We used our long-term annual bottom trawl survey (1973–2004) in Lake Michigan to reveal the response of the native fish community to the biological control of a dominant exotic fish, alewife (Alosa pseudoharengus), as well as to changes in total phosphorus and salmonine biomass. Through nonmetric multidimensional scaling, we documented a 1970s community largely dominated by alewife, and then a shift to a community dominated by several native species during the 1980s through 1990s, when alewife remained at relatively low levels. We argue that the recovery of burbot (Lota lota), deepwater sculpin (Myoxocephalus thompsonii), and yellow perch (Perca flavescens) was partially or fully aided by the alewife reduction. We argue that changes in phosphorus or salmonines were not directly related to abundance increases of native species. An additional community shift occurred during 1999–2004, which coincided with a reduction in species richness and total fish biomass in our trawl. The mechanisms underlying this latest shift may be related to reductions in nutrients, but further research is required. The restoration of the native fish community has been incomplete, however, as emerald shiner (Notropis atherinioides), cisco (Coregonus artedii), and lake trout (Salvelinus namaycush) have yet to demonstrate recovery.
