacommunity and metaecosystem perspectives.

How polymorphisms are maintained within populations over long periods of time remains debated, because genetic drift and various forms of selection are expected to reduce variation. Here, we study the genetic architecture and maintenance of phenotypic morphs that confer crypsis in Timema cristinae stick insects, combining phenotypic information and genotyping-by-sequencing data from 1,360 samples across 21 populations. We find two highly divergent chromosomal variants that span megabases of sequence and are associated with colour polymorphism. We show that these variants exhibit strongly reduced effective recombination, are geographically widespread and probably diverged millions of generations ago. We detect heterokaryotype excess and signs of balancing selection acting on these variants through the species' history. A third chromosomal variant in the same genomic region likely evolved more recently from one of the two colour variants and is associated with dorsal pattern polymorphism. Our results suggest that large-scale genetic variation associated with crypsis has been maintained for long periods of time by potentially complex processes of balancing selection.

Tychoparthenogenesis, a form of asexual reproduction in which a small proportion of unfertilized eggs can hatch spontaneously, could be an intermediate evolutionary link in the transition from sexual to parthenogenetic reproduction. The lower fitness of tychoparthenogenetic offspring could be due to either developmental constraints or to inbreeding depression in more homozygous individuals. We tested the hypothesis that in populations where inbreeding depression has been purged, tychoparthenogenesis may be less costly. To assess this hypothesis, we compared the impact of inbreeding and parthenogenetic treatments on eight life-history traits (five measuring inbreeding depression and three measuring inbreeding avoidance) in four laboratory populations of the desert locust, Schistocerca gregaria, with contrasted demographic histories. Overall, we found no clear relationship between the population history (illustrated by the levels of genetic diversity or inbreeding) and inbreeding depression, or between inbreeding depression and parthenogenetic capacity. First, there was a general lack of inbreeding depression in every population, except in two populations for two traits. This pattern could not be explained by the purging of inbreeding load in the studied populations. Second, we observed large differences between populations in their capacity to reproduce through tychoparthenogenesis. Only the oldest laboratory population successfully produced parthenogenetic offspring. However, the level of inbreeding depression did not explain the differences in parthenogenetic success between all studied populations. Differences in development constraints may arise driven by random and selective processes between populations.

Climate change is occurring across the world, with effects varying by ecosystem and region but already occurring quickly in high-latitude and high-altitude regions. Biotic interactions are important in determining ecosystem response to such changes, but few studies have been long-term in nature, especially in the High Arctic. Mesic tundra plots on Svalbard, Norway, were subjected to grazing at two different intensities by captive Barnacle geese from 2003–2005, in a factorial design with warming by Open Top Chambers. Warming manipulations were continued through 2014, when we measured vegetation structure and composition as well as growth and reproduction of three dominant species in the mesic meadow. Significantly more dead vascular plant material was found in warmed compared to ambient plots, regardless of grazing history, but in contrast to many short-term experiments no difference in the amount of living material was found. This has strong implications for nutrient and carbon cycling and could feed back into community productivity. Dominant species showed increased flowering in warmed plots, especially in those plots where grazing had been applied. However, this added sexual reproduction did not translate to substantial shifts in vegetative cover. Forbs and rushes increased slightly in warmed plots regardless of grazing, while the dominant shrub, Salix polaris, generally declined with effects dependent on grazing, and the evergreen shrub Dryas octopetala declined with previous intensive grazing. There were no treatment effects on community diversity or evenness. Thus despite no changes in total live abundance, a typical short-term response to environmental conditions, we found pronounced changes in dead biomass indicating that tundra ecosystem processes respond to medium- to long-term changes in conditions caused by 12 seasons of summer warming. We suggest that while high arctic tundra plant communities are fairly resistant to current levels of climate warming, underlying ecosystem processes are beginning to change. In addition, even short bouts of intense herbivory can have long-term consequences for some species in these communities.

