Department Fish Ecology and Evolution

Chromosomal fusions are hypothesized to facilitate adaptation to divergent environments, both by bringing together previously unlinked adaptive alleles and by creating regions of low recombination that facilitate the linkage of adaptive alleles. But, there is little empirical evidence to support this hypothesis. Here, we address this knowledge gap by studying threespine stickleback (Gasterosteus aculeatus), in which ancestral marine fish have repeatedly adapted to freshwater across the northern hemisphere. By comparing the threespine and ninespine stickleback (Pungitius pungitius) genomes to a de novo assembly of the fourspine stickleback (Apeltes quadracus) and an outgroup species, we find two chromosomal fusion events involving the same chromosomes have occurred independently in the threespine and ninespine stickleback lineages. On the fused chromosomes in threespine stickleback, we find an enrichment of quantitative trait loci (QTL) underlying traits that contribute to marine versus freshwater adaptation. By comparing whole genome sequences of freshwater and marine threespine stickleback populations, we also find an enrichment of regions under divergent selection on these two fused chromosomes. There is elevated genetic diversity within regions under selection in the freshwater population, consistent with a simulation study showing that gene flow can increase diversity in genomic regions associated with local adaptation and our demographic models showing gene flow between the marine and freshwater populations. Integrating our results with previous studies, we propose that these fusions created regions of low recombination that enabled the formation of adaptative clusters, thereby facilitating freshwater adaptation in the face of recurrent gene flow between marine and freshwater threespine sticklebacks.

1. Digital images are an intuitive way to capture, store and analyse organismal phenotypes. Many biologists are taking images to collect high-dimensional phenotypic information from specimens to investigate complex ecological, evolutionary and developmental phenomena, such as relationships between trait diversity and ecosystem function, multivariate natural selection or developmental plasticity. As a consequence, images are being collected at ever-increasing rates, but extraction of the contained phenotypic information poses a veritable analytical bottleneck.
2. phenopype is a high-throughput phenotyping pipeline for the programming language Python that aims at alleviating this bottleneck. The package facilitates immediate extraction of high-dimensional phenotypic data from digital images with low levels of background noise and complexity. At the core, phenopype provides functions for rapid signal processing-based image preprocessing and segmentation, data extraction, as well as visualization and data export. This functionality is provided by wrapping low-level computer vision libraries (such as OpenCV) into accessible functions to facilitate scientific image analysis. In addition, phenopype provides a project management ecosystem to streamline data collection and to increase reproducibility.
3. phenopype offers two different workflows that support users during different stages of scientific image analysis. The low-throughput workflow uses regular Python syntax and has greater flexibility at the cost of reproducibility, which is suitable for prototyping during the initial stages of a research project. The high-throughput workflow allows users to specify and store image-specific settings for analysis in human-readable YAML format, and then execute all functions in one step by means of an interactive parser. This approach facilitates rapid program-user interactions during batch processing, and greatly increases scientific reproducibility.
4. Overall, phenopype intends to make the features of powerful but technically involved low-level CV libraries available to biologists with little or no Python coding experience. Therefore, phenopype is aiming to augment, rather than replace the utility of existing Python CV libraries, allowing biologists to focus on rapid and reproducible data collection. Furthermore, image annotations produced by phenopype can be used as training data, thus presenting a stepping stone towards the application of deep learning architectures.

Hypostomus Lacépède, 1803, is a species-rich and widespread fish genus from the Neotropical region, but its evolutionary history and systematics remain largely unclear. In addition, species from regions with high levels of species richness and endemism such as the Northeastern Mata Atlântica (NMA) and São Francisco (SF) hydrographic freshwater ecoregions are underrepresented in phylogenetic studies so far. In this study, we performed a broad sampling of Hypostomus in NMA and SF to investigate the interspecific boundaries and phylogenetic relationships using a multilocus approach based on one mitochondrial and three nuclear markers. Seven genetic groups were found for both ecoregions, in addition to one lineage exclusive to the SF represented by populations of the species Hypostomus velhochico. Moreover, multilocus analyses validated 16 formally described species and two new lineages for the NMA and SF ecoregions, as well as putative cases of species complexes. In general, lineages with independent evolutionary histories were revealed within the same ecoregion alongside genetically related groups between NMA, SF, and other ecoregions. These data reinforce the intricate scenario of this group of Neotropical fish and are useful to outline further phylogeographic studies in Hypostomus.

Projet Lac was a large project conducted by Eawag and the University of Bern to quantitatively survey, for the first time, whole-lake fish communities in the large and deep lakes in and around the European Alps using multiple, standardised sampling methods. Starting in 2010, in total 35 lakes were investigated across Switzerland, Italy, France, Germany and Austria, with more than 106 fish species recorded. This report brings together key findings, compares fish communities among lakes, investigates their relationship to environmental parameters, and provides an overview of drivers of biodiversity and community structure in this important ecosystem.

Das Projet Lac war ein grosses Projekt der Eawag und der Universität Bern zur erstmaligen quantitativen Erfassung ganzer Fischgemeinschaften in grossen und tiefen Seen in und um die europäischen Alpen mit standardisierten Probenahmeverfahren. Ab 2010 wurden insgesamt 35 Seen in der Schweiz, Italien, Frankreich, Deutschland und Österreich untersucht und über 106 Fischarten erfasst. Dieser Bericht fasst die wichtigsten Ergebnisse zusammen, vergleicht die Fischgemeinschaften der einzelnen Seen, untersucht ihre Beziehung zu Umweltparametern und gibt einen Überblick über die Faktoren, welche die biologische Vielfalt und die Struktur der Gemeinschaften in diesem wichtigen Ökosystem beeinflussen.

Le Projet Lac était un grand projet de l'Eawag et de l'Université de Berne visant à recenser pour la première fois de manière quantitative des communautés entières de poissons dans les grands et profonds lacs des Alpes européennes et de leurs environs, à l'aide de méthodes d'échantillonnage standardisées. A partir de 2010, 35 lacs au total ont été étudiés en Suisse, en Italie, en France, en Allemagne et en Autriche et plus de 106 espèces de poissons ont été recensées. Ce rapport résume les principaux résultats, compare les communautés de poissons des différents lacs, examine leur relation avec les paramètres environnementaux et donne un aperçu des facteurs qui influencent la diversité biologique et la structure des communautés dans cet écosystème important.

Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.

Aquatische und terrestrische Ökosysteme sind eng miteinander verknüpft - sowohl durch die Bewegungen von Organismen wie auch durch den Austausch von Nährstoffen oder Schadstoffen. Dennoch werden in der Regel Wasser- und Land-Ökosysteme isoliert voneinander betrachtet und verwaltet. Diese Silo-Mentalität in Forschung, Praxis und Gesetzgebung behindert integrative Ansätze für den effektiveren Schutz der Biodiversität.

Interactions between organisms and their environments are central to how biological diversity arises and how natural populations and ecosystems respond to environmental change. These interactions involve processes by which phenotypes are affected by or respond to external conditions (e.g., via phenotypic plasticity or natural selection) as well as processes by which organisms reciprocally interact with the environment (e.g., via eco-evolutionary feedbacks). Organism-environment interactions can be highly dynamic and operate on different hierarchical levels, from genes and phenotypes to populations, communities, and ecosystems. Therefore, the study of organism-environment interactions requires integrative approaches and model systems that are suitable for studies across different hierarchical levels. Here, we introduce the freshwater isopod Asellus aquaticus, a keystone species and an emerging invertebrate model system, as a prime candidate to address fundamental questions in ecology and evolution, and the interfaces therein. We review relevant fields of research that have used A. aquaticus and draft a set of specific scientific questions that can be answered using this species. Specifically, we propose that studies on A. aquaticus can help understanding (i) the influence of host-microbiome interactions on organismal and ecosystem function, (ii) the relevance of biotic interactions in ecosystem processes, and (iii) how ecological conditions and evolutionary forces facilitate phenotypic diversification.

Long-chain polyunsaturated fatty acids are biologically important lipids that are unevenly distributed between and throughout environments. This heterogeneity can affect the evolution of metabolic processes, as populations adapt to the resource landscape that they encounter. Here, we compare fatty acid phenotypes of stickleback over two time scales of evolutionary divergence: between two lineages with different metabolic capacities for fatty acid synthesis (i.e. different copy number of the fatty acid desaturase gene; FADS2) that independently colonized European freshwaters during the Pleistocene and Holocene; and between two ecotypes within each lineage that have diverged more recently (~150 years) in different habitats (i.e. lake and stream). We measured fatty acid profiles of wild-caught and lab-reared fish for each lineage and ecotype combination after rearing lab fish on a diet deficient in omega-3 long-chain polyunsaturated fatty acids. Since these lineages hybridize in nature, we also measured profiles of lab-reared hybrids and backcrosses raised on the same deficient diet. Wild fish showed strong compositional differences in fatty acids between habitats, lineages and sexes. Common garden fish had generally lower polyunsaturated fatty acid levels than wild fish, and females had lower omega-6:omega-3 than males. Fish from the lineage with fewer FADS2 copies also had lower levels of docosahexaenoic acid. Overall, we document divergence in fatty acid phenotypes between stickleback lineages with different histories of freshwater colonization, and between ecotypes in the early stages of adaptive population divergence.

There is growing concern about the dire socioeco-logical consequences of abrupt transitions between alternative ecosystem states in response to environmental changes. At the same time, environmental change can trigger evolutionary responses that could stabilize or destabilize ecosystem dynamics. However, we know little about how coupled ecological and evolutionary processes affect the risk of transition between alternative ecosystem states. Using shallow lakes as a model ecosystem, we investigate how trait evolution of a key species affects ecosystem resilience under environmental stress. We find that adaptive evolution of macrophytes can increase ecosystem resilience by shifting the critical threshold, which marks the transition from a clear-water state to a turbid-water state to a higher level of environmental stress. However, following the transition, adaptation to the turbid-water state can delay the ecosystem recovery back to the clear-water state. This implies that restoration could be more effective when implemented early enough after a transition occurs and before organisms adapt to the alternative state. Our findings provide new insights into how to prevent and mitigate the occurrence of regime shifts in ecosystems and highlight the need to understand ecosystem responses to environmental change in the context of coupled ecological and evolutionary processes.

Horizontal bar rack bypass systems (HBR-BS) are characterized by a horizontal bar rack (HBR) with narrow clear bar spacing of 10–20 mm and an adjacent bypass (BS) to efficiently protect and guide downstream moving fish at water intakes. The small bar spacing may lead to operational challenges, such as clogging and high head losses. This study investigated whether combining an HBR with a low-voltage electric field (e-HBR) allows one to increase the clear bar spacing while maintaining a high standard of fish protection and guidance efficiency. To this end, an HBR-BS with 20 mm bar spacing and an e-HBR-BS with 20 and 51 mm bar spacing were tested with spirlin (Alburnoides bipunctatus) and European eel (Anguilla anguilla) in a laboratory flume. The racks were electrified with 38 V pulsed direct current. The protection efficiency of the e-HBR with 51 mm was 96% for spirlin and 86% for eels, which are similar results to those of the HBR with 20 mm. Some eels passed through the e-HBR, but only when they were parallel to the rack. Fish injuries of variable severeness due to the electrification were observed. The results highlight the potential of hybrid barriers for the protection of downstream moving fish. However, fish injuries due to electricity may occur; and reporting applied voltage, electrode geometry, resulting electric field strength and the pulse pattern of the electrified rack setup is necessary to ensure comparability among studies and to avoid injuries.

