DOI: 10.5061/dryad.8hq6qv2
title: Data from: Characterizing neutral and adaptive genomic differentiation in a changing climate: the most northerly freshwater fish as a model

description: Arctic freshwater ecosystems have been profoundly affected by climate
 change. Given that the Arctic charr (Salvelinus alpinus) is often the only
 fish species inhabiting these ecosystems, it represents a valuable model
 for studying the impacts of climate change on species life history
 diversity and adaptability. Using a genotyping-by-sequencing approach, we
 identified 5976 neutral single nucleotide polymorphisms (SNPs) and found
 evidence for reduced gene flow between allopatric morphs from two high
 Arctic lakes, Linne´vatn (Anadromous, Normal, and Dwarf) and Ellasjøen
 (Littoral and Pelagic). Within each lake, the degree of genetic
 differentiation ranged from low (Pelagic vs. Littoral) to moderate
 (Anadromous and Normal vs. Dwarf). We identified 17 highly diagnostic,
 putative adaptive SNPs that differentiated the allopatric morphs. Although
 we found no evidence for adaptive differences between morphs within
 Ellasjøen, we found evidence for moderate (Anadromous vs. Normal) to high
 genetic differentiation (Anadromous and Normal vs. Dwarf) among morphs
 within Linne´vatn based on two adaptive loci. As these freshwater
 ecosystems become more productive, the frequency of sympatric morphs in
 Ellasjøen will likely shift based on foraging opportunities, whereas the
 propensity to migrate may decrease in Linne´vatn, increasing the frequency
 of the Normal morph. The Dwarf charr was the most genetically distinct
 group. Identifying the biological basis for small body size should
 elucidate the potential for increased growth and subsequent interbreeding
 with sympatric morphs. Overall, neutral and adaptive genomic
 differentiation between allopatric and some sympatric morphs suggests that
 the response of Arctic charr to climate change will be variable across
 freshwater ecosystems.
description: Filtered Genepop
 fileGenepop file containing
 8,075 filtered SNPs among all five morphsFILTERED.genNeutral Genepop fileGenepop file containing 5,976 neutral SNPs among five morphs, as determined by BAYESCAN and LOSITANNEUTRAL.genAdaptive Genepop fileGenepop file containing 17 putative adaptive SNPs among five morphs, as determined by BAYESCAN and LOSITANADAPTIVE.genFig_S1HDplot (McKinney et al. 2016) illustrating the criteria used for identifying loci as putative paralogs (red points). Paralogs were categorized based upon a high proportion of heterozygotes and/or high read depth ratios. Loci retained for downstream analyses are colored black.Fig_S2Identifying the optimal number of clusters for the neutral dataset. BIC scores calculated following k-means clustering (a) and associated error for cross validation of ADMIXTURE values (b) for k (1 – 10).Fig_S3Allele frequencies among all five morphs for the 17 putative adaptive loci identified by both BAYESCAN and LOSITANFig_S4Pairwise comparison at neutral and adaptive loci (95% confidence intervals) for all five morphs, colored by sympatric (grey) and allopatric (black) pairs.Table_S1Locus-specific summary statistics for the filtered dataset (8,075 loci), calculated within each Arctic charr morph.Table_S2BAYESCAN and LOSITAN output used for partitioning the filtered dataset into neutral and putative adaptive loci.Table_S3Salvelinus alpinus coordinates for 11/17 outlier loci, alignment scores, annotation features, and associated functional group.