Human impacts on the community composition of Swiss rivers
For effective river management it is important to understand the role of different human impacts and environmental stressors on the structure and function of river ecosystems. In this project we want to explore Swiss monitoring data to identify the cause-effect relationship between anthropogenic stressors, e.g. pollution from agriculture and urban sources, habitat degradation, hydropower, and the community composition of macroinvertebrates and fish. We will take into account environmental variables like height, temperature, hydromorphological conditions, and dispersal limitation that influence the occurrence of organisms. We will analyze different community descriptors as response variables like taxonomic composition at different taxonomic levels, trait composition linking to community function, food web-network-properties to identify most sensitive indicators. We will use different statistical approaches.
The project consists of two main tasks:
The Identification of human impacts on macroinvertebrates and fish using different methods from multivariate statistics to identify influence factors on different community descriptors;
detailed food web analyzes for selected sites to combine structural and functional aspects to find out how food web properties and feeding habits of fish and macroinvertebrates are influenced by environmental conditions and human impacts.
The overall goal of this project is to derive guidance for the identification of human impacts on the aquatic communities of Swiss streams.
array(4 items)0 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=23436, pid=124)originalId => protected23436 (integer)
authors => protected'Caradima, B.; Scheidegger, A.; Brodersen, J.; Schuwirth,  ;N.' (79 chars)
title => protected'Bridging mechanistic conceptual models and statistical species distribution models of riverine fish' (99 chars)
journal => protected'Ecological Modelling' (20 chars)
year => protected2021 (integer)
volume => protected457 (integer)
issue => protected'' (0 chars)
startpage => protected'109680 (15 pp.)' (15 chars)
otherpage => protected'' (0 chars)
categories => protected'' (0 chars)
description => protected'Statistical species distribution models (SDMs) are widely used to quantify h ow taxa respond to environmental conditions and to predict their distributio n. However, the application of SDMs to freshwater fish taxa is complicated b y the active dispersal of fish taxa through river networks, and the species- and habitat-dependent observation process (i.e., the sampling method and ef fort) required to accurately sample their distributions. Many studies have a pplied presence-absence models (PAMs) to fish taxa, while more recent studie s have proposed zero-inflated models (ZIMs) to account for count observation s with many zeroes. However, relatively few studies have incorporated the ob servation process into the model structure, which would facilitate the combi nation of data from various monitoring programs that differ in their observa tion process. In this study, we use conceptual models to identify potentiall y dominant natural and anthropogenic environmental conditions with a direct, mechanistic effect on the distributions of freshwater fish taxa in Switzerl and, a region with a large range of environmental conditions, from alpine st reams that are mainly affected by hydromorphological alterations to lowland streams in densely populated areas with intensive agricultural land use. Mor eover, numerous barriers impede fish migration along the entire river networ k. Using combined data from two fish monitoring programs in Switzerland, we applied an exhaustive cross-validation procedure to select a set of environm ental variables with the highest (out-of-sample) predictive performance for the PAM and ZIM for fish density (individuals/m<sup>2</sup>) of the seven mo st prevalent fish taxa (<em>Salmo</em><em> spp., </em><em>Cottus</em><em> sp p., Squalius spp., Barbatula spp., </em><em>Barbus</em><em> spp., </em><em>P hoxinus</em><em> spp., Gobio spp.</em>). We used these variables to develop a PAM and ZIM for each taxon that accounts for differences in sampling metho ds and sampling effort. ...' (3464 chars)
serialnumber => protected'0304-3800' (9 chars)
doi => protected'10.1016/j.ecolmodel.2021.109680' (31 chars)
uid => protected23436 (integer)
_localizedUid => protected23436 (integer)modified_languageUid => protectedNULL
_versionedUid => protected23436 (integer)modifiedpid => protected124 (integer)1 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=21111, pid=124)originalId => protected21111 (integer)
authors => protected'Caradima, B.; Reichert, P.; Schuwirth, N.' (56 chars)
title => protected'Effects of site selection and taxonomic resolution on the inference of strea m invertebrate responses to environmental conditions' (128 chars)
journal => protected'Freshwater Science' (18 chars)
year => protected2020 (integer)
volume => protected39 (integer)
issue => protected'3' (1 chars)
startpage => protected'415' (3 chars)