Horizontal bar rack bypass systems (HBR-BS) are a state-of-the-art technology for fish downstream passage, which has been installed at many European hydropower plants in recent years. However, in-depth technical knowledge regarding hydraulics, operational aspects, and fish behavior has so far been missing. This research gap was filled with an extensive study conducted at the Laboratory of Hydraulics, Hydrology and Glaciology (VAW) of ETH Zurich. This article presents the most important research findings of the live fish laboratory tests and summarizes design recommendations, while the results from the hydraulic investigation and systematic foliage clogging experiments are presented in another paper. Further details can be found in the doctoral thesis of Meister.

Anomaly detection is the process of identifying unexpected data samples in datasets. Automated anomaly detection is either performed using supervised machine learning models, which require a labelled dataset for their calibration, or unsupervised models, which do not require labels. While academic research has produced a vast array of tools and machine learning models for automated anomaly detection, the research community focused on environmental systems still lacks a comparative analysis that is simultaneously comprehensive, objective, and systematic. This knowledge gap is addressed for the first time in this study, where 15 different supervised and unsupervised anomaly detection models are evaluated on 5 different environmental datasets from engineered and natural aquatic systems. To this end, anomaly detection performance, labelling efforts, as well as the impact of model and algorithm tuning are taken into account. As a result, our analysis reveals the relative strengths and weaknesses of the different approaches in an objective manner without bias for any particular paradigm in machine learning. Most importantly, our results show that expert-based data annotation is extremely valuable for anomaly detection based on machine learning.

In haplodiploids, (1) alleles spend twice as many generations in females as in males, (2) males are never heterozygous and therefore express recessive alleles, and (3) males sire daughters but not sons. Intralocus sexual conflict therefore operates differently in haplodiploids than in diploids and shares strong similarities with loci on X (or Z) chromosomes. The common co-occurrence of all three features makes it difficult to pinpoint their respective roles. However, they do not always co-occur in nature, and missing cases can be additionally studied with hypothetical life cycles. We model sexually antagonistic alleles in eight different sex determination systems and find that arguments 1 and 2 promote invasion and fixation of female-beneficial and male-beneficial alleles, respectively; argument 2 also improves prospects for polymorphism. Argument 3 harms the invasion prospects of sexually antagonistic alleles (irrespective of which sex benefits) but promotes fixation should invasion nevertheless occur. Disentangling the features helps to evaluate the validity of previous verbal arguments and yields better-informed predictions about intralocus sexual conflict under different sex determination systems, including hitherto undiscovered ones.

The trophic structure of food webs is primarily determined by the variation in trophic position among species and individuals. Temporal dynamics of food web structure are central to our understanding of energy and nutrient fluxes in changing environments, but little is known about how evolutionary processes shape trophic position variation in natural populations. We propose that trophic position, whose expression depends on both environmental and genetic determinants of the diet variation in individual consumers, is a quantitative trait that can evolve via natural selection. Such evolution can occur either when trophic position is correlated with other heritable morphological and behavioural traits under selection, or when trophic position is a target of selection, which is possible if the fitness effects of prey items are heterogeneously distributed along food chains. Recognising trophic position as an evolving trait, whose expression depends on the food web context, provides an important conceptual link between behavioural foraging theory and food web dynamics, and a useful starting point for the integration of ecological and evolutionary studies of trophic position.

Lakes Victoria, Kyoga, and Nabugabo ("the Lake Victoria region") are remarkable for hosting one of the largest assemblages of cichlid fishes among the African inland lakes. Here, we review the role and severity of anthropogenic and environmental stressors on the cichlid communities in the Lake Victoria region to understand the mechanisms leading to the persistence and resurgence of some of the cichlid fishes. Our review suggests that (1) the native Oreochromis species populations primarily collapsed due to overfishing and that the introduced species and habitat change suppressed their ability to recover; (2) without primary triggers associated with change in the environment and habitat conditions, particularly eutrophication and associated anoxia and reduced water transparency, Nile perch (Lates niloticus) predation alone may not have caused the massive loss of species diversity; and (3) the resurgence of haplochromine cichlids is due to a combination of general improvement in the environment and reduction in L. niloticus abundance, with additionally possibly some rapid ecological adaptations. We conclude that environmental stressors will likely continue to shape the ecosystems in which the remaining endemic cichlid fish diversity continue to evolve, clearly involving genetic exchange between species. If water clarity can be improved again, it is possible to maintain a diverse assemblage of endemic species.

While PIT-tag tracking using mobile antennas is being increasingly used to study fish movement and survival in streams, little is known about the limitations of the method, especially over longer periods of time and under different environmental settings. We used 6 years of data combining tagging, mobile antenna tracking and recaptures of Salmo trutta in multiple small streams in the Lake Lucerne drainage area in Switzerland to evaluate the relative importance of different environmental and intrinsic factors affecting the efficiency of the method. Our study system and experimental design allowed us to accurately verify the continuous presence and survival of recaptured fish in the stream after tracking, which meant that we could estimate detection probability with high confidence. The mean detection probability of tagged trout was 43%, but we found that fish length had a strong negative effect on detection probability, especially in males. Multivariate axes of stream environmental features did not predict efficiency but stream width alone was significantly positively correlated with efficiency. Additionally, stream temperature when tracking had a positive effect on fish detectability. Tag loss at recapture was globally rare (<8%) but common in large postspawn females (>30%). Based on the escape response of fish after detection, we could estimate the proportion of ghost tags, which reached a plateau of around 80% 2 years after tagging. We finally showed that our models of tag loss, fish detection and escape response are needed to interpret detection events. Our results highlight that individual variation in detection probability and tag loss is high and has to be considered for analysis.

Across ecosystems, resources vary in their nutritional composition and thus their dietary value to consumers. Animals can either access organic compounds, such as fatty acids, directly from diet or through internal biosynthesis, and the extent to which they use these two alternatives likely varies based on the availability of such compounds across the nutritional landscape. Cross-ecosystem subsidies of important dietary nutrients, like omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA), may provide consumers with the opportunity to relax the demands of synthesis and rely upon dietary flexibility rather than internal metabolic processes. Here, we examined how dietary flexibility and distance from a lake influenced the degree to which generalist insectivores relied upon dietary n-3 LC-PUFA from emergent aquatic insects versus n-3 LC-PUFA synthesized from precursor compounds found in terrestrial insects. We used bulk and compound-specific stable isotope analyses to understand spider and insectivorous bird (Blue Tit; Cyanistes caeruleus) reliance on aquatic and terrestrial resources, including dietary PUFA sources, along a riparian to upland gradient from a lake. We simultaneously investigated n-3 LC-PUFA synthesis ability in nestlings using ¹³C fatty acid labeling. We found that riparian spiders took advantage of emergent aquatic insect subsidies, deriving their overall diet and their n-3 PUFA from aquatic resources whereas nestling birds at all distances and upland spiders relied upon terrestrial resources, including PUFA. Our ¹³C labeling experiment demonstrated that nestling tits were able to synthesize the n-3 LC-PUFA docosahexaenoic acid from the dietary precursor α-linolenic acid, suggesting that they are not limited by aquatic resources to satisfy their LC-PUFA requirements. Overall, this study suggests that habitat generalist insectivores vary in the degree to which they can shift diet to take advantage of high-quality aquatic resources depending upon both their foraging flexibility and internal synthesis capacity.

Statistical species distribution models (SDMs) are widely used to quantify how taxa respond to environmental conditions and to predict their distribution. However, the application of SDMs to freshwater fish taxa is complicated by the active dispersal of fish taxa through river networks, and the species- and habitat-dependent observation process (i.e., the sampling method and effort) required to accurately sample their distributions. Many studies have applied presence-absence models (PAMs) to fish taxa, while more recent studies have proposed zero-inflated models (ZIMs) to account for count observations with many zeroes. However, relatively few studies have incorporated the observation process into the model structure, which would facilitate the combination of data from various monitoring programs that differ in their observation process. In this study, we use conceptual models to identify potentially dominant natural and anthropogenic environmental conditions with a direct, mechanistic effect on the distributions of freshwater fish taxa in Switzerland, a region with a large range of environmental conditions, from alpine streams that are mainly affected by hydromorphological alterations to lowland streams in densely populated areas with intensive agricultural land use. Moreover, numerous barriers impede fish migration along the entire river network. Using combined data from two fish monitoring programs in Switzerland, we applied an exhaustive cross-validation procedure to select a set of environmental variables with the highest (out-of-sample) predictive performance for the PAM and ZIM for fish density (individuals/m²) of the seven most prevalent fish taxa (Salmo spp., Cottus spp., Squalius spp., Barbatula spp., Barbus spp., Phoxinus spp., Gobio spp.). We used these variables to develop a PAM and ZIM for each taxon that accounts for differences in sampling methods and sampling effort. We quantified the quality of fit during calibration using all samples and predictive performance during 5-fold cross-validation of each model.
Results show that stream temperature and stream morphology within the accessible habitat commonly appear among the best predictive presence-absence models for multiple taxa. Spatial variables that account for migration barriers and quantify morphological conditions within the accessible habitat were selected for 6 out of 7 taxa. The selected PAMs performed well for all taxa with an intermediate prevalence (10–40%), with an explanatory power () of between 0.32 - 0.37 during calibration using all samples and only minor decreases in explanatory power during cross-validation (= 0.34 – 0.44). As expected, the PAM for the highly prevalent Salmo spp. (91%) failed to predict the few absence data points. By contrast, the ZIM model performed best for Salmo spp., with a standardized likelihood ratio of 1.56. For all other taxa besides Barbus spp. the ZIM models also had likelihood ratios above one, indicating a better predictive performance than the null model. We hope this study stimulates the development and application of fish species distribution models based on prior knowledge of causally linked environmental variables and incorporating observation errors to improve their predictive performance. This can facilitate learning from biomonitoring data to support management.

1. Animals may respond to ecological heterogeneity by genetic differentiation or phenotypic plasticity. Responses of organisms to their ecology can include adaptation at various levels of organization, including morphology, behaviour and social structure. Adaptations at one level might constrain or enhance adaptations on other levels, which highlights the importance of understanding their interactions.
2. In highly social animals, understanding the influence of their ecological niche on the evolution and maintenance of complex social organization poses an intriguing challenge. Predation risk and habitat characteristics determine social structure in the cooperatively breeding cichlid Neolamprologus pulcher. Here we examine how varying combinations of these ecological factors across eight distinct populations influence morphological differentiation.
3. We investigated the relationship between body shape and ecological parameters for 137 wild-caught individuals from eight distinct populations. Furthermore, we examined the genetic structure and differentiation among these populations using microsatellites. Finally, to disentangle heritable from plastic responses, we raised two successive generations from six populations in the laboratory under common garden conditions and screened 188 individuals for morphological differentiation.
4. We found that body shape of N. pulcher strongly correlates with the measured ecological parameters. Low predation risk, low habitat structure and small shelter size favoured shallow bodies, whereas at the opposite end of these environmental gradients deep body shapes prevail. These consistent morphological differences persisted over two laboratory-reared generations, revealing a heritable basis. In contrast to the significant effect of local ecology on morphological differentiation between populations, both geographical and genetic distance had little explanatory power, suggesting that morphological differentiation between populations is not a simple by-product of genetic isolation. Remarkably, the largest difference in body depth emerged between the two populations located closest to each other, but differing strongly in their ecological niche.
5. These results highlight that morphological variation is a key component of local adaptation in neighbouring populations of a highly social species. Such morphological differentiation has the potential to influence individual cooperative behaviour, which will eventually feed back on group structure and mediate the evolution and maintenance of complex social systems.