There is increasing evidence that closely related species have contrasting ecosystem effects, but very little is known about the temporal scale of these effects. When organisms' ecosystem-effects persist beyond or emerge after their presence in the ecosystem, this might increase the potential for eco-evolutionary feedbacks to accompany evolutionary diversification. Here we studied lab-raised whitefish of a benthic-limnetic species pair from a postglacial adaptive radiation to test whether closely related species have contrasting effects on mesocosm ecosystems (hereafter ecosystem effects). We found that the presence of whitefish (ecological effect) had strong effects on some ecosystem components, for example by reducing snail and mussel abundance and increasing phytoplankton abundance. Whitefish species had contrasting effects (evolutionary effect) on benthic algal cover, dissolved organic carbon, and zooplankton community composition, but these effects only emerged several months after whitefish were removed from the ecosystem. The effects of plasticity and the interactive effects of species and plasticity were relatively weak and, with one exception, not significant. Ecological and evolutionary effect sizes were uncorrelated over both phases of the experiment, as were effect sizes between phases for both ecological and evolutionary contrasts. Overall, our results suggest that adaptive radiation can have effects on the structure and functioning of ecosystems, but that the temporal dynamics and mechanistic basis of these effects are insufficiently understood.

Reports of viruses infecting insects have increased with the rapid emergence of new sequencing technologies. In this study, a newly discovered RNA virus infecting the parasitoid wasp Lysiphlebus fabarum (LysV) is investigated. Wasps were reared on aphid hosts (Aphis fabae) that are protected against parasitism by a suite of facultative endosymbionts, including the protective bacterium Hamiltonella defensa. During experimental evolution of wasps in three different aphid environments, either H. defensa free (H–) or carrying H. defensa strains 76 or 402, differences in viral presence were observed by RNA–seq. Following upon these results viral presence was found with PCR screenings in different sexually and asexually reproducing wasp lineages reared in the lab, albeit their infection percentages varied highly. Wasps evolving on hosts infected with H. defensa strain 76 had a higher infection rate than the other two evolution lineages. A qPCR assay was subsequently developed for quantification of viral presence, and showed that qPCR was more sensitive to low copy numbers of viral RNA than PCR. More detailed knowledge of viral infection thus requires a qPCR approach as PCR analyses may underestimate the degree of infection. Both horizontal and vertical transmission of the virus were demonstrated experimentally. Phylogenetic analyses classified the virus as belonging to the Iflaviridae family, with its closest known relatives all being parasitoid wasp–infecting viruses. Support is also provided for viral occurrence in wild populations at four sites located in western Switzerland, demonstrating its origin and introduction to the lab. Three haplotypes could be distinguished in the wild populations, of which two were also found in lab populations. Lastly, comparisons across time points suggest that this is a persistent infection in laboratory populations, without clear symptoms of the virus in infected wasps. This hints towards a possible commensal or mutualist relationship of the virus and its parasitoid host, although detailed fitness comparisons between infected and uninfected wasps will be required to verify this.

Reservoir siltation is a major problem worldwide, decreasing reservoir storage capacity, trapping entrained sediment, and altering the natural sediment regime. Sediment By-pass Tunnels (SBTs) are used to connect reservoirs with downstream receiving waters during high flows to reduce sediment accumulation in the reservoir. When operating, large volumes of sediment-laden waters are released into the receiving river for short periods of time (h). The aim of this study was to assess the impact of SBT events on the downstream riverine ecosystem. We measured physico-chemical properties, sediment respiration, periphyton biomass and chlorophyll-a, and macroinvertebrate assemblages along a 5-km stretch of river during the first two years of SBT operation. During the study, five major SBT events occurred. Few changes were found in physico-chemical properties, mainly due to the input of tributaries entering the system. Results showed a clear reduction in sediment respiration, an indicator of ecosystem metabolism, especially after large SBT events. Periphyton levels and macroinvertebrate density/richness also decreased after SBT events. A non-metric multidimensional scaling distinguished both temporal and spatial shifts in macroinvertebrate assemblages after SBT events, being related to downstream distance and SBT event magnitude. In summary, SBT events acted as a pulse disturbance, similarly to natural floods, followed by recovery of measured ecosystem indicators. Sediment By-pass Tunnel events can enhance sediment and flow connectivity, although the magnitude and frequency of operations should be controlled to prevent catastrophic disturbances.

