DOI: 10.5061/dryad.q83bk3jpq
title: Fine-scale environmentally associated spatial structure of Lumpfish ( Cyclopterus lumpus) across the Northwest Atlantic

description: Lumpfish, Cyclopterus lumpus, have historically been harvested throughout
 Atlantic Canada and are increasingly in demand as a solution to
 controlling sea lice in Atlantic salmon farms – a process which involves
 both the domestication and the transfer of lumpfish between geographic
 regions. Here, we have 70K SNP array data and whole genome re-sequencing
 data (WGS) for a variety of sample sites across the Northwest
 Atlantic. 
description: We sampled 1115 individuals
 from 79 locations throughout the North Atlantic from 2009 to 2019 (Fig.
 1a; S1) in conjunction with scientific research surveys (trawl and beach
 seines) and commercial fishing activities. Sampling locations included
 waters around Newfoundland (N=994), the Gulf of St. Lawrence (GSL)
 (N=108), waters around Grand Manan (N=13), and from the Gulf of Maine
 (N=83). Due to the different sampling approaches utilized, differences in
 the sexes and life stages collected were present. Research vessel surveys
 collected individuals using a bottom trawl and generally targeted adults
 of both sexes, commercial samples were largely adult females due to the
 selective nature of the fishery for roe, and coastal sites around
 Newfoundland (TNR, SPA, and NMS, Fig. 1a), sampled using a beach seine
 were juvenile lumpfish comprising both sexes. In all cases, fin clips were
 preserved in 95% ethanol for subsequent DNA
 extraction.             For the 70K SNP array data, 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; Holborn et al., 2022). 
             We conducted medium coverage (~8x),
 whole genome re-sequencing (WGS) of 848 lumpfish from multiple sites
 across North America (Fig. 1a; S1). The same individuals were used for WGS
 as in the array; however, individuals from sites US1, US2, CA and BHbr,
 were only present with array data. For whole genome re-sequencing library
 preparation, DNA extraction followed Mayjonade et al. (2016), using
 Longmire’s buffer (Longmire et al., 1997) for tissue lysis. Library
 preparation followed a modification of the protocol from Therkildsen and
 Palumbi (2017) by scaling down Nextera DNA Flex Library Prep Kits
 (Illumina) reaction volumes to 0.13x then used a standard volume in the
 Illumina protocol. We then used Kapa Hi-Fidelity Library Amplification
 Kits (Roche) for library amplification (20 ml reactions, 4 ml Nextera Unique Dual Indexes Set A (Illumina)).
 Libraries were quantified by Qubit (ThermoFisher) and an Agilent
 Bioanalyzer was used to check average fragment size. Libraries were
 normalized from 96-well plates to equimolar concentrations and pooled
 separately for each lane of sequencing. We sequenced pooled libraries at
 The Genome Quebec Centre d’expertise et de services on 11 lanes of an
 Illumina NovaSeq6000
 S4. 
description: We mainly used R to manipulate data files, however, also used
 PGDspider to convert file formats, as well as plink v1.9.