Motivation: fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site frequency spectrum under a maximum-likelihood framework.
Results: Other improvements include multi-threading, handling of population inbreeding, extended input file syntax facilitating the description of complex demographic scenarios, and more efficient simulations of sparsely structured populations and of large chromosomes.
Availability and implementation: fastsimcoal2 is freely available on http://cmpg.unibe.ch/software/fastsimcoal2/. It includes console versions for Linux, Windows and MacOS, additional scripts for the analysis and visualization of simulated and estimated scenarios, as well as a detailed documentation and ready-to-use examples.

In Lake Tanganyika, blooms of nitrogen-fixing (diazotrophic) cyanobacteria emerge, when the upper water column re-stratifies after a period of upwelling and convective mixing. During this seasonal transition, diazotrophic cyanobacteria exploit the abundant phosphate and fix nitrogen after other phytoplankton taxa have consumed the available nitrate. However, it remains less clear, which mechanisms favour diazotrophic cyanobacteria under more heavily stratified conditions with lower levels of excess phosphate and persistent nitrate-depletion. Here, we collected profiles of physicochemical parameters, nutrients and photo-pigments, as well as the medium- to large-sized phytoplankton community during two lake-wide cruises to elucidate to what extent the abundance of diazotrophic cyanobacteria in Lake Tanganyika may be controlled by the nitrate resupply through the thermocline into the euphotic zone. At stations where nitrate was depleted, but phosphate remained available near the surface, high densities of diazotrophic cyanobacteria were associated with a low nitrate supply to surface waters. Our data provide first support for two conceptual scenarios, where the relative position of the thermocline and the euphotic depth may create a functional niche for diazotrophic cyanobacteria: when the upward transport of nitrate into the euphotic zone is reduced by a subjacent thermocline, diazotrophic cyanobacteria, comprising Dolichospermum and Anabaenopsis, are key players in the medium-to large-sized phytoplankton community. By contrast, a thermocline located within the euphotic zone allows for a rapid vertical transport of nitrate for a thriving nitrate-assimilating phytoplankton community that evidently outcompetes diazotrophic cyanobacteria. This study highlights that, under nitrogen-depleted conditions, diazotrophic cyanobacteria can also grow in response to a reduced nutrient resupply to the productive surface waters.

Anthropogenic environmental changes are altering ecological and evolutionary processes of ecosystems. The possibility that ecosystems can respond abruptly to gradual environmental change when critical thresholds are crossed (i.e. tipping points) and shift to an alternative stable state is a growing concern. Here I show that fast environmental change can trigger regime shifts before environmental stress exceeds a tipping point in evolving ecological systems. The difference in the time scales of coupled ecological and evolutionary processes makes ecosystems sensitive not only to the magnitude of environmental changes, but also to the rate at which changes are imposed. Fast evolutionary change mediated by high trait variation can reduce the sensitivity of ecosystems to the rate of environmental change and prevent the occurrence of rate-induced regime shifts. This suggests that management measures to prevent rate-induced regime shifts should focus on mitigating the effects of environmental change and protecting phenotypic diversity in ecosystems.

Freshwater ecosystems are under new and increasing threats from anthropogenic change. Ability to detect and predict consequences of environmental perturbations on ecosystem function and water quality is limited by the lack of empirical data over relevant time scales. Paleoecological records present a unique opportunity to broaden understanding of ecological transitions over decadal to millennial timescales. This study tested the occurrence of regime shifts to track changes throughout the lake food web beyond the typical instrumental era, using both “traditional” paleoecological proxies (e.g., cladoceran zooplankton, zoobenthos, and pigments) and more recently developed molecular genetic methods based on sedimentary DNA. We used sediment cores from the perialpine Lake Joux (Swiss Jura), where the history of human settlement and land-use practices in the catchment has been well documented since the Medieval period. Paleoecological evidence revealed an abrupt and unprecedented biological reorganization in the second half of the 20th century, following several centuries of relatively stable communities despite growing human pressure. Time-varying autoregression computed using dynamic linear modelling identified this transition, triggered by the onset of rapid cultural eutrophication in the 1950s, as a true regime shift. Since this time, despite decades of re-oligotrophication, biotic communities of Lake Joux have not returned to pre-disturbance composition, most likely due to other confounding factors, including climate warming, that may prevent the lake from returning to an earlier equilibrium state. Paleoecological reconstruction further suggested that cladocerans responded earlier to disturbance, which is highly relevant for lake monitoring and management strategies.

Large-scale oil palm agriculture has caused deforestation in the tropics, but also degrades stream water quality and reduces aquatic biodiversity. Though the outcomes of industrial-scale oil palm plantations for biodiversity have been explored extensively, the consequences of small-scale oil palm agriculture for freshwater macroinvertebrate fauna are poorly understood. Here, we explored the impacts of small-scale oil palm agriculture on aerial adult Odonata (the dragonflies and damselflies), which, due to their inherent sensitivity to habitat degradation, represent useful indicators of wider ecosystem health. We surveyed riparian corridors of man-made waterways in natural habitats converted into agricultural lands in both peat swamp and mangrove forest, comprising a total of 60 sampling units across a region of Peninsular Malaysia where such small-scale agricultural practices are widespread. We hypothesized that physicochemical water quality of oil palm waterways together with riparian vegetation influence Odonata species richness and composition. Our results revealed that Odonata species richness increased with dissolved oxygen, water temperature and vegetation cover, but decreased with water level, pH, and total dissolved solids. Species composition was influenced by both dissolved oxygen and pH. The present study provides valuable insights into the effects of small-scale oil palm agriculture for water quality of associated aquatic habitats, and subsequent responses of adult Odonata. Therefore, smallholders should reduce the use of chemical pesticides and fertilizers to improve the conservation value of oil palm waterways for both Odonata and aquatic fauna more generally, in order to be certified as biodiversity-friendly agriculture.

Adaptive radiations are bursts of evolutionary species diversification that have contributed to much of the species diversity on Earth. An exception is modern Europe, where descendants of ancient adaptive radiations went extinct, and extant adaptive radiations are small, recent and narrowly confined. However, not all legacy of old radiations has been lost. Subterranean environments, which are dark and food-deprived, yet buffered from climate change, have preserved ancient lineages. Here we provide evidence of an entirely subterranean adaptive radiation of the amphipod genus Niphargus, counting hundreds of species. Our modelling of lineage diversification and evolution of morphological and ecological traits using a time-calibrated multilocus phylogeny suggests a major adaptive radiation, comprised of multiple subordinate adaptive radiations. Their spatio-temporal origin coincides with the uplift of carbonate massifs in South-Eastern Europe 15 million years ago. Emerging subterranean environments likely provided unoccupied, predator-free space, constituting ecological opportunity, a key trigger of adaptive radiation. This discovery sheds new light on the biodiversity of Europe.

The nutritional diversity of resources can affect the adaptive evolution of consumer metabolism and consumer diversification. The omega-3 long-chain polyunsaturated fatty acids eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) have a high potential to affect consumer fitness, through their widespread effects on reproduction, growth and survival. However, few studies consider the evolution of fatty acid metabolism within an ecological context. In this review, we first document the extensive diversity in both primary producer and consumer fatty acid distributions amongst major ecosystems, between habitats and amongst species within habitats. We highlight some of the key nutritional contrasts that can shape behavioural and/or metabolic adaptation in consumers, discussing how consumers can evolve in response to the spatial, seasonal and community-level variation of resource quality. We propose a hierarchical trait-based approach for studying the evolution of consumers' metabolic networks and review the evolutionary genetic mechanisms underpinning consumer adaptation to EPA and DHA distributions. In doing so, we consider how the metabolic traits of consumers are hierarchically structured, from cell membrane function to maternal investment, and have strongly environment-dependent expression. Finally, we conclude with an outlook on how studying the metabolic adaptation of consumers within the context of nutritional landscapes can open up new opportunities for understanding evolutionary diversification.

Multiple stressors linked to anthropogenic activities can influence how organisms adapt and evolve. So far, a consensus on how multiple stressors drive adaptive trajectories in natural populations has not been reached. Some meta-analysis reports show predominance of additive effects of stressors on ecological endpoints (e.g., fecundity, mortality), whereas others show synergistic effects more frequently. Moreover, it is unclear what mechanisms of adaptation underpin responses to complex environments. Here, we use populations of Daphnia magna resurrected from different times in the past to investigate mechanisms of adaptation to multiple stressors and to understand how historical exposure to environmental stress shapes adaptive responses of modern populations. Using common garden experiments on resurrected modern and historical populations, we investigate (1) whether exposure to one stress results in higher tolerance to a second stressor; (2) the mechanisms of adaptation underpinning long-term evolution to multistress (genetic evolution, plasticity, evolution of plasticity); and (3) the interaction effects of multiple stressors on fitness (synergism, antagonism, additivity). We measure the combined impact of different levels of resource availability (algae) and biocides on fitness-linked life-history traits and interpret these results in light of historical environmental exposures. We show that exposure to one stressor can alter tolerance to second stressors and that the interaction effect depends on the severity of either stressor. We also show that mechanisms of adaptation underpinning phenotypic evolution significantly differ in single-stress and multistress scenarios. These adaptive responses are driven largely by synergistic effects on fecundity and size at maturity, and additive effects on age at maturity. Exposure to multiple stressors shifts the trade-offs among fitness-linked life-history traits, with a stronger effect on Daphnia populations when low-resource availability and high biocide levels are experienced. Our study indicates that mitigation interventions based on single-stress analysis may not capture realistic threats.

Eutrophication is a persistent threat to aquatic ecosystems worldwide. Foundation species, namely those that play a central role in the structuring of communities and functioning of ecosystems, are likely important for the resilience of aquatic ecosystems in the face of disturbance. However, little is known about how interactions among such species influence ecosystem responses to nutrient perturbation. Here, using an array (N = 20) of outdoor experimental pond ecosystems (15,000 L), we manipulated the presence of two foundation species, the macrophyte Myriophyllum spicatum and the mussel Dreissena polymorpha, and quantified ecosystem responses to multiple nutrient disturbances, spread over two years. In the first year, we added five nutrient pulses, ramping up from 10 to 50 μg P/L over a 10-week period from mid-July to mid-October, and in the second year, we added a single large pulse of 50 μg P/L in mid-October. We used automated sondes to measure multiple ecosystems properties at high frequency (15-minute intervals), including phytoplankton and dissolved organic matter fluorescence, and to model whole-ecosystem metabolism. Overall, both foundation species strongly affected the ecosystem responses to nutrient perturbation, and, as expected, initially suppressed the increase in phytoplankton abundance following nutrient additions. However, when both species were present, phytoplankton biomass increased substantially relative to other treatment combinations: non-additivity was evident for multiple ecosystem metrics following the nutrient perturbations in both years but was diminished in the intervening months between our perturbations. Overall, these results demonstrate how interactions between foundation species can cause surprisingly strong deviations from the expected responses of aquatic ecosystems to perturbations such as nutrient additions.

Parasite infracommunities tend to be stochastic in nature, although environmental characteristics such as the type of water source in streams and host traits can have an effect on the biotic assemblages and by extension the parasite fauna. We examined the effect of water source and the rate of adult fish migration on the metazoan parasite infracommunities of conspecific juvenile brown trout, Salmo trutta L. among streams flowing into Lake Lucerne (Switzerland). Juvenile (1 to 2-year old) fish harboured higher parasite species richness in groundwater-fed than in surface water-fed streams, whereas the rate of fish migration did not affect infracommunity richness. Heteroxenous species were more common in groundwater-fed streams with high and medium rates of trout migration, whereas infracommunities in surface water-fed streams and streams with low rates of fish migration were dominated by one monoxenous parasite or lacked infections. Similarity in the parasite infracommunity composition of juvenile trout across streams was explained by the interaction between type of water source and adult migration rates. Our conclusions support that similarity in the parasite composition of resident freshwater conspecifics can be predicted by the local environmental settings and host migratory behaviour, whereas parasite richness is mainly influenced by the environmental characteristics.