Flow and sediment regimes are two of the main abiotic factors driving riverine ecosystems, interacting at different temporal and spatial scales. These interactions have a strong influence on habitat composition, ecosystem processes and community composition. Nowadays, flow and sediment regimes are highly altered due to anthropogenic modifications of rivers and floodplains, such as dams or river channelization, which disrupt the main properties of both regimes. The primary goal of this thesis was to understand the role of flow and sediment interactions on ecosystem structure and function in managed rivers and evaluate different techniques that mitigate the impact of rivers regulation. Hyporheic sediment respiration, periphyton biomass and chlorophyll-a were used as indicators of ecosystem function, whereas macroinvertebrates assemblages were used as a structural indicator.
The first chapter studied the variability of different indicators of ecosystem structure and function under different flow and geomorphology conditions. The study took place in a section of the river Thur, where a widening restoration was implemented by removing 1 km of lateral protections. This widening section characterized by newly established habitats such as gravel bars is fringed upstream and downstream by channelized sections. Channelized sites showed higher rates of sediment respiration, periphyton and macroinvertebrates compared to restored sites. Restored sites showed a greater temporal and spatial variability in the measured indicators due to the influence of flow disturbance, which was lower in channelized sites. Overall, sediment respiration and macroinvertebrate richness were related to flow variability and geomorphology, whereas periphyton and macroinvertebrate density was influenced mainly by flow variability.
The second chapter investigated the influence of flow regulation (residual flows and hydropeaking) on aquatic life stages that can persist in sediments during dry phases (i.e. macroinvertebrate seedbanks). Gravel bars affected by hydropeaking showed greater densities of organisms due to the high frequency of inundations, which increased the drift of animals onto gravel bars. The opposite trend was found in residual flow rivers, where there is a lack of flood occurrence.
The third chapter assessed the ecological impact of a Sediment Bypass Tunnel, a structure that routes upstream sediment input around dams, reducing the accumulation of sediments in the dam. Operations of the tunnel create a general decrease in measured indicators (sediment respiration, periphyton and macroinvertebrates), the decrease being related to the magnitude of flow and sediment released at the tunnel.
The fourth chapter described the interactions of flow and sediment inputs in two rivers with contrasting management programs (experimental floods and sediment bypass tunnel). Sediment lateral inputs caused local interactions with flow, generating morphological and biotic heterogeneity in the streambed, whereas upstream sediment inputs together with high flows by sediment bypass tunnel created a general decrease in biotic indicators in the system, reducing spatial variability..
The results from this thesis showed that each of the measured ecosystem properties is influenced in a specific way by flow-sediment interactions. The results indicated that different techniques can be used to mitigate the negative consequences of flow and sediment regime alterations on ecosystem functioning and structure, highlighting the important role of integrative objectives in river management.

The concept of life-history traits and the study of these traits are the hallmark of population biology. Acknowledging their variability and evolution has allowed us to understand how species adapt in response to their environment. The same traits are also involved in how species alter ecosystems and shape their dynamics and functioning. Some theories, such as the metabolic theory of ecology, ecological stoichiometry or pace-of-life theory, already recognize this junction, but only do so in an implicitly non-spatial context. Meanwhile, for a decade now, it has been argued that ecosystem properties have to be understood at a larger scale using meta-ecosystem theory because source–sink dynamics, community assembly and ecosystem stability are all modified by spatial structure. Here, we argue that some ecosystem properties can be linked to a single life-history trait, dispersal, i.e. the tendency of organisms to live, compete and reproduce away from their birth place. By articulating recent theoretical and empirical studies linking ecosystem functioning and dynamics to species dispersal, we aim to highlight both the known connections between life-history traits and ecosystem properties and the unknown areas, which deserve further empirical and theoretical developments.

