DOI: 10.5061/dryad.q771r
title: Data from: RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus).

description: Deciphering genetic structure and inferring connectivity in marine species
 have been challenging due to weak genetic differentiation and limited
 resolution offered by traditional genotypic methods. The main goal of this
 study was to assess how a population genomics framework could help
 delineate the genetic structure of the American lobster (Homarus
 americanus) throughout much of the species’ range and increase the
 assignment success of individuals to their location of origin. We
 genotyped 10 156 filtered SNPs using RAD sequencing to delineate genetic
 structure and perform population assignment for 586 American lobsters
 collected in 17 locations distributed across a large portion of the
 species’ natural distribution range. Our results revealed the existence of
 a hierarchical genetic structure, first separating lobsters from the
 northern and southern part of the range (FCT = 0.0011; P-value = 0.0002)
 and then revealing a total of 11 genetically distinguishable populations
 (mean FST = 0.00185; CI: 0.0007–0.0021, P-value &lt; 0.0002),
 providing strong evidence for weak, albeit fine-scale population
 structuring within each region. A resampling procedure showed that
 assignment success was highest with a subset of 3000 SNPs having the
 highest FST. Applying Anderson's (Molecular Ecology Resources, 2010,
 10, 701) method to avoid ‘high-grading bias’, 94.2% and 80.8% of
 individuals were correctly assigned to their region and location of
 origin, respectively. Lastly, we showed that assignment success was
 positively associated with sample size. These results demonstrate that
 using a large number of SNPs improves fine-scale population structure
 delineation and population assignment success in a context of weak genetic
 structure. We discuss the implications of these findings for the
 conservation and management of highly connected marine species,
 particularly regarding the geographic scale of demographic independence.
description: 10156 SNPs identified
 for Homarus americanusVCF output of the 10156
 SNPs identified for Homarus americanus through a RAD sequencing
 protocol.10156-586.recode.vcf8411snps-586indData containing 8411 SNPs successfully genotyped in 586 lobsters.8411-586.recode.vcfFST_GEOGRAPHICAL_DISTANCESGeographic distances and FST values between each pair of sampling locationBatch-catalogs for American lobsterbatch_1.catalog.tags.tsvAssignment results for 20 samples using THL methodassignment-20samples-regions.results.tsvAssignment results for 36 samples using THL methodassignment-36samples-regions.results.tsvAssignment results for 50 samples using THL methodassignment-50samples-regions.results.tsvAssignment results for 100 samples using THL methodassignment-100samples-regions.results.tsvAssignment results for the sites using LOO method (1 individual for ranking)assignment.summary.stats.no.imputation.ranked-THL1-sites.tsvAssignment results for regions using THL method (50% of individuals)assignment.summary.stats.no.imputation.ranked-regions-THL0.5.tsvAssignment results for sites using THL method (50% of individuals)assignment.summary.stats.no.imputation.ranked-sites-THL0.5.tsv