Data from: Putatively adaptive genetic variation in the giant California sea cucumber (Parastichopus californicus) as revealed by environmental association analysis of restriction‐site associated DNA sequencing data

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Description:
Understanding the spatial scale of local adaptation and the factors associated with adaptive diversity are important objectives for ecology and evolutionary biology, and have significant implications for effective conservation and management of wild populations and natural resources. In this study, we used an environmental association analysis (EAA) to identify important bioclimatic variables correlated with putatively adaptive genetic variation in a benthic marine invertebrate – the giant California sea cucumber (Parastichopus californicus) – spanning coastal British Columbia and southeastern Alaska. We used a redundancy analysis (RDA) with 3,699 SNPs obtained using RAD sequencing to detect candidate markers associated with 11 bioclimatic variables, including sea bottom and surface conditions, across two spatial scales (entire study area and within sub-regions). At the broadest scale, RDA revealed 59 candidate SNPs, 86% of which were associated with mean bottom temperature. Similar patterns were identified when population structure was accounted for. Additive polygenic scores, which provide a measure of the cumulative signal across all candidate SNPs, were strongly correlated with mean bottom temperature, consistent with spatially varying selection across a thermal gradient. At a finer scale, 23 candidate SNPs were detected, primarily associated with surface salinity (26%) and bottom current velocity (17%). Our findings suggest that environmental variables may play a role as drivers of spatially varying selection for P. californicus. These results provide context for future studies to evaluate the genetic basis of local adaptation in P. californicus and help inform the relevant scales and environmental variables for in situ field studies of putative adaptive variation in marine invertebrates.

Usage Notes:

01-RDA_candidate_snps

script to perform RDA for detecting candidate SNPs

02-compute_polygenic_scores

script to compute polygenic scores across candidate SNPs

3699snps_freqs

allele frequencies for RDA

candidates.frq

candidate frequencies for polygenic scores

meanbottomtemp_atsites

bottom temperature at sites for polygenic scores
Auteur(s) :
Xuereb, Amanda

Xuereb, Amanda

University of Toronto
, Kimber, Christopher M.

Kimber, Christopher M.

Linköping University
, Curtis, Janelle M.R.

Curtis, Janelle M.R.

University of Toronto
, Bernatchez, Louis

Bernatchez, Louis

Université Laval
0000-0002-8085-9709
, Fortin, Marie-Josée

Fortin, Marie-Josée

University of Toronto
et Curtis, Janelle M. R.

Curtis, Janelle M. R.

Fisheries and Oceans Canada
Dépôt source:
Dryad
Éditeur(s):
Dryad
Accès:
Public
URL:
http://datadryad.org/stash/dataset/doi:10.5061/dryad.b0p66dn
Date de publication:
2018-10-29
Mots-clés (en):
Echinoderms, Marine Invertebrate, redundancy analysis, environmental association analysis, Seascape Genomics, et Climate Data
Identificateur:
https://doi.org/10.5061/dryad.b0p66dn

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Citation selon les normes APA:
Data from: Putatively adaptive genetic variation in the giant California sea cucumber (Parastichopus californicus) as revealed by environmental association analysis of restriction‐site associated DNA sequencing data. (2018). [Data set]. Dryad. http://datadryad.org/stash/dataset/doi:10.5061/dryad.b0p66dn
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