Glaciers cover ~10% of the Earth's land surface, but they are shrinking rapidly across most parts of the world, leading to cascading impacts on downstream systems. Glaciers impart unique footprints on river flow at times when other water sources are low. Changes in river hydrology and morphology caused by climate-induced glacier loss are projected to be the greatest of any hydrological system, with major implications for riverine and near-shore marine environments. Here, we synthesize current evidence of how glacier shrinkage will alter hydrological regimes, sediment transport, and biogeochemical and contaminant fluxes from rivers to oceans. This will profoundly influence the natural environment, including many facets of biodiversity, and the ecosystem services that glacier-fed rivers provide to humans, particularly provision of water for agriculture, hydropower, and consumption. We conclude that human society must plan adaptation and mitigation measures for the full breadth of impacts in all affected regions caused by glacier shrinkage.

Anthropogenic global changes have affected almost all ecosystems on Earth and threatened biodiversity worldwide, but the extent of the impact of this pervasive influence is not fully understood. In aquatic ecosystems, eutrophication of lakes has led to the periodic dominance of cyanobacteria, which affects the services that lake ecosystems provide to human society (e.g., tourism, drinking water, fisheries), and sometimes directly threatens the health of animals, including humans. Many lakes in the European peri-Alpine region are regularly affected by the presence of cyanobacteria, but how rapid changes in local and regional lake conditions have contributed to determine their diversity and distribution, for example favouring toxic and bloom-forming taxa, is not well known. Peri-Alpine lakes, with their well-studied eutrophication and climate history, represent excellent study sites for reconstructing past assemblages of planktonic organisms and for investigating their diversity over long time scales of anthropogenic influence by applying molecular techniques to the sedimentary archive.
The general aim of this thesis project was to investigate the effects of environmental change, especially climate warming and alteration of nutrient regimes, over the distribution, the biodiversity, and the phylogenetic structure of lacustrine cyanobacterial communities. We used high-throughput sequencing on DNA extracted from dated sediment cores and performed phylogenetic and diversity analyses of the cyanobacterial communities over two centuries to cover the periods of pre-, mid- and post eutrophication of lakes. The first project (Chapter II) was to validate the sedimentary DNA-based reconstruction method by comparing the long-term diversity of cyanobacterial communities recovered from the sediments of two lakes (Greifensee and Lake Zurich) with the diversity assessed by microscopy in water samples collected over four decades as part of lake monitoring programmes. This study confirms the feasibility of the sedimentary DNA approach for assessing the richness and phylogenetic diversity of past communities of cyanobacteria.
The second project (Chapter III) was to investigate the biogeography of cyanobacteria and compare their community composition and phylogenetic structure across lakes. For that, the study region was expended to ten lakes across the peri-Alpine area. The results of this project show evidence for the homogenisation of lakes abiotic conditions due to climate warming and eutrophication, and reveal that over the past 150 years, the richness and similarity of cyanobacterial communities has generally increased, particularly gaining buoyant and colonial taxa.
The presence of cyanobacteria do not only impair water quality and ecosystem services, but they also have negative effects on other levels of lake food-webs. Chapter IV aims at linking the diversity of Daphnia and cyanobacteria in lakes impacted by anthropogenic eutrophication. This study using the sedimentary Daphnia egg bank and cyanobacterial DNA from two peri-alpine lakes (Switzerland) and a shallow lake in the Danube Biosphere Reserve (Romania) confirms the invasion of D. galeata and the subsequent replacement of native Daphnia lineages by D. galeata taxa in the two Swiss lakes. The results further suggest that D. galeata, D. cucullata, and their sexual descendants appear to have been favoured by the presence of filamentous cyanobacteria at all sites. These results provide novel insights into long-term community interactions between two important plankton groups.
During our investigation of cyanobacterial diversity in the sedimentary archive (chapters II & III), we detected two newly described clades of ancestral cyanobacteria called Melainabacteria and MLE635J-21. Chapter V presents a short literature review describing these nonphotosynthetic cyanobacteria, and explores their diversity within and across the same ten lakes investigated in chapter II, with the aim to compare their dynamics to the trends observed in cyanobacteria. This study reveals that, unlike cyanobacteria, the richness and composition of nonphotosynthetic cyanobacteria did not vary significantly over the past ~150 years, suggesting that the ladder are not governed by the same environmental factors as the photosynthetic clades.
Taken together, the results of these four studies reveal previously unreported patterns in the composition and structure of cyanobacterial communities over broad temporal and spatial scales, and highlight the effects of human-induced environmental changes on cyanobacterial assemblages in freshwater lakes that provide important ecosystem services to humans. Our results support the hypothesis that shifts in the diversity and distribution of taxa might not be reversible even after applying stringent remediation measures for the reduction of water eutrophication, and highlight the importance of increasing our understanding of the underlying mechanisms that regulate community structure to gain predictive ability for future lake management purposes.

