Fine-scale environmentally associated spatial structure of Lumpfish ( Cyclopterus lumpus) across the Northwest Atlantic
Data files
Sep 12, 2023 version files 1.11 GB
Abstract
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.
README
This README file was generated on 2023-09-08 by Barbara Langille
GENERAL INFORMATION
- Title of Dataset Fine-scale environmentally associated spatial structure of Lumpfish (Cyclopterus lumpus) across the Northwest Atlantic
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.caGeographic location of data collection: Northwest North America (from Gulf of Maine to Newfoundland)
DATA AND FILE OVERVIEW
- 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
- 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
- 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)
- 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
- 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).
- 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
- 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
- Data was derived from the following sources: A) 70K SNP array B) whole genome resequencing (WGS)
CODE/SOFTWARE
- Code can be found at Barbara Langille's github (https://github.com/babslangille).
- We mainly used plink v1.9 and R to manipulate files.
Methods
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.
Usage notes
We mainly used R to manipulate data files, however, also used PGDspider to convert file formats, as well as plink v1.9.