Marine Protected Areas (MPAs) are an important tool for management and conservation and play an increasingly recognised role in societal and human well-being. However, the assessment of MPAs often lacks a simultaneous consideration of ecological and socio-economic outcomes, and this can lead to misconceptions on the effectiveness of MPAs. In this perspective, we present a transdisciplinary approach based on the Delphi method for mapping and evaluating Marine Protected Areas for their ability to protect biodiversity while providing Ecosystem Services (ES) and related human well-being benefits – i.e., the ecosystem outputs from which people benefit. We highlight the need to include the human dimensions of marine protection in such assessments, given that the effectiveness of MPAs over time is conditional on the social, cultural and institutional contexts in which MPAs evolve. Our approach supports Ecosystem-Based Management and highlights the importance of MPAs in achieving restoration, conservation, and sustainable development objectives in relation to EU Directives such as the Marine Strategy Framework Directive (MSFD), the Maritime Spatial Planning Directive (MSPD), and the Common Fisheries Policy (CFP).

The visual systems of teleost fishes usually match their habitats and lifestyles. Since coral reefs are bright and colourful environments, the visual systems of their diurnal inhabitants have been more extensively studied than those of nocturnal species. In order to fill this knowledge gap, we conducted a detailed investigation of the visual system of the nocturnal reef fish family Holocentridae. Results showed that the visual system of holocentrids is well adapted to their nocturnal lifestyle with a rod-dominated retina. Surprisingly, rods in all species were arranged into 6-17 well-defined banks, a feature most commonly found in deep-sea fishes, that may increase the light sensitivity of the eye and/or allow colour discrimination in dim light. Holocentrids also have the potential for dichromatic colour vision during the day with the presence of at least two spectrally different cone types: single cones expressing the blue-sensitive SWS2A gene, and double cones expressing one or two green-sensitive RH2 genes. Some differences were observed between the two subfamilies, with Holocentrinae (squirrelfish) having a slightly more developed photopic visual system than Myripristinae (soldierfish). Moreover, retinal topography of both ganglion cells and cone photoreceptors showed specific patterns for each cell type, likely highlighting different visual demands at different times of the day, such as feeding. Overall, their well-developed scotopic visual systems and the ease of catching and maintaining holocentrids in aquaria, make them ideal models to investigate teleost dim-light vision and more particularly shed light on the function of the multibank retina and its potential for dim-light colour vision.

limate warming is causing rapid spatial expansion of ocean warm pools from equatorial latitudes towards the subtropics. Sedentary coral reef inhabitants in affected areas will thus be trapped in high temperature regimes, which may become the “new normal”. In this study, we used clownfish Amphiprion ocellaris as model organism to study reef fish mechanisms of thermal adaptation and determine how high temperature affects multiple lipid aspects that influence physiology and thermal tolerance. We exposed juvenile fish to two different experimental conditions, implemented over 28 days: average tropical water temperatures (26 °C, control) or average warm pool temperatures (30 °C). We then performed several analyses on fish muscle and liver tissues: i) total lipid content (%), ii) lipid peroxides, iii) fatty acid profiles, iv) lipid metabolic pathways, and v) weight as body condition metric. Results showed that lipid storage capacity in A. ocellaris was not affected by elevated temperature, even in the presence of lipid peroxides in both tissues assessed. Additionally, fatty acid profiles were unresponsive to elevated temperature, and lipid metabolic networks were consequently well conserved. Consistent with these results, we did not observe changes in fish weight at elevated temperature. There were, however, differences in fatty acid profiles between tissue types and over time. Liver showed enhanced α-linolenic and linoleic acid metabolism, which is an important pathway in stress response signaling and modulation on environmental changes. Temporal oscillations in fatty acid profiles are most likely related to intrinsic factors such as growth, which leads to the mobilization of energetic reserves between different tissues throughout time according to organism needs. Based on these results, we propose that the stability of fatty acid profiles and lipid metabolic pathways may be an important thermal adaptation feature of fish exposed to warming environments.

Ecologists and evolutionary biologists are well aware that natural and sexual selection do not operate on traits in isolation, but instead act on combinations of traits. This long-recognized and pervasive phenomenon is known as multivariate selection, or - in the particular case where it favours correlations between interacting traits - correlational selection. Despite broad acknowledgement of correlational selection, the relevant theory has often been overlooked in genomic research. Here, we discuss theory and empirical findings from ecological, quantitative genetic and genomic research, linking key insights from different fields. Correlational selection can operate on both discrete trait combinations and quantitative characters, with profound implications for genomic architecture, linkage, pleiotropy, evolvability, modularity, phenotypic integration and phenotypic plasticity. We synthesize current knowledge and discuss promising research approaches that will enable us to understand how correlational selection shapes genomic architecture, thereby linking quantitative genetic approaches with emerging genomic methods. We suggest that research on correlational selection has great potential to integrate multiple fields in evolutionary biology, including developmental and functional biology, ecology, quantitative genetics, phenotypic polymorphisms, hybrid zones and speciation processes.

Parasites threaten all free-living organisms, including molluscs. Understanding the evolution of immune defence traits in natural host populations is crucial for predicting their long-term performance under continuous infection risk. Adaptive trait evolution requires that traits are subject to selection (i.e. contribute to organismal fitness) and that they are heritable. Despite broad interest in the evolutionary ecology of immune activity in animals, the understanding of selection on and evolutionary potential of immune defence traits is far from comprehensive. For instance, empirical observations are only rarely in line with theoretical predictions of immune activity being subject to stabilizing selection. This discrepancy may be because ecoimmunological studies can typically cover only a fraction of the complexity of an animal immune system. Similarly, molecular immunology/immunogenetics studies provide a mechanistic understanding of immunity, but neglect variation that arises from natural genetic differences among individuals and from environmental conditions. Here, we review the current literature on natural selection on and evolutionary potential of immune traits in animals, signal how merging ecological immunology and genomics will strengthen evolutionary ecological research on immunity, and indicate research opportunities for molluscan gastropods for which well-established ecological understanding and/or 'immune-omics' resources are already available.

Sex determination systems are highly conserved among most vertebrates with genetic sex determination, but can be variable and evolve rapidly in some. Here, we study sex determination in a clade with exceptionally high sex chromosome turnover rates. We identify the sex determining chromosomes in three interspecific crosses of haplochromine cichlid fishes from Lakes Victoria and Malawi. We find evidence for different sex determiners in each cross. In the Malawi cross and one Victoria cross the same chromosome is sex-linked but while females are the heterogametic sex in the Malawi species, males are the heterogametic sex in the Victoria species. This chromosome has not previously been reported to be sex determining in cichlids, increasing the number of different chromosomes shown to be sex determining in cichlids to 12. All Lake Victoria species of our crosses are less than 15,000 years divergent, and we identified different sex determiners among them. Our study provides further evidence for the diversity and evolutionary flexibility of sex determination in cichlids, factors which might contribute to their rapid adaptive radiations.

Loss of resilience in population numbers in response to environmental perturbations may be predicted with statistical metrics called early warning signals (EWS) that are derived from abundance time series. These signals, however, have been shown to have limited success, leading to the development of trait‐based EWS that are based on information collected from phenotypic traits such as body size. Experimental work assessing the efficacy of EWS under varying ecological and environmental factors are rare. In addition, disentangling how such warning signals are affected under varying ecological and environmental factors is key to their application in biological conservation. Here, we experimentally test how different rates of environmental forcing (i.e. warming) and varying ecological factors (i.e. habitat quality and phenotypic diversity) affected population stability and predictive power of early warning signals of population collapse. We analyzed population density and body size time series data from three phenotypically different populations of a protozoan ciliate Askenasia volvox in two levels of habitat quality subjected to three different treatments of warming (i.e. no warming, fast warming and slow warming). We then evaluated how well abundance‐ and trait‐based EWS predicted population collapses under different levels of phenotypic diversity, habitat quality and warming treatments. Our results suggest that habitat quality and warming treatments had more profound effects than phenotypic diversity had on both population stability and on the performance of abundance‐based signals of population collapse. In addition, trait‐based EWS generally performed well, were reliable and more robust in forecasting population collapse than abundance‐based EWS, regardless of variation in environmental and ecological factors. Our study points towards the development of a predictive framework that includes information from phenotypic traits such as body size as an indicator of loss of resilience of ecological systems in response to environmental perturbations.

Developmental plasticity is ubiquitous in natural populations, but the underlying causes and fitness consequences are poorly understood. For consumers, nutritional variation of juvenile diets is probably associated with plasticity in developmental rates, but little is known about how diet quality can affect phenotypic trajectories in ways that might influence survival to maturity and lifetime reproductive output. Here, we tested how the diet quality of a freshwater detritivorous isopod (Asellus aquaticus), in terms of elemental ratios of diet (i.e. carbon : nitrogen : phosphorus; C : N : P), can affect (i) developmental rates of body size and pigmentation and (ii) variation in juvenile survival. We reared 1047 individuals, in a full-sib split-family design (29 families), on either a high- (low C : P, C : N) or low-quality (high C : P, C : N) diet, and quantified developmental trajectories of body size and pigmentation for every individual over 12 weeks. Our diet contrast caused strong divergence in the developmental rates of pigmentation but not growth, culminating in a distribution of adult pigmentation spanning the broad range of phenotypes observed both within and among natural populations. Under low-quality diet, we found highest survival at intermediate growth and pigmentation rates. By contrast, survival under high-quality diet survival increased continuously with pigmentation rate, with longest lifespans at intermediate growth rates and high pigmentation rates. Building on previous work which suggests that visual predation mediates the evolution of cryptic pigmentation in A. aquaticus, our study shows how diet quality and composition can generate substantial phenotypic variation by affecting rates of growth and pigmentation during development in the absence of predation.

If optimal investment in anti-predator defences depends on predation risk, invading new regions (and thus, encountering different predators) may favour shifts in that investment. Cane toads offer an ideal system to test this prediction: expensive anti-predator toxins are stored mainly in parotoid glands whose dimensions are easy to measure, and toad invasions have changed the suites of predators they encounter. Although plasticity may influence parotoid morphology, comparisons between parents and progeny revealed that gland dimensions were highly heritable. That heritability supports the plausibility of an evolved basis to variation in gland dimensions. Measurements of 3779 adult toads show that females have larger glands than males, invasive populations have larger glands than in the native-range, and that parotoid sexual size dimorphism varies strongly among invaded areas. Geographic variation in parotoid morphology may be driven by predation risk to both adult toads and offspring (provisioned with toxins by their mother), with toxins allocated to eggs exacerbating the risk of cannibalism but reducing the risk of interspecific predation. Investment into chemical defences has evolved rapidly during the cane toad’s international diaspora, consistent with the hypothesis that organisms flexibly adjust resource allocation to anti-predator tactics in response to novel challenges.

