DOI: 10.5061/dryad.5vb8v
title: Data from: Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus)

description: Investigating how environmental features shape the genetic structure of
 populations is crucial for understanding how they are potentially adapted
 to their habitats, as well as for sound management. In this study, we
 assessed the relative importance of spatial distribution, ocean currents
 and sea surface temperature (SST) on patterns of putatively neutral and
 adaptive genetic variation among American lobster from 19 locations using
 population differentiation (PD) approaches combined with environmental
 association (EA) analyses. First, PD approaches (using bayescan, arlequin
 and outflank) found 28 outlier SNPs putatively under divergent selection
 and 9770 neutral SNPs in common. Redundancy analysis revealed that spatial
 distribution, ocean current-mediated larval connectivity and SST explained
 31.7% of the neutral genetic differentiation, with ocean currents driving
 the majority of this relationship (21.0%). After removing the influence of
 spatial distribution, no SST were significant for putatively neutral
 genetic variation whereas minimum annual SST still had a significant
 impact and explained 8.1% of the putatively adaptive genetic variation.
 Second, EA analyses (using Pearson correlation tests, bayescenv and lfmm)
 jointly identified seven SNPs as candidates for thermal adaptation.
 Covariation at these SNPs was assessed with a spatial multivariate
 analysis that highlighted a significant temperature association, after
 accounting for the influence of spatial distribution. Among the 505
 candidate SNPs detected by at least one of the three approaches, we
 discovered three polymorphisms located in genes previously shown to play a
 role in thermal adaptation. Our results have implications for the
 management of the American lobster and provide a foundation on which to
 predict how this species will cope with climate change.
description: 13688snps-562individus.recodeThe file contains 13,688 SNPs and 562 individuals.RDA-selectionThe script used for performing RDA on the putatively under selection SNPs.scrip-rda-selection-legendre.RRDA-neutralThe script used for performing RDA on the putatively neutral SNPs.scrip-rda-neutral.R9770snps-neutral.frqThe file containing all the allele frequencies for the putatively neutral SNPs.28snps-562ind-freq.frqThe file containing all the allele frequencies for the putatively neutral SNPs.script-outflankThe script used for running OUTFLANKbayescan-13688snps-562ind 2The file used to run Bayescan.script_bayescan_lauraThe script used to analyse bayescan results.arlequin-13688snps-562indThe file use dot run Arlequin.AEM_vectorsThe output of the AEM analysis.aem-19popThe input to calculate AEM vectorsGeographical_dataThe spatial distribution data file used to calculate dbMEMEnvironmentalThe sea surface temperature data.script-AEMThe file used to visualize AEM vectors.freq-allelic-13688snps.txt.frqAll the allele frequencies at each SNP used to perform correlation tests.8094lociAll the sequence used to perform a BLAST search.