Data from: Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior

Understanding the emergence of species through the process of ecological
speciation is a central question in evolutionary biology which also has
implications for conservation and management. Lake Trout (Salvelinus
namaycush) is renowned for the occurrence of different ecotypes linked to
resource and habitat use throughout North America. We aimed to unravel the
fine genetic structure of the four Lake Trout ecotypes in Lake Superior. A
total of 486 individuals from four sites were genotyped at 6822 filtered
SNPs using RADseq technology. Our results revealed different extent of
morphological and genetic differentiation within the different sites.
Overall, genetic differentiation was weak but significant and was on
average three times higher between sites (Mean FST = 0.016) than between
ecotypes within sites (Mean FST = 0.005) indicating higher level of gene
flow or a more recent shared ancestor between ecotypes within each site
than between populations of the same ecotype. Evidence of divergent
selection was also found between ecotypes and/or in association with
morphological variation. Outlier loci found in genes related to lipid
metabolism and visual acuity were of particular interest in this context
of ecotypic divergence. However, we did not find clear indication of
parallelism at the genomic level, despite the presence of phenotypic
parallelism among some ecotypes from different sampling sites. Overall,
the occurrence of different levels of both genomic and phenotypic
differentiation between ecotypes within each site with several
differentiated loci linked to relevant biological functions support the
presence of a continuum of divergence in Lake Trout.