otherpage => protected'432' (3 chars)
categories => protected'benthic macroinvertebrates; indicator species; stream biomonitoring; stream biomonitoring; multiple stressors; hierarchical species distribution models' (151 chars)
description => protected'Key decisions in the design of biomonitoring programs include taxonomic reso lution, geographic extent, and site selection, each of which can affect our ability to infer human impacts on biodiversity from biomonitoring data. Thes e decisions are constrained by monitoring goals and budget limitations, whic h may require trade-offs between them. In this study, we use species distrib ution models (SDMs) to assess the effects of key decisions in biomonitoring design on our ability to infer the effects of natural and anthropogenic envi ronmental conditions on the occurrence of benthic macroinvertebrates in stre ams. We compared 4 datasets that differ in their site-selection strategy, ge ographic extent, and taxonomic resolution using data from Swiss federal and cantonal biomonitoring programs. We used individual SDMs with 3-fold cross v alidation to identify the environmental variables that best predict the prob ability of taxa occurrence across the datasets. We then used a hierarchical multi-species distribution model (hmSDM) to identify how key aspects of biom onitoring design influence the relative importance of the selected explanato ry (predictor) variables in the model as well as the model’s predictive pe rformance. The relative importance of the explanatory variables in the hmSDM s was lowest for the dataset with a grid-based site-selection approach and f amily-level resolution. An increase in predictive performance was achieved b y either using a species-level taxonomic resolution for Ephemeroptera, Pleco ptera, and Trichoptera or by combining different biomonitoring programs at t he family level to increase the number of sites and improve the coverage of environmental conditions. Selecting monitoring sites to provide a good cover age of environmental conditions, while also targeting sites with rare combin ations of environmental conditions, could further improve biomonitoring prog ram data. Models based on finer taxonomic resolution revealed that widesprea d families consist of sp...' (2578 chars)
serialnumber => protected'2161-9549' (9 chars)
doi => protected'10.1086/709024' (14 chars)
uid => protected21111 (integer)
_localizedUid => protected21111 (integer)modified_languageUid => protectedNULL
_versionedUid => protected21111 (integer)modifiedpid => protected124 (integer)2 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=19693, pid=124)originalId => protected19693 (integer)
authors => protected'Schuwirth, N.; Caradima, B.; Schindler Wildhaber, Y.; Sarbach -Remund, N.' (92 chars)
title => protected'Analyse schweizweiter Makrozoobenthosdaten. Erkenntnisse über anthropogene Einflüsse und Monitoring-Design' (108 chars)
journal => protected'Aqua & Gas' (10 chars)
year => protected2019 (integer)
volume => protected99 (integer)
issue => protected'12' (2 chars)
startpage => protected'55' (2 chars)
otherpage => protected'61' (2 chars)
categories => protected'' (0 chars)
description => protected'Mit einem statistischen Modell wurden schweizweite Monitoringdaten über die Zusammensetzung von Makrozoobenthosgemeinschaften in Schweizer Fliessgewäs sern ausgewertet. Temperatur, Landwirtschaft und Hydromorphologie wurden dab ei als wichtige Einflussfaktoren im Modell identifiziert. Arten aus der glei chen Familie reagieren in vielen Fällen unterschiedlich auf natürliche und menschliche Umwelteinflüsse. Neben der taxonomischen Auflösung wirkt sich auch die Stellenauswahl auf die Aussagekraft der Resultate aus.' (520 chars)
serialnumber => protected'2235-5197' (9 chars)
doi => protected'' (0 chars)
uid => protected19693 (integer)
_localizedUid => protected19693 (integer)modified_languageUid => protectedNULL
_versionedUid => protected19693 (integer)modifiedpid => protected124 (integer)3 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=19054, pid=124)originalId => protected19054 (integer)
authors => protected'Caradima, B.; Schuwirth, N.; Reichert, P.' (56 chars)
title => protected'From individual to joint species distribution models: a comparison of model complexity and predictive performance' (114 chars)
journal => protected'Journal of Biogeography' (23 chars)
year => protected2019 (integer)
volume => protected46 (integer)
issue => protected'10' (2 chars)
startpage => protected'2260' (4 chars)
otherpage => protected'2274' (4 chars)
categories => protected'benthic macroinvertebrates; biodiversity; hierarchical multispecies models; joint models; predictive modelling; richness; species distribution models; s tacked individual models' (176 chars)
