DOI: 10.5061/dryad.c3318
title: Data from: Population genomic analysis of the blue crab Callinectes sapidus using genotyping-by-sequencing

description: Previous genetic studies of the blue crab Callinectes sapidus along the
 U.S. Atlantic and Gulf coasts have reported weak or temporally variable
 spatial structure, suggesting high gene flow among distant populations
 possibly facilitated by long-distance larval dispersal or other features
 of blue crab life history. The use of relatively few genetic markers,
 however, may have limited power to detect subtle but significant structure
 that could inform fisheries management. In this study, the potential for
 genome-scale datasets to uncover subtle patterns of population structure
 in the blue crab was examined using a high-throughput genotyping approach
 (genotyping-by-sequencing) that generated data for more than 9,600 single
 nucleotide polymorphisms (SNPs) in crabs from three populations: Panama
 City Beach, FL, Agawam River, MA, and Porto Alegre, Brazil. Principle
 components analyses among the three populations revealed very distinct
 clustering of the Brazilian samples from U.S. populations, likely
 reflecting restricted gene flow across the equator. Detailed analysis of
 population structure between the two U.S. populations revealed low but
 significant genetic differentiation (FST = 0.0103), with FST values
 ranging from -0.05 to 0.48. Previous studies have failed to detect
 significant genetic structure on a similar geographic scale. FST outlier
 analysis identified 242 loci (2.45% of total) with statistically extreme
 values at the false discovery rate α = 0.05 level, only 16 of which showed
 significant sequence homology to annotated proteins via BLASTx alignment.
 Top BLASTx hits were to crustacean or arthropod sequences and 8 of the 16
 had high sequence similarity to transposable elements or related
 machinery. Finally, results of population assignment tests for the two
 U.S. populations showed that the full marker dataset provided good power
 to assign individuals back to their population of origin (∼83% and 92%
 success for Panama City Beach and Agawam River, respectively), which
 dropped significantly when using only 500 randomly selected SNPs (∼61% and
 72% success). Overall, this study demonstrates the great utility of
 high-throughput sequencing technologies for characterizing fine-scale
 patterns of genetic structure in blue crabs, and this approach should
 substantially improve the delineation of stock structure and further
 advance our understanding of blue crab population connectivity and
 ecology.
description: Filtered SNP genotype
 data set for Brazil, Massachussets and FloridaThis is a genepop
 formatted file (.gen) with SNP data for the three populations examined in
 this study (Porto Allegre, Brazil, Panama city beach FL, and Agawam river
 MA, USA). File contains data for 2,783 SNPs which were filtered for HWE,
 LD, and coverage. Genotype data was exported from the Stacks pipeline v.
 1.34 or higher.ld_hwe_pruned_crab.genFull SNP dataset for 2 North American populationsThis file contains SNP genotype data in genepop format (.gen) for 9864 loci from two blue crab populations : Agawam river MA (AR populatioN) and Panama City Beach, FL (PCB population). Genotype data were filtered for coverage and &gt;85% genotypes called for individuals, and HWE, but not for linkage disequilibrium (LD). Data were exported from Stacks v.1.34 or above.10K_FLA_CH.gen