The sympatric existence of genetically distinct populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves only certain parts of the genome. We return to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (coding for lactate dehydrogenase A) in brown trout in the small Lakes Bunnersjöarna, Sweden. First, we verify the existence of the two coexisting demes using a 96-SNP fluidigm array. We then apply whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; nucleotide diversity is higher in Deme I than in Deme II. Furthermore, strong genetic divergence is observed with genome-wide F_ST≈0.2. Comparing with similar data from other lakes, this divergence is of similar magnitude as that between reproductively isolated populations. Individual whole-genome resequencing of two individuals per deme suggests higher inbreeding in Deme II vs. Deme I, indicating different degree of isolation. Finally, we located two gene-copies for LDH-A and find divergence between demes in a regulatory section of one of these genes. However, we did not find a perfect fit between the sequence data and previous allozyme results, and this will require further research. Our data demonstrates genome-wide divergence governed mostly by genetic drift but also by diversifying selection in coexisting populations. This type of hidden biodiversity needs consideration in conservation management.

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