Invasive species can be powerful models for studying contemporary evolution in natural environments. As invading organisms often encounter new habitats during colonization, they will experience novel selection pressures. Threespine stickleback (Gasterosteus aculeatus complex) have recently colonized large parts of Switzerland and are invasive in Lake Constance. Introduced to several watersheds roughly 150 years ago, they spread across the Swiss Plateau (400–800 m a.s.l.), bringing three divergent hitherto allopatric lineages into secondary contact. As stickleback have colonized a variety of different habitat types during this recent range expansion, the Swiss system is a useful model for studying contemporary evolution with and without secondary contact. For example, in the Lake Constance region there has been rapid phenotypic and genetic divergence between a lake population and some stream populations. There is considerable phenotypic variation within the lake population, with individuals foraging in and occupying littoral, offshore pelagic, and profundal waters, the latter of which is a very unusual habitat for stickleback. Furthermore, adults from the lake population can reach up to three times the size of adults from the surrounding stream populations, and are large by comparison to populations globally. Here, we review the historical origins of the threespine stickleback in Switzerland, and the ecomorphological variation and genomic basis of its invasion in Lake Constance. We also outline the potential ecological impacts of this invasion, and highlight the interest for contemporary evolution studies.

• Phytosterols are primary plant metabolites that have fundamental structural and regulatory functions. They are also essential nutrients for phytophagous insects, including pollinators, that cannot synthesize sterols. Despite the well‐described composition and diversity in vegetative plant tissues, few studies have examined phytosterol diversity in pollen.
• We quantified 25 pollen phytosterols in 122 plant species (105 genera, 51 families) to determine their composition and diversity across plant taxa. We searched literature and databases for plant phylogeny, environmental conditions, and pollinator guilds of the species to examine the relationships with pollen sterols.
• 24‐methylenecholesterol, sitosterol and isofucosterol were the most common and abundant pollen sterols. We found phylogenetic clustering of twelve individual sterols, total sterol content and sterol diversity, and of sterol groupings that reflect their underlying biosynthesis pathway (C‐24 alkylation, ring B desaturation). Plants originating in tropical‐like climates (higher mean annual temperature, lower temperature seasonality, higher precipitation in wettest quarter) were more likely to record higher pollen sterol content. However, pollen sterol composition and content showed no clear relationship with pollinator guilds.
• Our study is the first to show that pollen sterol diversity is phylogenetically clustered and that pollen sterol content may adapt to environmental conditions.

1. Submerged macrophytes are important foundation species that can strongly influence the structure and functioning of aquatic ecosystems, but only little is known about the temporal variation and the timescales of these effects (i.e. from hourly, daily, to monthly).
2. Here, we conducted an outdoor experiment in replicated mesocosms (1,000 L) where we manipulated the presence and absence of macrophytes to investigate the temporal variability of their ecosystem effects. We measured several parameters (chlorophyll-a, phycocyanin, dissolved organic matter [DOM], and oxygen) with high-resolution sensors (15-min intervals) over several months (94 days from spring to autumn), and modelled metabolic rates of each replicate ecosystem in a Bayesian framework. We also implemented a simple model to explore competitive interactions between phytoplankton and macrophytes as a driver of variability in chlorophyll-a.
3. Over the entire experiment, macrophytes had a positive effect on mean DOM concentration, a negative effect on phytoplankton biomass, and either a weak or no effect on mean metabolic rates, DOM composition, and conductivity. We also found that macrophytes increased the variance of dissolved organic carbon composition and metabolic rates, and, occasionally in the observed period, increased the variance of phytoplankton biomass and conductivity. The observation that macrophytes decreased the mean but increased the variance of phytoplankton biomass was consistent with the model that we implemented.
4. Our high-resolution time series embedded within a manipulative experiment reveal how a foundation species can affect ecosystem properties and processes that have characteristically different timescales of response to environmental variation. Specifically, our results show how macrophytes can affect short-term dynamics of algal biomass, while also affecting the seasonal build-up of DOM and the variance of ecosystem metabolism.

Technological advances in DNA sequencing over the last decade now permit the production and curation of large genomic datasets in an increasing number of non‐model species. Additionally, this new data provides the opportunity for combining datasets, resulting in larger studies with a broader taxonomic range. Whilst the development of new sequencing platforms has been beneficial, resulting in a higher throughput of data at a lower per‐base cost, shifts in sequencing technology can also pose challenges for those wishing to combine new sequencing data with data sequenced on older platforms. Here, we outline the types of studies where the use of curated data might be beneficial, and highlight potential biases that might be introduced by combining data from different sequencing platforms. As an example of the challenges associated with combining data across sequencing platforms, we focus on the impact of the shift in Illumina's base calling technology from a four‐channel to a two‐channel system. We caution that when data is combined from these two systems, erroneous guanine base calls that result from the two‐channel chemistry can make their way through a bioinformatic pipeline, eventually leading to inaccurate and potentially misleading conclusions. We also suggest solutions for dealing with such potential artifacts, which make samples sequenced on different sequencing platforms appear more differentiated from one another than they really are. Finally, we stress the importance of archiving tissue samples and the associated sequences for the continued reproducibility and reusability of sequencing data in the face of ever‐changing sequencing platform technology.

Heterogeneous exposure to parasites may contribute to host species differentiation. Hosts often harbour multiple parasite species which may interact and thus modify each other’s effects on host fitness. Antagonistic or synergistic interactions between parasites may be detectable as niche segregation within hosts. Consequently, the within-host distribution of different parasite taxa may constitute an important axis of infection variation among host populations and species. We investigated the microhabitat distributions and species interactions of gill parasites (four genera) infecting 14 sympatric cichlid species in Lake Victoria, Tanzania. We found that the two most abundant ectoparasite genera (the monogenean Cichlidogyrus spp. and the copepod Lamproglena monodi) were non-randomly distributed across the host gills and their spatial distribution differed between host species. This may indicate microhabitat selection by the parasites and cryptic differences in the host–parasite interaction among host species. Relationships among ectoparasite genera were synergistic: the abundances of Cichlidogyrus spp. and the copepods L. monodi and Ergasilus lamellifer tended to be positively correlated. In contrast, relationships among morphospecies of Cichlidogyrus were antagonistic: the abundances of morphospecies were negatively correlated. Together with niche overlap, this suggests competition among morphospecies of Cichlidogyrus. We also assessed the reproductive activity of the copepod species (the proportion of individuals carrying egg clutches), as it may be affected by the presence of other parasites and provide another indicator of the species specificity of the host–parasite relationship. Copepod reproductive activity did not differ between host species and was not associated with the presence or abundance of other parasites, suggesting that these are generalist parasites, thriving in all cichlid species examined from Lake Victoria.

The present study documents, for the first time, the ingestion of microplastics (MPs) by Longnose stingrays in the Western Atlantic Ocean. We examined 23 specimens of Hypanus guttatus from the Brazilian Amazon coast and found microplastic particles in the stomach contents of almost a third of the individuals. Fibers were the most frequent item (82%), blue was the most frequent color (47%) and Polyethylene Terephthalate (PET) was the most frequent polymer recorded (35%), as identified by 2D imaging - Fourier Transform Infrared (FTIR). The ingestion of microplastics by Longnose stingray has not been previously recorded. The findings of the present study thus provide an important baseline for future studies of microplastic ingestion by dasyatid rays and other batoid species in the Atlantic Ocean, and contribute to the broader understanding of the spatial and temporal dimensions of the growing problem of plastic pollution in aquatic ecosystems and organisms.

Climate change in the Arctic is outpacing the global average and land-use is intensifying due to exploitation of previously inaccessible or unprofitable natural resources. A comprehensive understanding of how the joint effects of changing climate and productivity modify lake food web structure, biomass, trophic pyramid shape and abundance of physiologically essential biomolecules (omega-3 fatty acids) in the biotic community is lacking. We conducted a space-for-time study in 20 subarctic lakes spanning a climatic (+3.2°C and precipitation: +30%) and chemical (dissolved organic carbon: +10 mg/L, total phosphorus: +45 µg/L and total nitrogen: +1,000 µg/L) gradient to test how temperature and productivity jointly affect the structure, biomass and community fatty acid content (eicosapentaenoic acid [EPA] and docosahexaenoic acid [DHA]) of whole food webs. Increasing temperature and productivity shifted lake communities towards dominance of warmer, murky-water-adapted taxa, with a general increase in the biomass of primary producers, and secondary and tertiary consumers, while primary invertebrate consumers did not show equally clear trends. This process altered various trophic pyramid structures towards an hour glass shape in the warmest and most productive lakes. Increasing temperature and productivity had negative fatty acid content trends (mg EPA + DHA/g dry weight) in primary producers and primary consumers, but not in secondary nor tertiary fish consumers. The massive biomass increment of fish led to increasing areal fatty acid content (kg EPA + DHA/ha) towards increasingly warmer, more productive lakes, but there were no significant trends in other trophic levels. Increasing temperature and productivity are shifting subarctic lake communities towards systems characterized by increasing dominance of cyanobacteria and cyprinid fish, although decreasing quality in terms of EPA + DHA content was observed only in phytoplankton, zooplankton and profundal benthos.

Parasite-mediated selection may initiate or enhance differentiation between host populations that are exposed to different parasite infections. Variation in infection among populations may result from differences in host ecology (thereby exposure to certain parasites) and/or intrinsic immunological traits. Species of cichlid fish, even when recently diverged, often differ in parasite infection, but the contributions of intrinsic and extrinsic causes are unknown. Here, we compare infection patterns between two closely related host species from Lake Victoria (genus Pundamilia), using wild-caught and first-generation laboratory-reared fish, as well as laboratory-reared hybrids. Three of the commonest ectoparasite species observed in the wild were also present in the laboratory populations. However, the infection differences between the host species as observed in the wild were not maintained in laboratory conditions. In addition, hybrids did not differ in infection from either parental species. These findings suggest that the observed species differences in infection in the wild might be mainly driven by ecology-related effects (i.e. differential exposure), rather than by intrinsic species differences in immunological traits. Thus, while there is scope for parasite-mediated selection in Pundamilia in the wild, it has apparently not yet generated divergent evolutionary responses and may not enhance assortative mating among closely related species.

Higher order interactions (HOIs) have been suggested to stabilize diverse ecological communities. However, their role in maintaining species coexistence from the perspective of modern coexistence theory is not known. Here, using generalized Lotka-Volterra model, we derive a general rule for species coexistence modulated by HOIs. We show that where pairwise species interactions fail to promote species coexistence in regions of extreme fitness differences, negative HOIs that intensify pairwise competition, however, can promote coexistence provided that HOIs strengthen intraspecific competition more than interspecific competition. In contrast, positive HOIs that alleviate pairwise competition can stabilize coexistence across a wide range of fitness differences, irrespective of differences in strength of inter- and intraspecific competition. In addition, we extend our three-species analytical result to multispecies communities and show, using simulations, that multispecies coexistence is possible provided that strength of negative intraspecific HOIs is higher than interspecific HOIs. Our work sheds light on the underlying mechanisms through which HOIs can maintain species diversity.

Species diversity and trap success (abundance) between the two sites were assessed. Animals were sampled using four types of traps; Bucket pitfalls, Sherman, Tomahawk and Snap traps. A total of 103 animals comprising of 18 species in 8 families were captured; 73 of them from the Wooded Grassland and 30 from the Primary Forest. Species richness in the Wooded Grassland was 14 species and in the Primary Forest (11species). Using the Welch's t-test, species diversity between the Wooded Grassland (H'= 0.78) and that of the Primary Forest (H'= 0.71) did not differ significantly. The Sørensen Coefficient (CCs) value of 0.56 indicates a low similarity in the species inhabiting the two study sites. Small mammals species which disappeared for many years in the past could now be found inhabiting the Game Reserve. Most of it is still a secondary forest but it will recover into a primary forest in the near future if efforts to curb illegal tree harvesting and wild fires continue to be taken seriously.

