Reduced-representation sequencing detects trans-Arctic connectivity and local adaptation in polar cod (Boreogadus saida)

Information on connectivity and genetic structure of marine organisms remains sparse in frontier ecosystems such as the Arctic Ocean. Filling these knowledge gaps becomes increasingly urgent, as the Arctic is undergoing rapid physical, ecological, and socio-economic changes. The abundant and widely distributed polar cod (Boreogadus saida) is highly adapted to Arctic waters, and its larvae and juveniles live in close association with sea ice. Through a reduced-representation sequencing approach, this study explored the spatial genetic structure of polar cod at a circum-Arctic scale. Genomic variation was partitioned into neutral and adaptive components to respectively investigate genetic connectivity and local adaptation. Based on 922 high-quality single nucleotide polymorphism (SNP) markers genotyped in 611 polar cod, broad-scale differentiation was detected among three groups: (i) Beaufort-Chukchi seas, (ii) all regions connected by the Transpolar Drift, ranging from the Laptev Sea to ..., A total of 652 polar cod samples were collected in the Central Arctic Ocean, Fram Strait and the Arctic Ocean shelves bordering Alaska, Canada, Russia, Greenland and Northern Europe, during several expeditions between 2003 and 2021. Fish were collected using bottom trawl, bongo net, Young fish trawl, Surface and Under-Ice Trawl, ROVnet, Multpelt 832 pelagic trawl, or zooplankton net. We collected fin clips of all fish sampled and stored them in 96 % ethanol. Genomic DNA was extracted from fin clips using the NucleoSpin® Tissue kit (Macherey-Nagel), following manufacturer’s instructions. A modified version of the Elshire et al. (2011) genotyping-by-sequencing (GBS) method was used, with a single restriction enzyme (PstI) and size selection (320-720 bp).Three GBS libraries were paired-end sequenced on an Illumina Novaseq platform 6000 (PE100) at the Genomics Core Leuven (www.genomicscore.be). Sequences were quality checked using FastQC v0.11.8 and Stacks v2.5 was used to process the GBS d..., , # Data from: Reduced-representation sequencing detects trans-Arctic connectivity and local adaptation in polar cod (Boreogadus saida)

[https://doi.org/10.5061/dryad.fqz612k30](https://doi.org/10.5061/dryad.fqz612k30)

## Description of the data and file structure

This archive is linked to Maes, Verheye et al. (accepted), exploring connectivity patterns and local adaptation in Polar cod (*Boreogadus saida*), using single nucleotide polymorphisms (SNPs) datasets derived from RAD-sequencing.  Data cover 9 ecoregions of the Arctic Ocean. Genetic data include VCF format datasets of (1) 1192 SNPs, unfiltered for Hardy-Weinberg equilibrium (hwe) and used for outlier analyses, (2) 922 SNPs filtered for hwe, (3) 845 putatively neutral SNPs, obtained by removing all detected outliers to the 922 SNPs dataset and (4) 35 putatively adaptive SNPs identified by at least two outlier detection methods (PCAdapt, OutFLANK, BayeScan). The environmental matrix and allele frequencies of putatively neutr...