Ecological Segregation of Native and Alien Larval Fish Assemblages in the Southern Sacramento–San Joaquin Delta

—Fish larvae were sampled at multiple fixed sites from late winter to early summer over 6 years (1990–1995) in the southern Sacramento–San Joaquin Delta. A total of 394,797 fish larvae representing 15 species or taxonomic groups was collected. The assemblage was numerically dominated by three species that represented 98% of the total catch: alien shimofuri goby Tridentiger bifasciatus (71%), threadfin shad Dorosoma petenense (15%), and native prickly sculpin Cottus asper (12%). The abundance of native and alien species differentially clustered along environmental gradients of water temperature and river flow. Each native species (prickly sculpin, splittail Pogonichthys macrolepidotus, delta smelt Hypomesus transpacificus, longfin smelt Spirinchus thaleichthys, and Sacramento sucker Catostomus occidentalis) and one alien species (bigscale logperch Percina macrolepida) were associated with the early season conditions of cool water temperature and high river flow. Alien species (especially shimofuri goby, threadfin shad, and ictalurid catfishes) were associated with late season conditions of relatively warm water temperature and low river flow. Accordingly, native species dominated the assemblage February–March, while alien species dominated May–July. However, peak seasonal abundance of alien species was typically five times greater than that of native species. Seasonal succession of assemblage structure was persistent among years and was highly correlated with water temperature, a likely result of the differential spawning requirements of adult fishes. Interannually, the assemblage remained consistent over the study period despite considerable variability in delta inflow. I hypothesize, given the consistent temporal segregation between native and alien larval fish assemblages, that direct interactions such as competition between the two groups may not be a major factor influencing poor native fish recruitment in the south delta.