Discovery of adaptive genetic variation in recovering populations of lake trout in Lake Huron

Session: Application of Genomic Tools to Inform Management of the Great Lakes (1)

Seth Smith, Department of Fisheries & Wildlife, Michigan State University, [email protected]
Kim Scribner, Dept. Fisheries and Wildlife, Michigan State, [email protected]
Gordon Luikart, Flathead Lake Biological Station, [email protected]
Stephen Amish, University of Montana, [email protected]

Abstract

Lake trout (Salvelinus namaycush) were nearly extirpated from Lake Huron in the mid-20^th century as a result of sea lamprey predation, overfishing, and habitat alteration. An intensive stocking program was started in 1969 as a means of restoring self-sustaining populations; however, natural recruitment was not observed until the 1990s. Natural recruitment has steadily increased in recent years; however, the biological (genomic) basis for variation in fitness among individuals and hatchery strains remains unclear. In order to detect genes associated with survival and reproductive success in the wild, we used Restriction Site Associated DNA Capture (Rapture) to genotype 58,889 loci in 874 wild lake trout and 192 baseline samples from 7 hatchery progenitor populations. We used the program BAYPASS to test for evidence of selection in 11 wild cohorts produced in Lake Huron between 1995 and 2007. Depending on the cohort examined, we identified between 113 and 451 loci with changes in allele frequency with less than a 1% chance of occurring under neutral scenarios. Results suggest that selective pressures have fluctuated between 1995 and 2007, although, a subset of loci appear to be consistently associated with fitness across multiple cohorts, including genes related to immune function and circadian rhythm.