Eutrophication generally favours the growth of cyanobacteria over eukaryotic green algae in freshwater lakes. Cyanobacteria constitute a poor food source for the waterflea Daphnia, an important primary consumer of phytoplankton in lakes. While it is known that some Daphnia species are adapted to eutrophic conditions and can cope with cyanobacteria in their diet, it is less known whether cyanobacterial community composition can influence Daphnia population structure in lakes. We studied the variation in genetic diversity of Daphnia resting eggs and cyanobacterial DNA preserved in sediment cores from three European lakes impacted by eutrophication. Our retrospective analysis confirms that D. galeata invaded the two pre-alpine lakes around the middle of the twentieth century, hybridized with and became dominant over D. longispina. This coincides with the presence in all lakes and the increase in the proportion of colonial and filamentous cyanobacteria in the pre-alpine lakes. The recent re-oligotrophication of the lakes did not reverse the cyanobacterial and Daphnia assemblages to their pre-eutrophication composition and genetic structure, suggesting that both changed irreversibly due to anthropogenic influence on the ecosystems. Genetic analyses applied to lake sedimentary archives have the potential to unveil how different compartments of the food web covary in a changing environment.

1. Trait-based approaches are increasingly being used to test mechanisms underlying species assemblages and biotic interactions across a wide range of organisms including terrestrial arthropods and to investigate consequences for ecosystem processes. Such an approach relies on the standardized measurement of functional traits that can be applied across taxa and regions. Currently, however, unified methods of trait measurements are lacking for terrestrial arthropods and related macroinvertebrates (terrestrial invertebrates hereafter).
2. Here, we present a comprehensive review and detailed protocol for a set of 29 traits known to be sensitive to global stressors and to affect ecosystem processes and services. We give recommendations how to measure these traits under standardized conditions across various terrestrial invertebrate taxonomic groups.
3. We provide considerations and approaches that apply to almost all traits described, such as the selection of species and individuals needed for the measurements, the importance of intraspecific trait variability, how many populations or communities to sample and over which spatial scales.
4. The approaches outlined here provide a means to improve the reliability and predictive power of functional traits to explain community assembly, species diversity patterns and ecosystem processes and services within and across taxa and trophic levels, allowing comparison of studies and running meta-analyses across regions and ecosystems.
5. This handbook is a crucial first step towards standardizing trait methodology across the most studied terrestrial invertebrate groups, and the protocols are aimed to balance general applicability and requirements for special cases or particular taxa. Therefore, we envision this handbook as a common platform to which researchers can further provide methodological input for additional special cases.

