10.5061/DRYAD.C3318
Plough, Louis V.
University of Maryland, College Park
Data from: Population genomic analysis of the blue crab Callinectes
sapidus using genotyping-by-sequencing
Dryad
dataset
2017
Callinectes sapidus
FST
SNPs
2017-09-08T00:00:00Z
2017-09-08T00:00:00Z
en
https://doi.org/10.2983/035.036.0128
1633648 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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 >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
Brazil
North America