Skip to main content
U.S. flag

An official website of the United States government

Multi-species modeling of species-rich communities: assessing taxonomic, functional, and morphological diversity and change

Active
By Upper Midwest Environmental Sciences Center September 9, 2024

Joint species distribution models (JSDMs) allow researchers to model responses of large numbers of species to their environment while investigating the role of species traits and phylogenetic relationships in these responses. JSDMs can also estimate species associations (non-random co-occurrence patterns) in a way that accounts for differences in species niches. In this project we are applying existing and custom JSDMs to questions of community assembly, morphological change, and functional ecology across many different taxa and geographic areas. This method allows us to take a more holistic look at complex ecological communities, compared to studies and methods that focus only on one or a few species in isolation. 

This research uses a variety of custom and existing JSDMs. This includes the use of the Hierarchical modeling of species communities (Hmsc) modeling framework (Tikhonov et al. 2020), as well as expanding on a JSDM developed to allow modeling of imperfect detection by Tobler et al. (2019). We have expanded this imperfect detection model to allow for inclusion of detection covariates, species traits, and hierarchical random effects.

These models have been used to answer questions and analyze data collected on multiple taxa in different systems, locations, and species, including;

  • Modeling the consequences of climate change for 77 bird species in the Amazonian rainforest (Jirinec et al. 2021)
  • Quantifying the body size changes of 129 bird species in North and South America (Zimova et al. 2023)
  • Predicting the potential impact of extirpation of rare beetle species on the functional structure of forest beetle communities in northern and central Europe (Burner et al. 2022)
  • Comparing alternative measures of trait-niche relationships in forest beetles (Burner et al. 2023)

Lead investigator, Ryan Burner, leads workshops and co-teaches courses on the use of joint species distribution models. 

We are also currently modeling niches and distributions of floodplain forest birds along the Mississippi River, Himalayan River fish in India, alpine plants in Norway, forest and grassland birds in the central United States and in Uganda, arthropod species in bird diets in Jamaica, and global crop pests.

This work is ongoing and involves collaborators from the U.S. Fish and Wildlife Service, University of Michigan, Michigan Technological University, University of Oslo, Wageningen University, Indian Institute of Science Education and Research Kolkata, University of Helsinki, University of Jyväskylä, Norwegian University of Life Science, Swedish University of Agricultural Science, and the Research Centre in Biodiversity and Genetic Resources at the University of Porto.

Effects of species traits on morphological change through time. From Zimova et al. 2023.
Sources/Usage: Public Domain. View Media Details
Figure showing Bayesian hierarchical model estimates for the effects of species traits (body ‘size’ and generation length, ‘GL’) on rates of change in three bird morphological measurements through time. From Zimova et al. 2023.

References: 

Burner, R. C., Drag, L., Birkemoe, T., Wetherbee, B., Muller, J., Siitonen, J., Snäll T., Skarpaas, O., Potterf, M., Doerfler, I., Gossner, M. M., Schall, P., Weisser, W., & Sverdrup-Thygeson, A. (2022) Functional structure of European forest beetle communities is enhanced by rare species. Biological Conservation. 267(109491) 1-10 https://doi.org/10.1016/j.biocon.2022.109491

Burner, R. C., Stephan, J. G., Drag, L., Potterf, M., Birkemoe, T., Siitonen, J., Müller, J., Ovaskainen, O., Sverdrup-Thygeson, A., & Snäll, T. (2023). Alternative measures of trait-niche relationships: A test of dispersal traits in saproxylic beetles. Ecology and Evolution. 13:e10588 https://doi.org/10.1002/ece3.10588

Jirinec, V., Burner, R. C., Amaral, B. R., Bierregaard Jr. R. O., Fernández-Arellano, G., Hernández-Palma, A., Johnson, E. I., Lovejoy, T. E., Powell, L. L., Rutt, C. L., Wolfe, J. D., & Stouffer, P. C. (2021). Morphological consequences of climate change for resident birds in intact Amazonian rainforest. Science Advances. 7(eabk1743) 1-12 10.1126/sciadv.abk1743

Tikhonov, G., Opedal, Ø.H., Abrego, N., Lehikoinen, A., de Jonge, M.M., Oksanen, J. and Ovaskainen, O. (2020). Joint species distribution modelling with the R‐package Hmsc. Methods in Ecology and Evolution 11(3):442-447

Tobler, M. W., Kéry, M., Hui, F. K. C., Guillera-Arroita, G., Kanaus, P., & Sattler, T. (2019). Joint species distribution models with species correlations and imperfect detection. Ecology. 100(8) 1-14 https://doi.org/10.1002/ecy.2754

Zimova, M., Weeks, B. C., Willard, D. E., Giery, S. T., Jirinec, V., Burner, R. C., & Winger, B. M. (2023). Body size predicts the rate of contemporary morphological change in birds. Proceedings of the National Academy of Sciences (PNAS). 120(20) 1-9 https://doi.org/10.1073/pnas.2206971120

Joint species distribution models (JSDMs) allow researchers to model responses of large numbers of species to their environment while investigating the role of species traits and phylogenetic relationships in these responses. JSDMs can also estimate species associations (non-random co-occurrence patterns) in a way that accounts for differences in species niches. In this project we are applying existing and custom JSDMs to questions of community assembly, morphological change, and functional ecology across many different taxa and geographic areas. This method allows us to take a more holistic look at complex ecological communities, compared to studies and methods that focus only on one or a few species in isolation. 

