Data from: Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus

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Description:
Environmental factors can influence diversity and population structure in marine species and accurate understanding of this influence can both improve fisheries management and help predict responses to environmental change. We used 7163 SNPs derived from restriction site-associated DNA sequencing genotyped in 245 individuals of the economically important sea scallop, Placopecten magellanicus, to evaluate the correlations between oceanographic variation and a previously identified latitudinal genomic cline. Sea scallops span a broad latitudinal area (>10 degrees), and we hypothesized that climatic variation significantly drives clinal trends in allele frequency. Using a large environmental dataset, including temperature, salinity, chlorophyll a, and nutrient concentrations, we identified a suite of SNPs (285–621, depending on analysis and environmental dataset) potentially under selection through correlations with environmental variation. Principal components analysis of different outlier SNPs and environmental datasets revealed similar northern and southern clusters, with significant associations between the first axes of each (R2adj = .66–.79). Multivariate redundancy analysis of outlier SNPs and the environmental principal components indicated that environmental factors explained more than 32% of the variance. Similarly, multiple linear regressions and random-forest analysis identified winter average and minimum ocean temperatures as significant parameters in the link between genetic and environmental variation. This work indicates that oceanographic variation is associated with the observed genomic cline in this species and that seasonal periods of extreme cold may restrict gene flow along a latitudinal gradient in this marine benthic bivalve. Incorporating this finding into management may improve accuracy of management strategies and future predictions.

Usage Notes:

VanWyngaardenM_etal_SeascapeGen_RADseq_SNPs

This VCF file contains 7216 RAD-seq derived SNPs detected among 12 Northwest Atlantic Ocean populations of the sea scallop, Placopecten magellanicus. The program stacks v0.9999 was used to call variants.
VanWyngaardenM_etal_SeascapeGen_SNPMap4b.vcf

VanWyngaardenM_etal_SeascapeGen_RADseq_Barcodes_Index

This file contains population information and the sequences for the P1 Barcodes and the P2 Indexes for all adult sea scallops collected and used in the analysis. This information will allow readers to demultiplex the data from the raw sequence reads archived in NCBI SRA and repeat the SNP calling analysis.
VanWyngaardenM_etal_SeascapeGen_Barcode.xlsx

VanWyngaardenM_etal_SeascapeGen_FinalEnvironmentalData

This file contains data for the final 90 environmental variables used to compare genetic and environmental variation among sea scallop populations as well as the latitude and longitude of all 12 sample sites. Data have been standardized to 0 mean and unit variance.

VanWyngaardenM_et_al_SeascapeGen_SampleSiteDistance

This file contains distances (in kilometers) from the furthest north sample site (SUN) for all populations of Placopecten magellanicus sampled along a one dimensional transect (estimated using Google Earth).

VanWyngaardenM_etal_SeascapeGen_RCode

This R file contains pseudocode for the main analyses used in the publication "Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus" by Van Wyngaarden, M et al. Not all steps are included in the code but examples of the major analyses (outlier selection, PCA, RDA, and multiple linear regressions) are presented. Running this code will not repeat all the analyses used in the publication but will allow readers to see what functions were used.
VanWyngaardenM_etal_SeascapeGen_Code.R
Author(s):
Van Wyngaarden, Mallory

Van Wyngaarden, Mallory

Memorial University of Newfoundland
, Snelgrove, Paul V. R.

Snelgrove, Paul V. R.

Memorial University of Newfoundland
, DiBacco, Claudio

DiBacco, Claudio

Bedford Institute of Oceanography
, Hamilton, Lorraine C.

Hamilton, Lorraine C.

Bedford Institute of Oceanography
, Rodriguez-Ezpeleta, Naiara

Rodriguez-Ezpeleta, Naiara

Marine Research Division; AZTI; Sukarrieta Bizkaia Spain
, Zhan, Luyao

Zhan, Luyao

Dalhousie University
, Beiko, Robert

Beiko, Robert

Dalhousie University
, Bradbury, Ian R.

Bradbury, Ian R.

Dalhousie University
, and Beiko, Robert G.

Beiko, Robert G.

Dalhousie University
Source Repository:
Dryad
Publisher(s):
Dryad
Access:
Public
URL:
http://datadryad.org/stash/dataset/doi:10.5061/dryad.c15v5
Publication date:
2019-01-02
Keywords:
single nucleotide polymorphism, outlier loci, Placopecten magellanicus, and sea scallop
Identifier:
https://doi.org/10.5061/dryad.c15v5

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Citation

APA Citation:
Van Wyngaarden, M., Snelgrove, P. V. R., DiBacco, C., Hamilton, L. C., Rodriguez-Ezpeleta, N., Zhan, L., Beiko, R., Bradbury, I. R., & Beiko, R. G. (2019). Data from: Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus [Data set]. Dryad. http://datadryad.org/stash/dataset/doi:10.5061/dryad.c15v5
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