New types of fish guidance structures with vertical curved bars and a subsequent bypass system represent a promising technical solution for the protection and guidance of downstream moving fish at run-of-river hydropower plants and water intakes. These so-called "curved-bar rack bypass systems" (CBR-BSs) function as a mechanical behavioral barrier and are characterized by low hydraulic losses, a symmetrical downstream flow field and an overall high fish guidance efficiency in the laboratory for a wide array of European freshwater fish species. This paper presents the results of the hydraulic and live-fish laboratory tests of an optimized CBR-BS configuration with a bar spacing of 50 mm and 30° rack angle to the flow direction. The tests were conducted with six different fish species in an ethohydraulic laboratory flume at different approach flows (0.5 m/s, 0.7 m/s) and different bypass entrance velocities (0.6-1.0 m/s). A numerical model was used to simulate the flow fields in the CBR-BS in order to link the fish behavior to the hydrodynamic cues created by the CBR-BS. Lower approach flow velocities decreased the hydraulic cues of the CBR, which led to more rack passages. A 20% velocity increase towards the bypass entrance significantly increased the fish guidance efficiency compared to a 40% velocity increase. The tested CBR-BS resulted in overall higher interspecies fish protection and guidance efficiencies compared to the more commonly applied horizontal-bar rack with a narrow bar spacing of 20 mm. Recommendations for a sustainable and cost-effective application of CBR-BSs are given.

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.

According to the competitive exclusion principle, species with low competitive abilities should be excluded by more efficient competitors; yet, they generally remain as rare species. Here, we describe the positive and negative spatial association networks of 326 disparate assemblages, showing a general organization pattern that simultaneously supports the primacy of competition and the persistence of rare species. Abundant species monopolize negative associations in about 90% of the assemblages. On the other hand, rare species are mostly involved in positive associations, forming small network modules. Simulations suggest that positive interactions among rare species and microhabitat preferences are the most probable mechanisms underpinning this pattern and rare species persistence. The consistent results across taxa and geography suggest a general explanation for the maintenance of biodiversity in competitive environments.

African cichlid fishes are a prime model for studying speciation mechanisms. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for cichlid phenotypic variation. One of their most variable phenotypes is visual sensitivity, with some of the largest spectral shifts among vertebrates. These shifts arise primarily from differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi cichlids, we previously identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or an opsin gene. In this comprehensive study, we show that these indels are the result of the movement of transposable elements (TEs) that correlate with opsin expression variation across the Malawi flock. In tracking the evolutionary history of these particular indels, we found they are endemic to Lake Malawi, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. However, an independent indel has arisen at a similar genomic location in one locus outside of the Malawi flock. The convergence in TE movement suggests these loci are primed for TE insertion and subsequent deletions. Increased TE mobility may be associated with interspecific hybridization, which disrupts mechanisms of TE suppression. This might provide a link between cichlid hybridization and accelerated regulatory variation. Overall, our study suggests that TEs may be an important driver of key regulatory changes, facilitating rapid phenotypic change and possibly speciation in African cichlids.

Among vertebrates, teleost eye diversity exceeds that found in all other groups. Their spectral sensitivities range from ultraviolet to red, and the number of visual pigments varies from 1 to over 40. This variation is correlated with the different ecologies and life histories of fish species, including their variable aquatic habitats: murky lakes, clear oceans, deep seas and turbulent rivers. These ecotopes often change with the season, but fish may also migrate between ecotopes diurnally, seasonally or ontogenetically. To survive in these variable light habitats, fish visual systems have evolved a suite of mechanisms that modulate spectral sensitivities on a range of timescales. These mechanisms include: (1) optical media that filter light, (2) variations in photoreceptor type and size to vary absorbance and sensitivity, and (3) changes in photoreceptor visual pigments to optimize peak sensitivity. The visual pigment changes can result from changes in chromophore or changes to the opsin. Opsin variation results from changes in opsin sequence, opsin expression or co-expression, and opsin gene duplications and losses. Here, we review visual diversity in a number of teleost groups where the structural and molecular mechanisms underlying their spectral sensitivities have been relatively well determined. Although we document considerable variability, this alone does not imply functional difference per se. We therefore highlight the need for more studies that examine species with known sensitivity differences, emphasizing behavioral experiments to test whether such differences actually matter in the execution of visual tasks that are relevant to the fish.

The potent defensive chemicals of cane toads (Rhinella marina) protect them against predators that lack coevolved physiological tolerance to those toxins. That relative invulnerability may explain why major injuries (such as limb loss) appear to be rare in cane toads from most of their global range; however, we noted frequent predator-induced injuries (>4% of adults) in samples from within the toad's native range (in French Guiana) and from a site (Lake Argyle) in north-western Australia. Toads at Lake Argyle enter the edge of the lake at night to rehydrate, exposing them to foraging freshwater crocodiles (Crocodylus johnstoni). Crocodiles rarely consume toads, but the attacks often result in loss of a limb. Because limbs contain relatively little toxin, attacks to the limbs expose a crocodile to nauseating but non-lethal amounts of toxin; and hence, facilitate taste aversion learning by the predator. The context of the encounters, such as differences in geography, may help to explain why the invasion of cane toads has not significantly impacted on crocodile populations at this site, in contrast to heavy impacts reported from nearby riverine systems.

Salmonids are of particular interest to evolutionary biologists due to their incredible diversity of life-history strategies and the speed at which many salmonid species have diversified. In Switzerland alone, over 30 species of Alpine whitefish from the subfamily Coregoninae have evolved since the last glacial maximum, with species exhibiting a diverse range of morphological and behavioural phenotypes. This, combined with the whole genome duplication which occurred in the ancestor of all salmonids, makes the Alpine whitefish radiation a particularly interesting system in which to study the genetic basis of adaptation and speciation and the impacts of ploidy changes and subsequent rediploidization on genome evolution. Although well curated genome assemblies exist for many species within Salmonidae, genomic resources for the subfamily Coregoninae are lacking. To assemble a whitefish reference genome, we carried out PacBio sequencing from one wild-caught Coregonus sp. "Balchen" from Lake Thun to ~90x coverage. PacBio reads were assembled independently using three different assemblers, Falcon, Canu and wtdbg2 and subsequently scaffolded with additional Hi-C data. All three assemblies were highly contiguous, had strong synteny to a previously published Coregonus linkage map, and when mapping additional short-read data to each of the assemblies, coverage was fairly even across most chromosome-scale scaffolds. Here, we present the first de novo genome assembly for the Salmonid subfamily Coregoninae. The final 2.2 Gb wtdbg2 assembly included 40 scaffolds, an N50 of 51.9 Mb, and was 93.3% complete for BUSCOs. The assembly consisted of ~52% TEs and contained 44,525 genes.

Assessing the migratory behaviour of individual and groups of animals is key to understand the function of migration, its evolution, and how it is affected by environment and human activities. In the eastern North Atlantic, killer whales (Orcinus orca) presumably track herring stocks as they migrate between across the region. However, the detailed migratory and foraging behaviour of eastern North Atlantic killer whales is poorly understood. We report on the behaviour of 15 adult male killer whales equipped with Argos satellite transmitters during the winter of 2015-2016 along the coast of Troms, northern Norway. The animals were tracked for 8-104 days (mean: 41 days), during which they migrated 302-7608 Km (mean: 2646 Km). The observed movement of killer whales south to 64.2°N along the Norwegian coast following NSS-herring to their spawning grounds is in agreement with previous studies. However, our study is the first to also document northern migration of three of the Norwegian killer whales into the Barents Sea region towards Novaya Zemlya Island about 900 km from the Norwegian coast approaching 77.0°N. Importantly, using a Bayesian state-space model, we offer new insights on killer whale searching and transit movements, as well as diurnal patterns in swimming speed, preferred foraging habitat and feeding behaviour. The 15 tagged killer whales spend 75.0% of the time in an area restricted search (ARS) mode (range: 55.2-95.2%), 3.9% of the time in a transit mode (range: 0.0-16.1%) and 21.1% (range: 4.8-36.3%) in uncertain mode. The restricted search behaviour peaked at the end of January and beginning of February, after which the killer whales gradually performing transit behaviour as they followed the migrating herring out of the region, or shifted to other prey items.

The Spanish government declared the lockdown on March 14th, 2020 to tackle the fast-spreading of COVID-19. As a consequence, the Balearic Islands remained almost fully isolated due to the closing of airports and ports, these isolation measures and the home-based confinement have led to a low prevalence of COVID-19 in this region. We propose a compartmental model for the spread of COVID-19 including five compartments (Susceptible, Exposed, Presymptomatic Infective, Diseased, and Recovered), and the mobility between municipalities. The model parameters are calibrated with the temporal series of confirmed cases provided by the Spanish Ministry of Health. After calibration, the proposed model captures the trend of the official confirmed cases before and after the lockdown. We show that the estimated number of cases depends strongly on the initial dates of the local outbreak onset and the number of imported cases before the lockdown. Our estimations indicate that the population has not reached the level of herd immunization necessary to prevent future outbreaks. While the low prevalence, in comparison to mainland Spain, has prevented the saturation of the health system, this low prevalence translates into low immunization rates, therefore facilitating the propagation of new outbreaks that could lead to secondary waves of COVID-19 in the region. These findings warn about scenarios regarding after-lockdown-policies and the risk of second outbreaks, emphasize the need for widespread testing, and could potentially be extrapolated to other insular and continental regions.

One hallmark of the East African cichlid radiations is the rapid evolution of reproductive isolation that is robust to full sympatry of many closely related species. Theory predicts that species persistence and speciation in sympatry with gene flow are facilitated if loci of large effect or physical linkage (or pleiotropy) underlie traits involved in reproductive isolation. Here, we investigate the genetic architecture of a key trait involved in behavioural isolation, male nuptial coloration, by crossing two sister species pairs of Lake Victoria cichlids of the genus Pundamilia and mapping nuptial coloration in the F2 hybrids. One is a young sympatric species pair, representative of an axis of colour motif differentiation, red-dorsum versus blue, that is highly recurrent in closely related sympatric species. The other is a species pair representative of colour motifs, red-chest versus blue, that are common in allopatric but uncommon in sympatric closely related species. We find significant quantitative trait loci (QTLs) with moderate to large effects (some overlapping) for red and yellow in the sympatric red-dorsum × blue cross, whereas we find no significant QTLs in the non-sympatric red-chest × blue cross. These findings are consistent with theory predicting that large effect loci or linkage/pleiotropy underlying mating trait differentiation could facilitate speciation and species persistence with gene flow in sympatry.

The East African cichlid radiations are characterized by repeated and rapid diversification into many distinct species with different ecological specializations and by a history of hybridization events between nonsister species. Such hybridization might provide important fuel for adaptive radiation. Interspecific hybrids can have extreme trait values or novel trait combinations and such transgressive phenotypes may allow some hybrids to explore ecological niches neither of the parental species could tap into. Here, we investigate the potential of second-generation (F2) hybrids between two generalist cichlid species from Lake Malawi to exploit a resource neither parental species is specialized on: feeding by sifting sand. Some of the F2 hybrids phenotypically resembled fish of species that are specialized on sand sifting. We combined experimental behavioral and morphometric approaches to test whether the F2 hybrids are transgressive in both morphology and behavior related to sand sifting. We then performed a quantitative trait loci (QTL) analysis using RADseq markers to investigate the genetic architecture of morphological and behavioral traits. We show that transgression is present in several morphological traits, that novel trait combinations occur, and we observe transgressive trait values in sand sifting behavior in some of the F2 hybrids. Moreover, we find QTLs for morphology and for sand sifting behavior, suggesting the existence of some loci with moderate to large effects. We demonstrate that hybridization has the potential to rapidly generate novel and ecologically relevant phenotypes that may be suited to a niche neither of the parental species occupies. Interspecific hybridization may thereby contribute to the rapid generation of ecological diversity in cichlid radiations.