This research uses a variety of custom and existing JSDMs. This includes the use of the Hierarchical modeling of species communities (Hmsc) modeling framework (Tikhonov et al. 2020), as well as expanding on a JSDM developed to allow modeling of imperfect detection by Tobler et al. (2019). We have expanded this imperfect detection model to allow for inclusion of detection covariates, species traits, and hierarchical random effects.

These models have been used to answer questions and analyze data collected on multiple taxa in different systems, locations, and species, including;

  • Modeling the consequences of climate change for 77 bird species in the Amazonian rainforest (Jirinec et al. 2021)
  • Quantifying the body size changes of 129 bird species in North and South America (Zimova et al. 2023)
  • Predicting the potential impact of extirpation of rare beetle species on the functional structure of forest beetle communities in northern and central Europe (Burner et al. 2022)
  • Comparing alternative measures of trait-niche relationships in forest beetles (Burner et al. 2023)

Lead investigator, Ryan Burner, leads workshops and co-teaches courses on the use of joint species distribution models. 

We are also currently modeling niches and distributions of floodplain forest birds along the Mississippi River, Himalayan River fish in India, alpine plants in Norway, forest and grassland birds in the central United States and in Uganda, arthropod species in bird diets in Jamaica, and global crop pests.

This work is ongoing and involves collaborators from the U.S. Fish and Wildlife Service, University of Michigan, Michigan Technological University, University of Oslo, Wageningen University, Indian Institute of Science Education and Research Kolkata, University of Helsinki, University of Jyväskylä, Norwegian University of Life Science, Swedish University of Agricultural Science, and the Research Centre in Biodiversity and Genetic Resources at the University of Porto.

Effects of species traits on morphological change through time. From Zimova et al. 2023.
Sources/Usage: Public Domain. View Media Details
Figure showing Bayesian hierarchical model estimates for the effects of species traits (body ‘size’ and generation length, ‘GL’) on rates of change in three bird morphological measurements through time. From Zimova et al. 2023.

References: 

Burner, R. C., Drag, L., Birkemoe, T., Wetherbee, B., Muller, J., Siitonen, J., Snäll T., Skarpaas, O., Potterf, M., Doerfler, I., Gossner, M. M., Schall, P., Weisser, W., & Sverdrup-Thygeson, A. (2022) Functional structure of European forest beetle communities is enhanced by rare species. Biological Conservation. 267(109491) 1-10 https://doi.org/10.1016/j.biocon.2022.109491

Burner, R. C., Stephan, J. G., Drag, L., Potterf, M., Birkemoe, T., Siitonen, J., Müller, J., Ovaskainen, O., Sverdrup-Thygeson, A., & Snäll, T. (2023). Alternative measures of trait-niche relationships: A test of dispersal traits in saproxylic beetles. Ecology and Evolution. 13:e10588 https://doi.org/10.1002/ece3.10588

Jirinec, V., Burner, R. C., Amaral, B. R., Bierregaard Jr. R. O., Fernández-Arellano, G., Hernández-Palma, A., Johnson, E. I., Lovejoy, T. E., Powell, L. L., Rutt, C. L., Wolfe, J. D., & Stouffer, P. C. (2021). Morphological consequences of climate change for resident birds in intact Amazonian rainforest. Science Advances. 7(eabk1743) 1-12 10.1126/sciadv.abk1743

Tikhonov, G., Opedal, Ø.H., Abrego, N., Lehikoinen, A., de Jonge, M.M., Oksanen, J. and Ovaskainen, O. (2020). Joint species distribution modelling with the R‐package Hmsc. Methods in Ecology and Evolution 11(3):442-447

Tobler, M. W., Kéry, M., Hui, F. K. C., Guillera-Arroita, G., Kanaus, P., & Sattler, T. (2019). Joint species distribution models with species correlations and imperfect detection. Ecology. 100(8) 1-14 https://doi.org/10.1002/ecy.2754

Zimova, M., Weeks, B. C., Willard, D. E., Giery, S. T., Jirinec, V., Burner, R. C., & Winger, B. M. (2023). Body size predicts the rate of contemporary morphological change in birds. Proceedings of the National Academy of Sciences (PNAS). 120(20) 1-9 https://doi.org/10.1073/pnas.2206971120

Was this page helpful?