Population structure and genomic variation of ecological life history diversity in wild-caught Lake Superior brook trout, Salvelinus fontinalis

Abstract Delineating patterns of extant genetic diversity is crucial for understanding the evolutionary history of populations and how they can be conserved. Brook trout ( Salvelinus fontinalis ; n  = 173) were sampled from 11 locations in Nipigon Bay, Lake Superior to evaluate genetic differentiation between migratory (coaster) and non-migratory (resident) individuals. Stable isotope data were used to classify the trophic ecology of individuals, rather than relying on size or capture location and timing to classify ecotypes. Genome-wide association analysis of 4676 single nucleotide polymorphism (SNP) markers was conducted to test if phenotypic and behavioral differences within and among populations of brook trout were linked to allelic variation in the genome. Population genetic structure was also evaluated to determine the source of migratory coasters based on multilocus genotypes from a subset of 906 SNP markers. Significant population genetic structure was revealed among the sampled tributaries, and the population genetic structure suggests that a single, larger stream in the study area, Cypress River, was the primary source of migratory brook trout in Nipigon Bay. There was little evidence of genetic differentiation between sympatric migrant and stream-resident brook trout; across the genome only 11 SNP loci ( Data statement Raw RADseq is deposited in the NCBI Genbank Sequence Read Archive (PRJNA486545). Biological metadata and processed genotypes are found in the Electronic Supplementary Material (ESM).