Adaptive radiation plays a fundamental role in our understanding of the evolutionary process. However, the concept has provoked strong and differing opinions concerning its definition and nature among researchers studying a wide diversity of systems. Here, we take a broad view of what constitutes an adaptive radiation, and seek to find commonalities among disparate examples, ranging from plants to invertebrate and vertebrate animals, and remote islands to lakes and continents, to better understand processes shared across adaptive radiations. We surveyed many groups to evaluate factors considered important in a large variety of species radiations. In each of these studies, ecological opportunity of some form is identified as a prerequisite for adaptive radiation. However, evolvability, which can be enhanced by hybridization between distantly related species, may play a role in seeding entire radiations. Within radiations, the processes that lead to speciation depend largely on (1) whether the primary drivers of ecological shifts are (a) external to the membership of the radiation itself (mostly divergent or disruptive ecological selection) or (b) due to competition within the radiation membership (interactions among members) subsequent to reproductive isolation in similar environments, and (2) the extent and timing of admixture. These differences translate into different patterns of species accumulation and subsequent patterns of diversity across an adaptive radiation. Adaptive radiations occur in an extraordinary diversity of different ways, and continue to provide rich data for a better understanding of the diversification of life.

In recent years, due to an increased need for non-intrusive sampling techniques, hydroacoustics has attracted attention in fishery science and management. Efforts to promote standardisation are increasing the accuracy, efficiency, and comparability of this method. The European Water Framework Directive and the Standard Operating Procedures for Fisheries Hydroacoustic Surveys in North American Great Lakes has recommended that surveys be conducted at night. At night, fish usually disperse in the water column, thus allowing for single echo detection and subsequent accurate fish size estimation, while day-time schooling behaviour hampers the estimation of fish size. However, sampling during the day would often be safer and cheaper. This study analyses how fisheries hydroacoustic results differ between day-time and night-time surveys, using data from 14 natural temperate lakes of various size. Data collected during the day and night at two depth layers linked to thermal stratification were compared in terms of acoustic scattering strength, target strength, and biomass estimates. The results showed a significant correlation between day-time and night-time estimates, though biomass in the upper layer was biased for day-time surveys, mainly due to incorrect fish size estimates resulting from rare single echo detections and schooling behaviour. Biomass estimates for the lower depth layer did not significantly differ between the two diel periods. Thus, this study confirms that hydroacoustic sampling in temperate lakes should be performed at night for accurate fish stock biomass estimates.

Parasites may have strong eco-evolutionary interactions with their hosts. Consequently, they may contribute to host diversification. The radiation of cichlid fish in Lake Victoria provides a good model to study the role of parasites in the early stages of speciation. We investigated patterns of macroparasite infection in a community of 17 sympatric cichlids from a recent radiation and 2 older species from 2 nonradiating lineages, to explore the opportunity for parasite-mediated speciation. Host species had different parasite infection profiles, which were only partially explained by ecological factors (diet, water depth). This may indicate that differences in infection are not simply the result of differences in exposure, but that hosts evolved species-specific resistance, consistent with parasite-mediated divergent selection. Infection was similar between sampling years, indicating that the direction of parasite-mediated selection is stable through time. We morphologically identified 6 Cichlidogyrus species, a gill parasite that is considered a good candidate for driving parasite-mediated speciation, because it is host species-specific and has radiated elsewhere in Africa. Species composition of Cichlidogyrus infection was similar among the most closely related host species (members of the Lake Victoria radiation), but two more distantly related species (belonging to nonradiating sister lineages) showed distinct infection profiles. This is inconsistent with a role for Cichlidogyrus in the early stages of divergence. To conclude, we find significant interspecific variation in parasite infection profiles, which is temporally consistent. We found no evidence that Cichlidogyrus-mediated selection contributes to the early stages of speciation. Instead, our findings indicate that species differences in infection accumulate after speciation.

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.

Patterns of animal migration and the ecological forces that shape them have been studied for centuries. Yet ecological impacts caused by the migration, such as altered predator–prey interactions and effects on community structure, remain poorly understood. This is to a large extent due to the scarcity of naturally replicated migration systems with negative controls, that is, ecosystems without migration. In this study, we tested whether partial migration of certain species within the overall prey community affects foraging ecology of top predators and thereby alters energy pathways in food webs. We carried out the study in independent replicated freshwater lake systems, four with and four without opportunity for prey migration. Specifically, we compared predator foraging mode in lakes where cyprinid prey fish perform seasonal partial migrations into connected streams with lakes lacking migratory opportunities for prey fish. We found clear seasonal bottom-up effects of prey migration on predators, including changes in size structure and total biomass of ingested prey, size-specific changes in littoral versus pelagic origin of diet, and a higher degree of feast-and-famine for predators in systems with migratory prey. Our analyses further showed that partially migratory prey species constitute a larger part of the prey community in systems that allow migration. Hence, prey migrations have important implications for predator foraging ecology and may cause seasonal shifts in the importance of their supporting energy pathways. We suggest that such bottom-up effects of partial migration may be a widespread phenomenon both in aquatic and in terrestrial ecosystems.

As is common in biological invasions, the rate at which cane toads (Rhinella marina) have spread across tropical Australia has accelerated through time. Individuals at the invasion front travel further than range-core conspecifics and exhibit distinctive morphologies that may facilitate rapid dispersal. However, the links between these morphological changes and locomotor performance have not been clearly documented. We used raceway trials and high-speed videography to document locomotor traits (e.g. hop distances, heights, velocities, and angles of take-off and landing) of toads from range-core and invasion-front populations. Locomotor performance varied geographically, and this variation in performance was linked to morphological features that have evolved during the toads' Australian invasion. Geographical variation in morphology and locomotor ability was evident not only in wild-caught animals, but also in individuals that had been raised under standardized conditions in captivity. Our data thus support the hypothesis that the cane toad's invasion across Australia has generated rapid evolutionary shifts in dispersal-relevant performance traits, and that these differences in performance are linked to concurrent shifts in morphological traits.

Objectives: The aim of the present study was to clarify the association between the degree of development of pregnancy parturition scars (PPSs) and the total number of pregnancies and parturitions (TNPPs) on the basis of new identification standards for PPS in the preauricular area.
Materials and Methods: Preauricular grooves were macroscopically observed on the pelves of 103 early modern males and 295 females (62 early modern females; 233 present‐day females). Three categories of PPS in the preauricular area were defined. The association between the degree of development of PPS in the preauricular area and the TNPP was analyzed in 90 present‐day females with detailed lifetime data.
Results: PPS could not estimate the exact TNPP. However, it was shown that no PPS indicated no TNPP, weak PPS indicated a lower TNPP, and developed PPS indicated a higher TNPP.
Discussion: Even though the possibility remains that some PPS indicate no TNPP, the results showed that the percentage of each PPS category indicated fertility in the population, suggesting that the strength of the association between the degree of development of PPS and the TNPP was affected by the classification system, the reliability of lifetime data, and the statistical methods used for analysis.

Identifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced-representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyika's two sardine species, Limnothrissa miodon and Stolothrissa tanganicae. Samples of these ecologically and economically important species were collected across the length of Lake Tanganyika, as well as from nearby Lake Kivu, where L. miodon was introduced in 1959. Our results reveal differentiation within both S. tanganicae and L. miodon that is not explained by geography. Instead, this genetic differentiation is due to the presence of large sex-specific regions in the genomes of both species, but involving different polymorphic sites in each species. Our results therefore indicate rapidly evolving XY sex determination in the two species. Additionally, we found evidence of a large chromosomal rearrangement in L. miodon, creating two homokaryotypes and one heterokaryotype. We found all karyotypes throughout Lake Tanganyika, but the frequencies vary along a north–south gradient and differ substantially in the introduced Lake Kivu population. We do not find evidence for significant isolation by distance, even over the hundreds of kilometres covered by our sampling, but we do find shallow population structure.

Adaptive radiations (ARs) frequently show remarkable repeatability where single lineages undergo multiple independent episodes of AR in distant places and long-separate time points. Genetic variation generated through hybridization between distantly related lineages can promote AR. This mechanism, however, requires rare coincidence in space and time between a hybridization event and opening of ecological opportunity, because hybridization generates large genetic variation only locally and it will persist only for a short period. Hence, hybridization seems unlikely to explain recurrent AR in the same lineage. Contrary to these expectations, our evolutionary computer simulations demonstrate that admixture variation can geographically spread and persist for long periods if the hybrid population becomes separated into isolated sub-lineages. Subsequent secondary hybridization of some of these can reestablish genetic polymorphisms from the ancestral hybridization in places far from the birthplace of the hybrid clade and long after the ancestral hybridization event. Consequently, simulations revealed conditions where exceptional genetic variation, once generated through a rare hybridization event, can facilitate multiple ARs exploiting ecological opportunities available at distant points in time and space.

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.

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.

Speciation rates vary considerably among lineages, and our understanding of what drives the rapid succession of speciation events within young adaptive radiations remains incomplete. The cichlid fish family provides a notable example of such variation, with many slowly speciating lineages as well as several exceptionally large and rapid radiations. Here, by reconstructing a large phylogeny of all currently described cichlid species, we show that explosive speciation is solely concentrated in species flocks of several large young lakes. Increases in the speciation rate are associated with the absence of top predators; however, this does not sufficiently explain explosive speciation. Across lake radiations, we observe a positive relationship between the speciation rate and enrichment of large insertion or deletion polymorphisms. Assembly of 100 cichlid genomes within the most rapidly speciating cichlid radiation, which is found in Lake Victoria, reveals exceptional 'genomic potential' - hundreds of ancient haplotypes bear insertion or deletion polymorphisms, many of which are associated with specific ecologies and shared with ecologically similar species from other older radiations elsewhere in Africa. Network analysis reveals fundamentally non-treelike evolution through recombining old haplotypes, and the origins of ecological guilds are concentrated early in the radiation. Our results suggest that the combination of ecological opportunity, sexual selection and exceptional genomic potential is the key to understanding explosive adaptive radiation.

