Loss of genetic diversity and reduction of genetic distance among lake trout Salvelinus namaycush ecomorphs, Lake Superior 1959 to 2013

North America's northern lakes are undergoing major changes. Lake Superior is the coldest and northernmost of the Laurentian Great Lakes. Here, we present an extension of a long-term data set that monitors genetic and phenotypic diversity of lake trout Salvelinus namaycush in Lake Superior. Hypotheses were investigated pertaining to loss of genetic diversity and genetic homogenization among three lake trout ecomorphs in Lake Superior during their recovery several decades after a major fishery collapse in the early 1960s. Comparison of a contemporary (2004-2013) microsatellite DNA data set to a previously published, post-collapse recovery period data set (1995-1999) indicated substantive losses in genetic diversity. Allelic richness decreased by 5.7%, 12.3%, and 6.8% at Isle Royale, Stannard Rock, and Klondike Reef, respectively. A 60.7% reduction in genetic distance among ecomorphs since the 1990s was detected. Comparisons with a third data set of samples collected during the fishery collapse (1959) indicated an overall 18.2% loss in allelic richness at Isle Royale. The amount of introgression among ecomorphs has likely increased over time. Apparent losses in genetic diversity could be a consequence of historical fishery harvests (early 1900s) exacerbated by intensive stocking (1950s-1980s) and invasions of non-native species (1960s-1990s). Overlap in foraging and breeding areas may have contributed to increasing levels of hybridization among ecomorphs. Knowledge of these processes will help to identify impediments and strategies for the maintenance of lake trout biodiversity in northern Great Lakes, and their re-establishment in the Laurentian Great Lakes.