Using joint species distribution models to establish biological benchmarks for streams and rivers of the contiguous United States

Using reference sites to establish appropriate biological benchmarks is challenging because of the ubiquity of anthropogenic impacts. We circumvent the need for reference sites using joint species distribution models to predict the benthic macroinvertebrate assemblage expected (E) to occur if gradients of nutrients, salinity, climate, and physical habitat were minimally influenced by human activities. We then compare E to the observed (O) assemblage to assess the taxonomic completeness of assessed sites. At the genus level, the models accurately explained occurrences for all taxa (AUC > 0.70) and at the assemblage level; regressing observed richness against predicted richness revealed intercepts close to 0 (± 1.5) and slopes close to 1 (± 0.15). We modeled the minimally disturbed state for several chemical gradients using random forest models to account for natural and anthropogenic gradients in observed values and then reduced or removed the anthropogenic effects by setting them to zero. Depending on the ecoregion, random forest models explained 22 to 79% of the variation in the chemical gradients and hindcasted values were typically lower than present-day observations. For each site we generated a distribution of plausible observed-to-expected ratios (O:E) by comparing O to 1250 random samples from the posterior predictive distribution of E. We then measured biological condition as the probability that the observed assemblage is different from the assemblage expected to occur if the site was in its minimally disturbed state. We found that the assemblages observed at 57% of sites across the contiguous United States had a probability > 0.5 of being different from the expected assemblage after accounting for model uncertainty. This presentation demonstrates an alternative method for establishing biological benchmarks without relying on reference sites and we discuss its advantages, disadvantages, and complexities. The views expressed in this presentation are those of the authors and do not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

Impact/Purpose

A central objective of biological assessments is to determine whether an assemblage of organisms is comparable in terms of diversity and composition to that of natural habitats in the region. Typically, the assemblage expected to occur under natural conditions, is derived from a suite of reference sites that are minimally disturbed by human activities.  Unfortunately, because of the ubiquity of human alterations, reference sites meeting minimally disturbed criteria can be difficult to find and complicate biological assessments. In this presentation we propose an alternative approach to establishing biological benchmarks using joint species distribution models and data collected by the National Rivers and Streams Assessment program. We found that this approach, based on taxon-environment relationships, could elucidate new patterns in the biological condition of rivers and streams in the contiguous United States. Importantly, this study supports the development of new biological assessment techniques by establishing biological benchmarks without relying on reference sites.

Citation

Kopp, D., J. Stoddard, Ryan A Hill, J. Doyle, Phil Kaufmann, A. Herlihy, AND Steve Paulsen. Using joint species distribution models to establish biological benchmarks for streams and rivers of the contiguous United States. National Monitoring Conference, Virginia Beach, VA, April 24 - 28, 2023.