Simpson's fossil-record inspired model of 'adaptive zones' proposes that evolution is dominated by small fluctuations within adaptive zones, occasionally punctuated by larger shifts between zones. This model can help explain why the process of population divergence often results in weak or moderate reproductive isolation (RI), rather than strong RI and distinct species. Applied to the speciation process, the adaptive zones hypothesis makes two inter-related predictions: (i) large shifts between zones are relatively rare, (ii) when large shifts do occur they generate stronger RI than shifts within zones. Here, we use ecological, phylogenetic and behavioural data to test these predictions in Timema stick insects. We show that host use in Timema is dominated by moderate shifts within the systematic divisions of flowering plants and conifers, with only a few extreme shifts between these divisions. However, when extreme shifts occur, they generate greater RI than do more moderate shifts. Our results support the adaptive zones model, and suggest that the net contribution of ecological shifts to diversification is dependent on both their magnitude and frequency. We discuss the generality of our findings in the light of emerging evidence from diverse taxa that the evolution of RI is not always the only factor determining the origin of species diversity.
This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

1. Different migratory species have evolved distinct migratory characteristics that improve fitness in their particular ecological niches. However, when such species hybridize, migratory traits from parental species can combine maladaptively and cause hybrids to fall between parental fitness peaks, with potential consequences for hybrid viability and species integrity.
2. Here, we take advantage of a natural cross‐breeding incident to study migratory behaviour in naturally occurring hybrids as well as in their parental species and explore links between migratory traits and predation risk.
3. To achieve this, we used electronic tags and passive telemetry to record detailed individual migration patterns (timing and number of migratory trips) in two common freshwater fish species, roach Rutilus rutilus, common bream Abramis brama as well as their hybrids. Next, we scanned for tags regurgitated by a key avian predator (great cormorant Phalacrocorax carbo) at nearby roosting sites, allowing us to directly link migratory behaviour to predation risk in the wild.
4. We found that hybrid individuals showed a higher number of short, multi‐trip movements between lake and stream habitats as compared to both parental species. The mean date of first lake departure differed between bream and roach by more than 10 days, while hybrids departed in two distinct peaks that overlapped with the parental species' averages. Moreover, the probability of cormorant predation increased with multi‐trip movement frequency across species and was higher for hybrids.
5. Our data provide novel insights into hybrid viability, with links to predator‐mediated ecological selection. Increased exposure to predators via maladaptive migratory behaviour reduces hybrid survival and can thereby reinforce species integrity.

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.

The alpha taxonomy of the endemic whitefish of lakes Brienz and Thun, Switzerland, is revised. We evaluate the status of seven known species: Coregonus steinmanni sp. nov., Coregonus profundus sp. nov. and Coregonus acrinasus sp. nov. are endemic to Lake Thun; Coregonus Brienzii sp. nov. is endemic to Lake Brienz; and C. alpinus, C. albellus, and C. fatioi from lakes Brienz and Thun are redescribed. One of these species, C. alpinus, is revised, since the lectotype for this species is incongruent with the species description given by Kottelat (1997) and Kottelat and Freyhof (2007). The name C. alpinus is thus retained for the lectotype designated by Kottelat (1997) and a new description of this taxon provided. For the species otherwise described by Kottelat (1997) and Kottelat and Freyhof (2007) as C. alpinus the new name C. profundus is designated. Coregonus acrinasus is genetically partially of allochthonous origin, closely related to the radiation of Lake Constance, and we therefore compare it to all recognized species of Lake Constance, C. wartmanni, C. macrophthalmus, C. arenicolus, and C. gutturosus.

Passive integrated transponder (PIT)‐tagging is commonly used in behavioural studies of fish, although long‐term evaluations of effects from tagging under natural conditions are scarce. We PIT‐tagged common bream Abramis brama, European perch Perca fluviatilis, pike Esox lucius and roach Rutilus rutilus, released them in their lakes of origin and recaptured them after 103-3269 days. Overall, tagged fish did not differ in condition from non‐tagged fish, except for small R. rutilus that had a lower length‐specific body mass in one lake in 1 year. We conclude that PIT‐tagging in general has negligible long‐term effects on fish condition.

The harbour porpoise Phocoena phocoena is a small marine predator with a high conservation status in Europe and the USA. To protect the species effectively, it is crucial to understand its movement patterns and how the distribution of intensively used foraging areas can be predicted from environmental conditions. Here, we investigated the influence of both static and dynamic environmental conditions on large-scale harbour porpoise movements in the North Sea. We used long-term movement data from 57 individuals tracked during 1999-2017 in a state-space model to estimate the underlying behavioural states, i.e. whether animals used area-restricted or directed movements. Subsequently, we assessed whether the probability of using area-restricted movements was related to environmental conditions using a generalized linear mixed model. Harbour porpoises were more likely to use area-restricted movements in areas with low salinity levels, relatively high chlorophyll a concentrations and low current velocity, and in areas with steep bottom slopes, suggesting that such areas are important foraging grounds for porpoises. Our study identifies environmental parameters of relevance for predicting harbour porpoise foraging hot spots over space and time in a dynamic system. The study illustrates how movement patterns and data on environmental conditions can be combined, which is valuable to the conservation of marine mammals.

1. Most carnivores undergo diet shift from smaller to larger prey items during ontogeny. The trophic relationship between a growing carnivore and larger prey is representative of a size-structured predator–prey interaction. The strength of this interaction is, in part, determined by the recruitment of individuals from smaller predatory size classes into larger predatory size classes. Therefore, it is interesting to investigate how larger prey alter the recruitment of smaller predator size classes into larger predator size classes, since this can affect their own future predation risk.
2. Past empirical studies have exclusively documented that large prey reduce predator recruitment by decreasing growth and/or survival of the smaller predators. In this study, we provide empirical evidence of the contrasting pattern: large prey enhance the recruitment of smaller predators into larger predators even though they increase cannibalism mortality of the smaller predators. We have done this here by studying the trophic interaction between predatory salamander larvae Hynobius retardatus and the frog tadpoles Rana pirica that represent their large prey.
3. In a field experiment in which salamander hatchlings were exposed to the presence or absence of large frog tadpoles, we found that more giant salamanders emerged in the presence of frog tadpoles than in their absence. Reassignment of frog tadpoles (to both treatments) in the subsequent experimental period showed that the enhanced emergence of giant salamanders in the presence of frog tadpoles leads to the intensification of salamander predation on the frog tadpoles.
4. In an additional laboratory experiment, to better understand the underlying mechanisms, we manipulated both the presence of frog tadpoles and the occurrence of cannibalism between salamander hatchlings. This experiment revealed that frog tadpoles intensify the cannibalism of salamander larvae during their hatchling stage, thus allowing more salamander larvae to become large-sized predators.
5. Our results suggest that frog tadpoles can inadvertently intensify their own future predation risk by intensifying cannibalistic interactions among predatory salamander hatchlings, thereby enhancing the degree of predator recruitment to a larger size class. Hence, large prey can enhance the recruitment of individuals from small predator size classes into larger predator size classes.

The types of mutations affecting adaptation in the wild are only beginning to be understood. In particular, whether structural changes shape adaptation by suppressing recombination or by creating new mutations is unresolved. Here, we show that multiple linked but recombining loci underlie cryptic color morphs of Timema chumash stick insects. In a related species, these loci are found in a region of suppressed recombination, forming a supergene. However, in seven species of Timema, we found that a megabase-size "supermutation" has deleted color loci in green morphs. Moreover, we found that balancing selection likely contributes more to maintaining this mutation than does introgression. Our results show how suppressed recombination and large-scale mutation can help to package gene complexes into discrete units of diversity such as morphs, ecotypes, or species.

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.

Reintroduction, stocking and translocation of freshwater fish are of growing concern given their importance for biodiversity conservation and ecosystem functioning. For successful management and stocking programmes, it is essential to incorporate genetics-based approaches. The nase (Chondrostoma nasus) constituted one of the most common fish species in European rivers. Its highly specialised and migratory nature exposed the species to human pressures, and thus, promoted its decline. Current knowledge of the genetic structure of C. nasus is considerably limited for Europe as a whole and for Germany specifically. To overcome this lack of information we present original data on C. nasus from different tributaries of the River Rhine. We analysed nine microsatellite markers and mtDNA Cytochrome b sequences to assess the distribution of genetic diversity and structure of this species across the study area. With the exception of the Lake Constance/Alpine Rhine population, C. nasus exhibited high gene flow within the Rhine system, and therefore, limited geographical genetic differences between populations where migration is not prevented by human intervention. The present study provides new insights into the levels of genetic variability of C. nasus in the Rhine system, providing useful information for guiding reintroduction and stocking programmes. Population genetic information will improve future preservation and management of this valuable freshwater fish species in Germany and beyond.

La réintroduction, l'empoissonnement et le transfert de poissons d'eau douce sont de plus en plus préoccupants compte tenu de leur importance pour la conservation de la biodiversité et le fonctionnement des écosystèmes. Pour que les programmes de gestion et de repeuplement soient efficaces, il est essentiel d'intégrer des approches fondées sur la génétique. Le hotu (Chondrostoma nasus) constitue l'une des espèces de poissons les plus communes dans les rivières européennes. Sa biologie hautement spécialisée et migratoire a exposé l'espèce aux pressions humaines, et a donc favorisé son déclin. Les connaissances actuelles sur la structure génétique de C. nasus sont considérablement limitées pour l'Europe dans son ensemble et pour l'Allemagne en particulier. Pour pallier ce manque d'informations, nous présentons des données originales sur C. nasus provenant de différents affluents du Rhin. Nous avons analysé neuf marqueurs microsatellites et des séquences d'ADNmt du cytochrome b pour évaluer la répartition de la diversité génétique et la structure de cette espèce dans la zone d'étude. À l'exception de la population du lac de Constance et du Rhin alpin, C. nasus présentait un flux génétique élevé dans le système rhénan et, par conséquent, des différences génétiques géographiques limitées entre les populations où la migration n'est pas empêchée par l'intervention humaine. La présente étude apporte de nouvelles connaissances sur les niveaux de variabilité génétique de C. nasus dans le système rhénan, fournissant des informations utiles pour orienter les programmes de réintroduction et d'empoissonnement. L'information génétique des populations permettra d'améliorer la préservation et la gestion futures de cette précieuse espèce de poisson d'eau douce en Allemagne et au-delà.

Ecological speciation is facilitated when divergent adaptation has direct effects on selective mating. Divergent sensory adaptation could generate such direct effects, by mediating both ecological performance and mate selection. In aquatic environments, light attenuation creates distinct photic environments, generating divergent selection on visual systems. Consequently, divergent sensory drive has been implicated in the diversification of several fish species. Here, we experimentally test whether divergent visual adaptation explains the divergence of mate preferences in Haplochromine cichlids. Blue and red Pundamilia co‐occur across south‐eastern Lake Victoria. They inhabit different photic conditions and have distinct visual system properties. Previously, we documented that rearing fish under different light conditions influences female preference for blue versus red males. Here, we examine to what extent variation in female mate preference can be explained by variation in visual system properties, testing the causal link between visual perception and preference. We find that our experimental light manipulations influence opsin expression, suggesting a potential role for phenotypic plasticity in optimizing visual performance. However, variation in opsin expression does not explain species differences in female preference. Instead, female preference covaries with allelic variation in the long‐wavelength‐sensitive opsin gene (LWS), when assessed under broad‐spectrum light. Taken together, our study presents evidence for environmental plasticity in opsin expression and confirms the important role of colour perception in shaping female mate preferences in Pundamilia. However, it does not constitute unequivocal evidence for the direct effects of visual adaptation on assortative mating.

Although metamorphosis is widespread in the animal kingdom, several species have evolved life-cycle modifications to avoid complete metamorphosis. Some species, for example, many salamanders and newts, have deleted the adult stage via a process called paedomorphosis. Others, for example, some frog species and marine invertebrates, no longer have a distinct larval stage and reach maturation via direct development. Here we study which ecological conditions can lead to the loss of metamorphosis via the evolution of direct development. To do so, we use size-structured consumer-resource models in conjunction with the adaptive-dynamics approach. In case the larval habitat deteriorates, individuals will produce larger offspring and in concert accelerate metamorphosis. Although this leads to the evolutionary transition from metamorphosis to direct development when the adult habitat is highly favorable, the population will go extinct in case the adult habitat does not provide sufficient food to escape metamorphosis. With a phylogenetic approach we furthermore show that among amphibians the transition of metamorphosis to direct development is indeed, in line with model predictions, conditional on and preceded by the evolution of larger egg sizes.