DOI: 10.5061/dryad.3f1c8
title: Data from: Genome architecture enables local adaptation of Atlantic cod despite high connectivity

description: Adaptation to local conditions is a fundamental process in evolution;
 however, mechanisms maintaining local adaptation despite high gene flow
 are still poorly understood. Marine ecosystems provide a wide array of
 diverse habitats that frequently promote ecological adaptation even in
 species characterized by strong levels of gene flow. As one example,
 populations of the marine fish Atlantic cod (Gadus morhua) are highly
 connected due to immense dispersal capabilities but nevertheless show
 local adaptation in several key traits. By combining population genomic
 analyses based on 12K single nucleotide polymorphisms with larval
 dispersal patterns inferred using a biophysical ocean model, we show that
 Atlantic cod individuals residing in sheltered estuarine habitats of
 Scandinavian fjords mainly belong to offshore oceanic populations with
 considerable connectivity between these diverse ecosystems. Nevertheless,
 we also find evidence for discrete fjord populations that are genetically
 differentiated from offshore populations, indicative of local adaptation,
 the degree of which appears to be influenced by connectivity. Analyses of
 the genomic architecture reveal a significant overrepresentation of a
 large ~5 Mb chromosomal rearrangement in fjord cod, previously proposed to
 comprise genes critical for the survival at low salinities. This suggests
 that despite considerable connectivity with offshore populations, local
 adaptation to fjord environments may be enabled by suppression of
 recombination in the rearranged region. Our study provides new insights
 into the potential of local adaptation in high gene flow species within
 fine geographical scales and highlights the importance of genome
 architecture in analyses of ecological adaptation.
description: SNP array data including
 linked loci (7,783 SNPs)SNP array data of 527
 Atlantic cod (Gadus morhua), genotyped at 7,783 loci (dataset including
 linked SNPs). Genepop format
 (http://genepop.curtin.edu.au/help_input.html): first line: datafile
 information; second line: loci names (dbSNP accession numbers); line 3-543
 genotypes for each locus (01=A, 02=C, 03=G, 04=T), one individual per row,
 sampling sites are separated by “pop”. All SNPs are referred to by their
 database of Single Nucleotide Polymorphisms (dbSNP) accession numbers,
 available from: http://www.ncbi.nlm.nih.gov/SNP. First three characters of
 individual names correspond to population IDs: ENG, English Channel; NOR,
 North Sea; TVE, Tvedestrand; SOP, Soppekilen; HEL, Hellefjord; FRI/GRE,
 Grenland; OSL, Oslofjord; IDD, Iddefjord; SKA, Skagerrak; GUL,
 Gullmarsfjord; HAV, Havstensfjord; KAT, Kattegat; ORE, Öresund; BEL, Belt
 Sea.barth_atlantic_cod_7783_SNPs.txtSNP array data excluding linked loci (6,658 SNPs)SNP array data of 527 Atlantic cod (Gadus morhua), genotyped at 6,658 loci (dataset excluding linked SNPs). Genepop format (http://genepop.curtin.edu.au/help_input.html): first line: datafile information; second line: loci names (dbSNP accession numbers); line 3-543 genotypes for each locus (01=A, 02=C, 03=G, 04=T), one individual per row, sampling sites are separated by “pop”. All SNPs are referred to by their database of Single Nucleotide Polymorphisms (dbSNP) accession numbers, available from: http://www.ncbi.nlm.nih.gov/SNP. First three characters of individual names correspond to population IDs: ENG, English Channel; NOR, North Sea; TVE, Tvedestrand; SOP, Soppekilen; HEL, Hellefjord; FRI/GRE, Grenland; OSL, Oslofjord; IDD, Iddefjord; SKA, Skagerrak; GUL, Gullmarsfjord; HAV, Havstensfjord; KAT, Kattegat; ORE, Öresund; BEL, Belt Sea.barth_atlantic_cod_6658_SNPs.txt