San Francisco Estuary and Watershed Science

The loss of biodiversity and biotic homogenization are on the rise in ecosystems around the world as a result of species invasions, habitat degradation, and the effects of climate change. In the Sacramento–San Joaquin Delta, non-native species make up the majority of the fish community, and declines in native species have been well documented; however, little is known about whether these trends have resulted in biotic homogenization. In this study, we used data from a long-term beach seine survey to analyze regional beta diversity trends of nearshore fish assemblages in the Delta from 1995 to 2019. Overall, we found no evidence of regional biotic homogenization occurring over the study period. Regional beta diversity increased moderately over time and was significantly influenced by the high interannual variability of freshwater inflow. These beta diversity patterns were driven by the non-native Mississippi Silverside that has proliferated in the system in recent years, but also by a handful of native fish species such as the Sacramento Sucker, Tule Perch, and Splittail. Overall, our results offer a contrast to other highly invaded ecosystems around the world and suggest that despite the near extinction of some native fish species, there remain pockets of suitable habitat in the Delta that may play a key role in the conservation of remnant native fish diversity.