DOI: 10.5061/dryad.k713n
title: Data from: Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior

description: 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.
description: Geometric morphometric
 data for body shape for Big ReefLandmarks and
 semi-landmarks for body shape for Big Reef fishBig_Reef_104indv_body.TPSGenotype data in .vcf formatFiltered SNPs in .vcf format from 486 individuals genotyped at 6822 SNPSdata_6822filtered_snp_486indv_4pop.vcfGeometric morphometric data for head shape for Big ReefLandmarks and semi-landmarks for head shape for Big ReefBig_Reef_104indv_head.TPSGeometric morphometric data for body shape for Isle RoyaleLandmarks and semi-landmarks for body shape for Isle Royale in .tps formatIsle_Royale_144indv_body.TPSGeometric morphometric data for head shape for Isle RoyaleLandmarks and semi-landmarks for head shape for Isle Royale in .tps formatIsle_Royale_144indv_head.TPSGeometric morphometric data for body shape for Stannard RockLandmarks and semi-landmarks for body shape for Stannard Rock in .tps formatStannard_Rock_128indv_body.TPSGeometric morphometric data for head shape for Stannard RockLandmarks and semi-landmarks for head shape for Stannard Rock in .tps formatStannard_Rock_128indv_head.TPSGeometric morphometric data for body shape for Superior ShoalsLandmarks and semi-landmarks for body shape for Superior Shoals in .tps formatSuperior_Shoals_125indv_body.TPSGeometric morphometric data for head shape for Superior ShoalsLandmarks and semi-landmarks for head shape for Superior Shoals in .tps formatSuperior_Shoals_125indv_head.TPSsample_informationInformation for each genotyped individuals