Data from: Seascape genomics of eastern oyster (Crassostrea virginica) along the Atlantic coast of Canada.
- Description:
- Interactions between environmental factors and complex life-history characteristics of marine organisms produce the genetic diversity and structure observed within species. Our main goal was to test for genetic differentiation among eastern oyster populations from the coastal region of Canadian Maritimes against expected genetic homogeneity caused by historical events, taking into account spatial and environmental (temperature, salinity, turbidity) variation. This was achieved by genotyping 486 individuals originating from 13 locations using RADSeq. A total of 11 321 filtered SNPs were used in a combination of population genomics and environmental association analyses. We revealed significant neutral genetic differentiation (mean FST= 0.009) between sampling locations, and the occurrence of six major genetic clusters within the studied system. Redundancy analyses (RDA) revealed that spatial and environmental variables explained 3.1% and 4.9% of the neutral genetic variation and 38.6% and 12.2% of the putatively adaptive genetic variation, respectively. These results indicate that these environmental factors play a role in the distribution of both neutral and putatively adaptive genetic diversity in the system. Moreover, polygenic selection was suggested by genotype–environment association analysis and significant correlations between additive polygenic scores and temperature and salinity. We discuss our results in the context of their conservation and management implications for the eastern oyster.
Usage Notes:genepop_6SNPs_divergent_notimputed
Genotypes data (not imputed) for potentially selected SNPs in Genepop formatgenepop_6SNPs_divergent_IMPUTED
Imputed genotypes data for potentially selected SNPs in Genepop formatgenepop_8246SNPs_NEUTRAL_notimputed
Genotypes data for putatively neutral SNPs in Genepop formatgenepop_8246SNPs_NEUTRAL_IMPUTED
Imputed genotypes data for putatively neutral SNPs in Genepop formatgenepop_11321SNPs_IMPUTED
Imputed genotypes data for all filtered SNPs in Genepop formatgenepop_11321SNPs_notimputed
Genotypes data for all filtered SNPs in Genepop formatgenepop_11321SNP_6clusters_IMPUTED_33indv
Imputed genotypes data for putatively all filtered SNPs with individuals in 6 cluters (equal sample size, n=33) in Genepop formatgenepop_11321SNP_6clusters_IMPUTED
Imputed genotypes data for putatively all filtered SNPs with individuals in 6 clutersin Genepop formatenvironmental_data_polygenicRDA
Environmental data for the polygenic RDA analysis11321SNPs_matrix012
Matrix (genotypes coded as 012) data for all filtered SNPs in Genepop formathaplotypes_4307
Haplotypes data for genetic diversity in tsv formatenvironmental_data_pcnmRDA
Environmental data for the PCNM+RDA analysismatrix012_6SNPs_divergent_IMPUTED
Matrix (genotypes coded as 012) data for potentially selected SNPsmatrix012_8246SNPs_NEUTRAL_IMPUTED
Matrix (genotypes coded as 012) data for putatively neutral SNPspopulation_map
Individual's population membershipread_me
Description of all files. - , Xuereb, Amanda, , , , , Bernatchez, Louis, and
- Source Repository:
- Dryad
- Publisher(s):
- Dryad
- Access:
- Public
- URL:
- http://datadryad.org/stash/dataset/doi:10.5061/dryad.g487s21
- Publication date:
- 2018-11-20
- Keywords:
- Identifier:
- https://doi.org/10.5061/dryad.g487s21
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