description: This README file was generated on 2023-09-08 by Barbara Langille GENERAL
 INFORMATION 1. Title of Dataset Fine-scale environmentally associated
 spatial structure of Lumpfish (Cyclopterus lumpus) across the Northwest
 Atlantic 2. Author information ``` A. Primary Author Contact Information
 Name: Barbara Langille Institution while conducting this research:
 Department of Fisheries and Oceans Address: Bedford Institute of
 Oceanography, Challenger drive, Dartmouth, NS, Canada Current Insitution:
 Huntsman Marine Science Center Address: Lower Campus rd, St. Andrews, NB,
 Canada Email: bll845@mun.ca B. Main Co-investigator Information Name: Ian
 Bradbury Institution: Department of Fisheries and Oceans Address: Bedford
 Institute of Oceanography, Challenger drive, Dartmouth, NS, Canada Email:
 Ian.Bradbury@dfo-mpo.gc.ca ``` 3. Geographic location of data collection:
 Northwest North America (from Gulf of Maine to Newfoundland) DATA AND FILE
 OVERVIEW 1. File list: <br> A)
 SNParray\_Lumpfish\_recluster\_filterNA\_norelated.ped B)
 SNParray\_Lumpfish\_recluster\_filterNA\_norelated.map C)
 Cyclopterus\_lumpus\_sizechecked\_phased\_NA\_exon.ped D)
 Cyclopterus\_lumpus\_sizechecked\_phased\_NA\_exon.map 2. Both files the
 start with 'SNParray...' are the data from the 70K snp array,
 while the files labelled 'Cyclopterus...' are the whole genome
 resequencing (WGS) data. More information on how the datasets were
 generated can be found in the associated publication in Evolutionary
 Applications entitled: Fine-scale environmentally associated spatial
 structure of Lumpfish (Cyclopterus lumpus) across the Northwest Atlantic
 3. Both Ped files have the same format of information - Family ID,
 Individual ID, Paternal ID, Maternal ID, Sex, Phenotype, Genotype -no data
 for paternal or maternal ID and is set to zero -no info for sex of
 phenotype and is set to zero and -9, respectively -genotype is the list of
 snps for each individual - is in the same order as the map file (which
 tells you exactly where the snp is in the genome) 4. Both Map files have
 the same format of information - Chromosome, SNP name, Genetic distance
 (all zero in this case), Base-pair position (bp units) -any missing data
 will be filtered out when you filter by maf, geno, and mind in plink -any
 extra rows will be ignored in plink and R 5. Population/Family ID codes
 Region Location Population N Newfoundland Baine Harbour BAI 55 Baine
 Harbour BHbr 48 Witless Bay CA 14 Champneys CHA 46 Cooks Harbour COH 50
 Fortune FTN 98 Gooseberry Cove GBC 98 Greenspond GRE 58 Musgrave Harbour
 MUG 50 Nippers Harbour NIP 50 Newman Sound NMS\* 10 Multi-species
 Survey3Ps S3P 35 Placentia Bay SPA\* 22 Terra Nova TNR\* 50 Twillingate
 TWI 50 Witless Bay WIT 118 Wild Cove WLN 59 Gulf of St. Lawrence TE1
 combination - see supplementary files of publication for information on
 how sites were combined TE2 combination - see supplementary files of
 publication for information on how sites were combined TE3 combination -
 see supplementary files of publication for information on how sites were
 combined New Brunswick Pond Point Grand Manan PPG 13 United States Bay
 East of Beals Island BIM 16 Frenchmans Bay FBM 29 Scantums Basin MSB 17
 Cobscook Bay US1 15 Frenchmans Bay US2 14 * The asterix indicates a
 juvenile sample site. * These codes are found in the individual ID in the
 WGS data. * The same individuals are found in both datasets (although
 there are a few less sample sites in the WGS data). 6. Citation for this
 dataset: Langille, Barbara et al. (2023). Fine-scale environmentally
 associated spatial structure of Lumpfish ( Cyclopterus lumpus) across the
 Northwest Atlantic [Dataset]. Dryad.
 https://doi.org/10.5061/dryad.q83bk3jpq SHARING/ACCESS INFORMATION 1.
 Links to publications that cite or use the data: Langille BL, Kess T,
 Brachmann M, Nugent CM, Messmer A, Duffy SJ, Holborn MK, Van Wyngaarden M,
 Knutsen TM, Kent M, Boyce D, Gregory RS, Gauthier J, Fairchild EA, Pietrak
 M, Eddy S, Bentzen P, Bradbury IR. (2023). Fine-scale environmentally
 associated spatial structure of Lumpfish (Cyclopterus lumpus) across the
 Northwest Atlantic. Evolutionary Applications 2. Data was derived from the
 following sources: A) 70K SNP array B) whole genome resequencing (WGS)
 CODE/SOFTWARE 1. Code can be found at Barbara Langille's github
 (https://github.com/babslangille). 2. We mainly used plink v1.9 and R to
 manipulate files.