Joint Species Distribution Modelling (JSDM)

Modelling multiple species simultaneously to capture ecological co-occurrence patterns and species interactions.

JSDM species co-occurrence correlation matrix heatmap

Residual correlation matrix among species derived from a joint species distribution model. Red indicates positive co-occurrence; blue indicates negative co-occurrence.

References

  1. Boulangeat, I., Philippe, P., Abdulhak, S., Douzet, R., Garraud, L., Lavergne, S., Lavorel, S., Van Es, J., Vittoz, P., & Thuiller, W. (2012). Improving plant functional groups for dynamic models of biodiversity: At the crossroads between functional and community ecology. Global Change Biology, 18(11), 3464–3475. https://doi.org/10.1111/j.1365-2486.2012.02783.x
  2. Doser, J. W., Finley, A. O., Banerjee, S. (2023). Joint species distribution models with imperfect detection for high-dimensional spatial data. Ecology, 104(9), e4137. https://doi.org/10.1002/ecy.4137
  3. Doser, J. W., Finley, A. O., Kéry, M., & Zipkin, E. F. (2022). spOccupancy: An R package for single-species, multi-species, and integrated spatial occupancy models. Methods in Ecology and Evolution, 13(8), 1670–1678. https://doi.org/10.1111/2041-210X.13897
  4. Hu, Y., Si-Moussi, S., & Thuiller, W. (2025). Introduction to deep learning methods for multi-species predictions. Methods in Ecology and Evolution, 16(1), 228–246. https://doi.org/10.1111/2041-210X.14466
  5. Khaliq, I., Hof, C., Prinzinger, R., Böhning-Gaese, K., & Pfenninger, M. (2014). Global variation in thermal tolerances and vulnerability of endotherms to climate change. Proceedings of the Royal Society B: Biological Sciences, 281(1789), 20141097. https://doi.org/10.1098/rspb.2014.1097
  6. Komatsu, K. J., Avolio, M. L., Padullés Cubino, J., Schrodt, F., Auge, H., Cavender-Bares, J., Clark, A. T., Flores-Moreno, H., Grman, E., Harpole, W. S., Kattge, J., Kimmel, K., Koerner, S. E., Korell, L., Langley, J. A., Münkemüller, T., Ohlert, T., Onstein, R. E., Roscher, C., Soudzilovskaia, N. A., Taylor, B. N., Tedersoo, L., Terry, R. S., & Wilcox, K. (2024). CoRRE Trait Data: A dataset of 17 categorical and continuous traits for 4079 grassland species worldwide. Scientific Data, 11, 795. https://doi.org/10.1038/s41597-024-03637-x
  7. Maitner, B. (2025). BIEN: Tools for accessing the Botanical Information and Ecology Network Database (R package version 1.2.7). CRAN.
  8. Maitner, B. S., Boyle, B., Casler, N., Condit, R., Donoghue, J., Duran, S. M., Guaderrama, D., Hinchliff, C. E., Jorgensen, P. M., Kraft, N. J. B., McGill, B., Merow, C., Morueta-Holme, N., Peet, R. K., Sandel, B., Schildhauer, M., Smith, S. A., Svenning, J.-C., Thiers, B., Violle, C., Wiser, S., & Enquist, B. J. (2018). The BIEN R package: A tool to access the Botanical Information and Ecology Network (BIEN) database. Methods in Ecology and Evolution, 9(2), 373–379. https://doi.org/10.1111/2041-210X.12861
  9. Ovaskainen, O., Tikhonov, G., Norberg, A., Blanchet, F. G., Duan, L., Dunson, D., Roslin, T., & Abrego, N. (2017). How to make more out of community data? A conceptual framework and its implementation as models and software. Ecology Letters, 20(5), 561–576. https://doi.org/10.1111/ele.12757
  10. Pollock, L. J., Tingley, R., Morris, W. K., Golding, N., O'Hara, R. B., Parris, K. M., Vesk, P. A., & McCarthy, M. A. (2014). Understanding co-occurrence by modelling species simultaneously with a joint species distribution model (JSDM). Methods in Ecology and Evolution, 5(5), 397–406. https://doi.org/10.1111/2041-210X.12180
  11. Tikhonov, G., Opedal, Ø. H., Abrego, N., Lehikoinen, A., de Jonge, M. M. J., Oksanen, J., & Ovaskainen, O. (2020). Joint species distribution modelling with the R-package Hmsc. Methods in Ecology and Evolution, 11(3), 442–447. https://doi.org/10.1111/2041-210X.13345
  12. Willis, S. G., Foden, W., Baker, D. J., Belle, E., Burgess, N. D., Carr, J. A., Doswald, N., Garcia, R. A., Hartley, A., Hof, C., Newbold, T., Rahbek, C., Smith, R. J., Visconti, P., Young, B. E., & Butchart, S. H. M. (2015). Integrating climate change vulnerability assessments from species distribution models and trait-based approaches. Biological Conservation, 190, 167–178. https://doi.org/10.1016/j.biocon.2015.05.001

Palette