description => protected'<em>Aim:</em> Species distribution models (SDMs) are widely used to study ge ographic distributions of taxa in response to natural and anthropogenic envi ronmental conditions. For a community, common approaches include fitting ind ividual SDMs (iSDMs) to all taxa or directly modelling community properties such as richness. However, the parameters of iSDMs are difficult to identify for rare taxa, and community properties do not reveal taxon‐specific resp onses. Individual models can be combined into a hierarchical multispecies di stribution model (mSDM) that constrains taxon‐specific parameters accordin g to overarching community parameters, or a joint model (jSDM) in which inte rdependencies between taxa are jointly inferred. We compare how individual, hierarchical multispecies and joint SDMs differ in quality of fit, explanato ry power and predictive performance, and analyse how these properties depend on the prevalence of taxa.<br /><em>Taxa:</em> Presence–absence observati ons of 245 benthic macroinvertebrate taxa identified at a mixed taxonomic re solution.<br /><em>Location:</em> Four hundred and ninety‐two sites in riv ers throughout Switzerland.<br /><em>Methods:</em> Individual, hierarchical and joint hierarchical generalized linear models (GLM) were developed for al l taxa. Parameters were estimated using maximum likelihood estimation or Bay esian inference with Hamiltonian Markov chain Monte Carlo simulations. Predi ctive performance was assessed with cross‐validation. In addition, the pre dicted family and species richness of the models was compared with a GLM for richness.<br /> Results: Individual models show a slightly higher quality o f fit largely due to overfitting for rare taxa. The mSDM achieves a similar quality of fit and explanatory power, mitigates overfitting for rare taxa an d considerably improves predictive performance over the whole community. The joint models further improve the quality of fit, but decrease predictive pe rformance and increase p...' (2371 chars)
serialnumber => protected'0305-0270' (9 chars)
doi => protected'10.1111/jbi.13668' (17 chars)
uid => protected19054 (integer)
_localizedUid => protected19054 (integer)modified_languageUid => protectedNULL
_versionedUid => protected19054 (integer)modifiedpid => protected124 (integer)
Bridging mechanistic conceptual models and statistical species distribution models of riverine fish
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.
Caradima, B.; Scheidegger, A.; Brodersen, J.; Schuwirth, N. (2021) Bridging mechanistic conceptual models and statistical species distribution models of riverine fish, Ecological Modelling, 457, 109680 (15 pp.), doi:10.1016/j.ecolmodel.2021.109680, Institutional Repository
Effects of site selection and taxonomic resolution on the inference of stream invertebrate responses to environmental conditions
Key decisions in the design of biomonitoring programs include taxonomic resolution, geographic extent, and site selection, each of which can affect our ability to infer human impacts on biodiversity from biomonitoring data. These decisions are constrained by monitoring goals and budget limitations, which may require trade-offs between them. In this study, we use species distribution models (SDMs) to assess the effects of key decisions in biomonitoring design on our ability to infer the effects of natural and anthropogenic environmental conditions on the occurrence of benthic macroinvertebrates in streams. We compared 4 datasets that differ in their site-selection strategy, geographic extent, and taxonomic resolution using data from Swiss federal and cantonal biomonitoring programs. We used individual SDMs with 3-fold cross validation to identify the environmental variables that best predict the probability of taxa occurrence across the datasets. We then used a hierarchical multi-species distribution model (hmSDM) to identify how key aspects of biomonitoring design influence the relative importance of the selected explanatory (predictor) variables in the model as well as the model’s predictive performance. The relative importance of the explanatory variables in the hmSDMs was lowest for the dataset with a grid-based site-selection approach and family-level resolution. An increase in predictive performance was achieved by either using a species-level taxonomic resolution for Ephemeroptera, Plecoptera, and Trichoptera or by combining different biomonitoring programs at the family level to increase the number of sites and improve the coverage of environmental conditions. Selecting monitoring sites to provide a good coverage of environmental conditions, while also targeting sites with rare combinations of environmental conditions, could further improve biomonitoring program data. Models based on finer taxonomic resolution revealed that widespread families consist of species and genera with different and stronger responses to environmental conditions. However, many families include species that are too rare to allow inference of significant responses to environmental conditions. We show that hmSDMs of stream invertebrates can contribute to the selection of specific taxa for identification at finer taxonomic resolution. This strategy could facilitate the standardization and combination of multiple biomonitoring datasets and improve the identifiability of stream invertebrate responses to environmental conditions in biomonitoring programs.
