DOI: 10.5061/dryad.c15v5
title: Data from: Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus

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 (&gt;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.
description: VanWyngaardenM_etal_SeascapeGen_RADseq_SNPsThis 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.vcfVanWyngaardenM_etal_SeascapeGen_RADseq_Barcodes_IndexThis 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.xlsxVanWyngaardenM_etal_SeascapeGen_FinalEnvironmentalDataThis 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_SampleSiteDistanceThis 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_RCodeThis 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