Genotyping By Sequencing for Examining Genomic Divergence and Defining Management Units in Wild Lake Trout Populations

Increasing the number of genetic markers by using advanced genotyping by sequencing techniques extend the resolution and utility of population genomics for fisheries management. Here, we examined genomic divergence among Lake tout (Salvelinus namaycush) populations in Quebec in order to help defining biologically meaningful management units in this species. We applied a two-enzyme genotyping by sequencing protocol to 800 adult Lake trout sampled in 38 unstocked lakes widely distributed in the Province of Quebec. A total of 3000 single-nucleotide-polymorphisms were chosen based on quality criteria. High genetic differentiation between lakes (Fst ranging from 0.05 to 0.30) and Bayesian clustering analyses suggested that almost each lake harbored a distinct population. High level of non-parallel loss of polymorphism was found in each population, further illustrating the central effect of genetic drift within these isolated populations. Nevertheless, several allelic variants were found associated to environmental features and could mirror adaptation processes despite of massive drift. Altogether, these results have important implications for the delineation of management units in Lake trout, primarily through the definition of the lake as the optimal unit for a biologically relevant management of wild lake trout populations.