Caradima, B.; Reichert, P.; Schuwirth, N. (2020) Effects of site selection and taxonomic resolution on the inference of stream invertebrate responses to environmental conditions, Freshwater Science, 39(3), 415-432, doi:10.1086/709024, Institutional Repository
Analyse schweizweiter Makrozoobenthosdaten. Erkenntnisse über anthropogene Einflüsse und Monitoring-Design
Mit einem statistischen Modell wurden schweizweite Monitoringdaten über die Zusammensetzung von Makrozoobenthosgemeinschaften in Schweizer Fliessgewässern ausgewertet. Temperatur, Landwirtschaft und Hydromorphologie wurden dabei als wichtige Einflussfaktoren im Modell identifiziert. Arten aus der gleichen Familie reagieren in vielen Fällen unterschiedlich auf natürliche und menschliche Umwelteinflüsse. Neben der taxonomischen Auflösung wirkt sich auch die Stellenauswahl auf die Aussagekraft der Resultate aus.
Schuwirth, N.; Caradima, B.; Schindler Wildhaber, Y.; Sarbach-Remund, N. (2019) Analyse schweizweiter Makrozoobenthosdaten. Erkenntnisse über anthropogene Einflüsse und Monitoring-Design, Aqua & Gas, 99(12), 55-61, Institutional Repository
From individual to joint species distribution models: a comparison of model complexity and predictive performance
Aim: Species distribution models (SDMs) are widely used to study geographic distributions of taxa in response to natural and anthropogenic environmental conditions. For a community, common approaches include fitting individual SDMs (iSDMs) to all taxa or directly modelling community properties such as richness. However, the parameters of iSDMs are difficult to identify for rare taxa, and community properties do not reveal taxon‐specific responses. Individual models can be combined into a hierarchical multispecies distribution model (mSDM) that constrains taxon‐specific parameters according to overarching community parameters, or a joint model (jSDM) in which interdependencies between taxa are jointly inferred. We compare how individual, hierarchical multispecies and joint SDMs differ in quality of fit, explanatory power and predictive performance, and analyse how these properties depend on the prevalence of taxa. Taxa: Presence–absence observations of 245 benthic macroinvertebrate taxa identified at a mixed taxonomic resolution. Location: Four hundred and ninety‐two sites in rivers throughout Switzerland. Methods: Individual, hierarchical and joint hierarchical generalized linear models (GLM) were developed for all taxa. Parameters were estimated using maximum likelihood estimation or Bayesian inference with Hamiltonian Markov chain Monte Carlo simulations. Predictive performance was assessed with cross‐validation. In addition, the predicted family and species richness of the models was compared with a GLM for richness. Results: Individual models show a slightly higher quality of fit largely due to overfitting for rare taxa. The mSDM achieves a similar quality of fit and explanatory power, mitigates overfitting for rare taxa and considerably improves predictive performance over the whole community. The joint models further improve the quality of fit, but decrease predictive performance and increase predictive uncertainty. Main conclusions: We show that even a relatively simple mSDM combines many of the analytical capabilities of iSDMs and improves predictive performance. Increasingly complex mSDMs and jSDMs provide additional analytical possibilities, but depending on the data and research questions, different levels of complexity may be appropriate.
Caradima, B.; Schuwirth, N.; Reichert, P. (2019) From individual to joint species distribution models: a comparison of model complexity and predictive performance, Journal of Biogeography, 46(10), 2260-2274, doi:10.1111/jbi.13668, Institutional Repository
