70K SNP array data for Lumpfish (Cyclopterus lumpus) across the trans-Atlantic

In marine species with large populations and high dispersal potential, large-scale genetic differences and clinal trends in allele frequency can provide insight into the evolutionary processes that shape diversity. Lumpfish, Cyclopterus lumpus, is found throughout the North Atlantic and has traditionally been harvested for roe and more recently used as a cleaner fish in salmon aquaculture. We used a 70K SNP array to evaluate trans-Atlantic differentiation, genetic structuring, and clinal variation across the North Atlantic. Basin-scale structuring between the Northeast and Northwest Atlantic was significant, with enrichment for loci associated with developmental/mitochondrial function. We identified a putative structural variant on chromosome 2, likely contributing to differentiation between Northeast and Northwest Atlantic Lumpfish, and consistent with post-glacial trans-Atlantic secondary contact. Redundancy Analysis identified climate associations both in the Northeast (N = 1269 loci..., Sampling and DNA preparation
A total of 570 individuals were sampled from 26 locations across the North Atlantic Ocean from 2009 to 2019 (Fig. 1, Table 1) in conjunction with scientific research surveys (trawl and beach seines) and commercial fishing activities. There was a total of 11 sites in the NW Atlantic (the same NW sites as in Langille et al. (2023), although in this study samples have been downsampled): Newfoundland (N = 369), Gulf of Saint Lawrence (GSL; N = 108), New Brunswick (N = 13), and the Gulf of Maine (N = 70). There were a total of 15 sites in the NE Atlantic: Iceland (N = 134), the Faroe Islands (N = 15), Norway (N = 30), Denmark (N = 8), Sweden (N = 5), Scotland (N = 13), Ireland (N = 43), and the United Kingdom (N = 30). One site from Iceland (IC), one from Norway (NO2), and one from Newfoundland (TNR) were samples of juveniles; all other samples were of adults. Tissue samples were preserved in 95% ethanol and subsequent DNA extractions were performed using DNeasy ..., , # 70K SNP array data for Lumpfish (Cyclopterus lumpus) across the trans-Atlantic

[https://doi.org/10.5061/dryad.j3tx95xp3](https://doi.org/10.5061/dryad.j3tx95xp3)

This dataset contains SNPs in .ped/.map format.

Lumpfish has been listed as near threatened in the North Atlantic, however this assessment has not ben updated since 2013 (IUCN Red List). Therefore in the below table, we have provided approximate latitude and longitudes in order to prevent unintended risks to these potentially threatened populations.

## Description of the data and file structure

The data is in .ped/.map format. The ped file contains columns with data in the following order: Family ID, Individual ID, Paternal ID, Maternal ID, Sex, Affection, and Genotypes. The order of the genotypes is explained by the .map file which has columns in the following order: Chromosome, SNP name, Genetic position, and Physical position. There is no data present for Paternal ID, Maternal ID, Sex, and Genetic position, therefore ...