Floodplains are vital components of river ecosystems and play an important role in carbon cycling and storage at catchment and global scales. For efficient river management and conservation, it is critical to understand the functional role of spatiotemporally complex and dynamic habitat mosaics of river floodplains. Unfortunately, the fundamental understanding of mineralization and carbon flux patterns across complex floodplains is still fragmentary. In this study, respiratory potential (i.e., electron transport system activity [ETSA]) was quantified seasonally across different aquatic and terrestrial habitats (wetted channels, gravel bars, islands, riparian forests, and grasslands) of 2 Alpine floodplains differing in climate, altitude, discharge, flow alteration intensity, and land use (Soča [natural flow regime, 12% grassland area] and Urbach [mean annual discharge reduction by 30% due to water abstraction, 69% grassland area]). In situ respiration (R) was measured, and ETSA–R ratios were calculated to examine differences in exploitation intensity of the overall respiratory capacity among floodplain habitats and seasons. ETSA and R provided potential and actual estimates, respectively, of organic matter mineralization in the different floodplain habitats. Hierarchical linear regression across habitat types showed that organic matter, grain sizes <0.063 mm, and water content were the most important predictors of ETSA in both floodplains, and grain sizes 2–0.063 and >8 mm were also highly important for the Soča floodplain. The combination of ETSA and R measurements conducted in contrasting floodplains increased our understanding of the relationships between floodplain habitat heterogeneity, organic matter mineralization and human impacts, that is, structural–functional linkages in floodplains. These data are integral towards predicting changes in floodplain function in response to environmental alterations from increasing human pressures and environmental change.

Micropollutants enter surface waters through various pathways, of which wastewater treatment plants (WWTPs) are a major source. The large diversity of micropollutants and their many modes of toxic action pose a challenge for assessing environmental risks. In this study, we investigated the potential impact of WWTPs on receiving ecosystems by describing concentration patterns of micropollutants, predicting acute risks for aquatic organisms and validating these results with macroinvertebrate biomonitoring data. Grab samples were taken upstream, downstream and at the effluent of 24 Swiss WWTPs during low flow conditions across independent catchments with different land uses. Using liquid chromatography high resolution tandem mass spectrometry, a comprehensive target screening of almost 400 organic substances, focusing mainly on pesticides and pharmaceuticals, was conducted at two time points, and complemented with the analysis of a priority mixture of 57 substances over eight time points. Acute toxic pressure was predicted using the risk assessment approach of the multi-substance potentially affected fraction, first applying concentration addition for substances with the same toxic mode of action and subsequently response addition for the calculation of the risk of the total mixture. This toxic pressure was compared to macroinvertebrate sensitivity to pesticides (SPEAR index) upstream and downstream of the WWTPs. The concentrations were, as expected, especially for pharmaceuticals and other household chemicals higher downstream than upstream, with the detection frequency of plant protection products upstream correlating with the fraction of arable land in the catchments. While the concentration sums downstream were clearly dominated by pharmaceuticals or other household chemicals, the acute toxic pressure was mainly driven by pesticides, often caused by the episodic occurrence of these compounds even during low flow conditions. In general, five single substances explained much of the total risk, with diclofenac, diazinon and clothianidin as the main drivers. Despite the low predicted acute risk of 0%–2.1% for affected species, a significant positive correlation with macroinvertebrate sensitivity to pesticides was observed. However, more effect data for pharmaceuticals and a better quantification of episodic pesticide pollution events are needed for a more comprehensive risk assessment.

