Integrating uncertain prior knowledge regarding ecological preferences into multi-species distribution models: Effects of model complexity on predictive performance
Abstract
Species distribution models (SDMs) are often criticised for lacking explicit linkage to ecological concepts. We aim to improve the ecological basis of SDMs by integrating prior knowledge about ecological preferences of organisms. Additionally, we aim to support a systematic, data-driven review of such prior knowledge by confronting it with independent monitoring data using Bayesian inference. We developed a series of multi-species distribution models (MSDMs) with increasing complexity to predict the probability of occurrence of taxa at sampling sites based on habitat suitability functions that are parameterized with prior ecological knowledge. We subsequently assessed the models`predictive performance with 3-fold cross-validation. So far, if ecological preferences or functional traits have been used in SDMs, they were mainly used as fixed inputs without considering their uncertainty. We take the additional step of considering uncertainty about preference parameters by including them as uncertain prior information that is subsequently updated with Bayesian inference. We apply the series of models in a case study on macroinvertebrates in Swiss streams. We analyse differences in the quality of fit, changes in predictive performance, and the potential to learn about the parameters from the data. We consider ecological preferences for natural and human modified environmental factors including temperature, flow velocity, organic matter concentration, insecticide pollution, and substratum. Results indicate that updating prior knowledge on ecological preferences with Bayesian inference, rather than using it as fixed input, improves model fit and predictive performance. For example, the predictive performance measured by the deviance for validation data improves by 17 % and the explanatory power increases 3.8 times from a model that treats ecological preferences as fixed scores to a model that treats them as uncertain parameters. The spatial distribution of many taxa, including rare taxa with frequencies of occurrence down to about 5 %, which are difficult to model with SDMs that do not consider prior information, can be captured by the new models. Integrating prior knowledge as uncertain parameters in a Bayesian framework establishes ecological interpretable links between taxa and their environment and supports a systematic revision and complementation of databases on ecological preferences, even in case of poor or missing prior knowledge. Model outputs need to be carefully interpreted by modellers and experts on ecological preferences. Increased exchange between these research fields will benefit further integration of ecological preferences into SDMs.
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BibTeX
@article{vermeiren2026integrating,
title = {{Integrating uncertain prior knowledge regarding ecological preferences into multi-species distribution models: Effects of model complexity on predictive performance}},
author = {Peter Vermeiren and Peter Reichert and Nele Schuwirth},
journal = {Ecological Modelling},
year = {2026},
month = sep,
doi = {10.1016/j.ecolmodel.2020.108956},
url = {https://hal.inrae.fr/hal-05738365v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Integrating uncertain prior knowledge regarding ecological preferences into multi-species distribution models: Effects of model complexity on predictive performance
AU - Peter Vermeiren
AU - Peter Reichert
AU - Nele Schuwirth
PY - 2026
DA - 2026/09/04
JO - Ecological Modelling
DO - 10.1016/j.ecolmodel.2020.108956
UR - https://hal.inrae.fr/hal-05738365v1
AB - Species distribution models (SDMs) are often criticised for lacking explicit linkage to ecological concepts. We aim to improve the ecological basis of SDMs by integrating prior knowledge about ecological preferences of organisms. Additionally, we aim to support a systematic, data-driven review of such prior knowledge by confronting it with independent monitoring data using Bayesian inference. We developed a series of multi-species distribution models (MSDMs) with increasing complexity to predict the probability of occurrence of taxa at sampling sites based on habitat suitability functions that are parameterized with prior ecological knowledge. We subsequently assessed the models`predictive performance with 3-fold cross-validation. So far, if ecological preferences or functional traits have been used in SDMs, they were mainly used as fixed inputs without considering their uncertainty. We take the additional step of considering uncertainty about preference parameters by including them as uncertain prior information that is subsequently updated with Bayesian inference. We apply the series of models in a case study on macroinvertebrates in Swiss streams. We analyse differences in the quality of fit, changes in predictive performance, and the potential to learn about the parameters from the data. We consider ecological preferences for natural and human modified environmental factors including temperature, flow velocity, organic matter concentration, insecticide pollution, and substratum. Results indicate that updating prior knowledge on ecological preferences with Bayesian inference, rather than using it as fixed input, improves model fit and predictive performance. For example, the predictive performance measured by the deviance for validation data improves by 17 % and the explanatory power increases 3.8 times from a model that treats ecological preferences as fixed scores to a model that treats them as uncertain parameters. The spatial distribution of many taxa, including rare taxa with frequencies of occurrence down to about 5 %, which are difficult to model with SDMs that do not consider prior information, can be captured by the new models. Integrating prior knowledge as uncertain parameters in a Bayesian framework establishes ecological interpretable links between taxa and their environment and supports a systematic revision and complementation of databases on ecological preferences, even in case of poor or missing prior knowledge. Model outputs need to be carefully interpreted by modellers and experts on ecological preferences. Increased exchange between these research fields will benefit further integration of ecological preferences into SDMs.
SN - 0304-3800
SN - 1872-7026
ER -