DOI: 10.5061/dryad.j3tx95xp3
title: 70K SNP array data for Lumpfish (Cyclopterus lumpus) across the trans-Atlantic

description: 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) and Northwest (N = 1637 loci), with 103 shared loci between them.
 Clinal patterns in allele frequencies were observed in some loci (15% -
 Northwest and 5% - Northeast) of which 708 loci were shared and involved
 with growth, developmental processes, and locomotion. The combined
 evidence of trans-Atlantic differentiation, environmental associations,
 and clinal loci, suggests that both regional and large-scale
 potentially-adaptive population structuring is present across the North
 Atlantic.
description: <strong>Sampling and DNA
 preparation</strong> 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
 <em>et al</em>. (2023), although in this study samples have
 been downsampled): Newfoundland (<em>N</em> = 369), Gulf of
 Saint Lawrence (GSL; <em>N</em> = 108), New Brunswick
 (<em>N </em>= 13), and the Gulf of Maine (<em>N
 </em>= 70). There were a total of 15 sites in the NE Atlantic:
 Iceland (<em>N</em> = 134), the Faroe Islands
 (<em>N</em> = 15), Norway (<em>N</em> = 30),
 Denmark (<em>N</em> = 8), Sweden (<em>N</em> = 5),
 Scotland (<em>N</em> = 13), Ireland (<em>N</em> =
 43), and the United Kingdom (<em>N</em> = 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 Blood and Tissue kits (Qiagen) according to
 manufacturer’s protocols. Genomic DNA was visualized by 1% agarose gel
 electrophoresis and quantified using Quant-iT PicoGreen ds-DNA Assay kits
 (Thermofisher) on a fluorescent plate reader. Genomic DNA was normalized
 to 15 ng/ml and sent to the Centre of Integrative Genomics (CIGENE, Ås,
 Norway) for genotyping on the Lumpfish 70K SNP Affymetrix Axiom array
 (produced by CIGENE and Aquagen). <strong>70K SNP
 array filtering</strong> A custom Affymtrix 70K
 SNP array (developed by Aquagen and CIGENE) was mapped to the Lumpfish
 genome from North America (Holborn <em>et al</em>., 2022).
 Sample/SNP level filtering was performed as quality control in Plink 1.9
 (Chang <em>et al</em>., 2015); the SNP set was filtered by
 individuals with high genotyping (<em>--mind</em>) 0.05,
 sample call rates (<em>--geno</em>) 0.05, and minor allele
 frequency (<em>--maf</em>) 0.01. Individuals were filtered by
 relatedness in Plink, using the <em>–genome </em>flag and a
 pi-hat threshold of 0.35. 
description: # 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 all these columns contain zeros. Missing data for Affection (all of it is missing) is represented by a -9. Even though there is no data in these columns, they need to be present for different programs to be able to read the files in these formats. Column headers cannot be present in the files, otherwise they will not work in different programs. Example line #1 from .ped file: BAI BAI_2019_001_K8.CEL 0 0 0 -9 G G C C G G C T T C T C A G... Where **BAI** is the Family ID, **BAI_2019_001_K8.CEL** is the Individual ID, **0 0 0 -9** is the missing data for Paternal ID, Maternal ID, Sex, and Affection, and **G G C C G G C T T C T C A G**... is the genotype for this individual. Example line #1 from .map file: 1 AX-298066833 0 22038 Where **1** is the chromosome, **AX-298066833** is the SNP name, **0** is the genetic position, and **22038** is the physical position. The following table contains all information required for translating Family IDs in the SNP data, including population codes, latitude and longitude, and the number of sampled individuals per location (N): | Continent | Location | Code | Latitude | Longitude | N | | :------------ | :--------------------------- | :---- | :----------------- | :----------------- | :-- | | Europe | Iceland | IC\* | 63.9 | -22.6 | 14 | | Europe | Iceland | ISH | 65.8 | -20.3 | 30 | | Europe | Iceland | IVO | 65.7 | -14.8 | 30 | | Europe | Faroe Isl. | FI | 62.1 | -6.5 | 15 | | Europe | Norway | NO1 | 63.0 | 7.4 | 15 | | Europe | Norway | NO2\* | 64.4 | 11.3 | 8 | | Europe | Norway | NO3 | 59.0 | 5.8 | 7 | | Europe | Denmark | DE | 55.5 | 12.2 | 8 | | Europe | Sweden | SW | 58.3 | 19.1 | 5 | | Europe | Scotland | OH | 57.2 | -6.1 | 13 | | Europe | Ireland | IR | 52.1 | -10.3 | 13 | | Europe | Ireland | KEI | 51.8 | -10.3 | 30 | | Europe | United Kingdom | UK1 | 49.4 | -2.6 | 15 | | Europe | United Kingdom | UK2 | 50.6 | -2.4 | 15 | | North America | NL, Canada | COH | 51.5 | -55.5 | 30 | | North America | NL, Canada | NIP | 49.7 | -55.8 | 30 | | North America | NL, Canada | TNR\* | 48.6 | -53.5 | 30 | | North America | NL, Canada | CHA | 48.3 | -53.2 | 30 | | North America | NL, Canada | WIT | 47.2 | -52.7 | 30 | | North America | NL, Canada | BAI | 47.1 | -54.8 | 30 | | North America | Gulf of St. Lawrence, Canada | GSL | various (53 sites) | various (53 sites) | 105 | | North America | NS, Canada | PPG | 44.6 | -66.8 | 13 | | North America | Gulf of Maine, USA | US1 | 44.9 | -67.0 | 14 | | North America | Gulf of Maine, USA | BIM | 44.5 | -67.6 | 6 | | North America | Gulf of Maine, USA | FBM | 44.4 | -68.2 | 19 | | North America | Gulf of Maine, USA | US2 | 44.4 | -68.2 | 14 | | North America | Gulf of Maine, USA | MSB | 42.8 | -70.5 | 15 | ## **Code/Software** Code that has been used in this submission can be found at [https://github.com/babslangille/Genomic-differentiation-structural-variants-and-clinal-variation](https://github.com/babslangille/Genomic-differentiation-structural-variants-and-clinal-variation)