Migration allows animals to track the environmental conditions that maximize growth, survival, and reproduction [1–3]. Improved understanding of the mechanisms underlying migrations allows for improved management of species and ecosystems [1–4]. For centuries, the catadromous European eel (Anguilla anguilla) has provided one of Europe's most important fisheries and has sparked considerable scientific inquiry, most recently owing to the dramatic collapse of juvenile recruitment [5]. Larval eels are transported by ocean currents associated with the Gulf Stream System from Sargasso Sea breeding grounds to coastal and freshwater habitats from North Africa to Scandinavia [6, 7]. After a decade or more, maturing adults migrate back to the Sargasso Sea, spawn, and die [8]. However, the migratory mechanisms that bring juvenile eels to Europe and return adults to the Sargasso Sea remain equivocal [9, 10]. Here, we used a “magnetic displacement” experiment [11, 12] to show that the orientation of juvenile eels varies in response to subtle differences in magnetic field intensity and inclination angle along their marine migration route. Simulations using an ocean circulation model revealed that even weakly swimming in the experimentally observed directions at the locations corresponding to the magnetic displacements would increase entrainment of juvenile eels into the Gulf Stream System. These findings provide new insight into the migration ecology and recruitment dynamics of eels and suggest that an adaptive magnetic map, tuned to large-scale features of ocean circulation, facilitates the vast oceanic migrations of the Anguilla genus [7, 13, 14].

1. Phenotypic variation controls the species interactions which determine whether or not species coexist. Long-standing hypotheses in ecology and evolution posit that phenotypic differentiation enables coexistence by increasing the size of niche differentiation. This hypothesis has only been tested using macroscopic traits to date, but niche differentiation, particularly of microscopic organisms, also occurs at the molecular and metabolic level.
2. We examined how phenotypic variation that arises at the level of gene expression over evolutionary time affects phytoplankton species interactions and coexistence.
3. We predicted that similarity in gene expression among species would decline with phylogenetic distance, and that reduced similarity in gene expression would weaken competition, increase facilitation and promote coexistence.
4. To test this, we grew eight species of freshwater green algae in monocultures and bicultures for 46 days in a laboratory microcosm experiment. We quantified the strength of species interactions by: (i) fitting Lotka–Volterra models to time-series densities and estimating interaction coefficients, and (ii) calculating relative densities that compare species’ steady-state densities in biculture to those in monoculture. We used Illumina high throughput sequencing to quantify the expression of 1253 families of homologous genes, including a set of 17 candidate genes that we hypothesized a priori to be involved in competition or facilitation.
5. Synthesis. We found that closely related species had greater similarity in gene expression than did distantly related species, but as gene expression became more similar, species experienced weaker competition or greater facilitation, and were more likely to coexist. We identified gene functional categories that were uniquely differentially regulated in association with particular species interaction types. Contrary to common thinking in ecology and evolution, similarity in gene expression, and not differentiation, was associated with weaker competition, facilitation and coexistence.

Water temperature is known to influence individual animal metabolism, development, and reproduction. However, in situ studies aiming to demonstrate the link between water temperature and community structure in complex ecosystems such as large river floodplains are still rare. In particular, we have little indication about how an increase in temperature affects the density of native and invasive species within a community. Large river floodplains cover a varied range of environmental conditions, are rich in species, and therefore potentially useful ecosystems to study the effect of water temperature at the community level. Moreover, as freshwater communities are increasingly impacted by global warming and biological invasions, an improved understanding of the possible interaction between these drivers would be beneficial. First, we studied during two years the thermal heterogeneity of 36 sites in a large river (Rhone) floodplain. Second, we compared the thermal regimes of sites having different levels of hydrological connectivity with the main river channel. Third, we studied the combined and separated effects of the thermal regime and the hydrological connectivity on the presence and densities of native and non-native species of macroinvertebrates. The studied large river floodplain covered a wide range of thermal regimes, with some sites displaying a yearlong constant temperature of about 10°C, whereas others experienced thermal amplitude of over 25°C. The thermal regime was independent of the level of hydrological connectivity of the sites. The increase in hydrological connectivity had a significant and positive effect on the richness of non-native species within sites. The thermal regime had a positive influence on the density of non-native species but no effect on the total density of native taxa within communities. This study showed that large river floodplains possess a wide range of thermal conditions and that the increase in water temperature can have a positive influence on the presence of non-native populations of macroinvertebrates. This study provides a first set of empirical results to establish models predicting the effect of increasing temperatures on the establishment of non-native and native species in a complex ecosystem and underline the problem of biological invasions under climate change.