10.5061/DRYAD.V4Q83
Baetscher, Diana S.
University of California System
Southwest Fisheries Science Center
Hasselman, Daniel J.
University of California, Santa Cruz
Reid, Kerry
University of California System
Southwest Fisheries Science Center
Palkovacs, Eric P.
University of California, Santa Cruz
Garza, John Carlos
University of California System
Southwest Fisheries Science Center
Data from: Discovery and characterization of single nucleotide
polymorphisms in two anadromous alosine fishes of conservation concern
Dryad
dataset
2018
Alosa pseudoharengus
river herring
Alosa aestivalis
Single nucleotide polymorphisms
Holocene
2018-06-26T00:00:00Z
2018-06-26T00:00:00Z
en
https://doi.org/10.1002/ece3.3215
11455120 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Freshwater habitat alteration and marine fisheries can affect anadromous
fish species, and populations fluctuating in size elicit conservation
concern and coordinated management. We describe the development and
characterization of two sets of 96 single nucleotide polymorphism (SNP)
assays for two species of anadromous alosine fishes, alewife and blueback
herring (collectively known as river herring), that are native to the
Atlantic coast of North America. We used data from high-throughput DNA
sequencing to discover SNPs and then developed molecular genetic assays
for genotyping sets of 96 individual loci in each species. The two sets of
assays were validated with multiple populations that encompass both the
geographic range and the known regional genetic stocks of both species.
The SNP panels developed herein accurately resolved the genetic stock
structure for alewife and blueback herring that was previously identified
using microsatellites and assigned individuals to regional stock of origin
with high accuracy. These genetic markers, which generate data that are
easily shared and combined, will greatly facilitate ongoing conservation
and management of river herring including genetic assignment of marine
caught individuals to stock of origin.
Alewife SNP genotypesAlewife SNP
genotypes-twocolumnformatALEVAL323_93_twocolumn.txtBlueback Herring SNP
genotypesBlueback Herring SNP genotypes-twocolumn
formatBBH_VAL_431_96_twocolumn.txtAlewife FASTA fileFASTA file with
consensus sequences from all alewife ddRAD loci with at least one
SNPalewife_batch_1.faBlueback Herring FASTA fileFASTA file with consensus
sequences from all Blueback Herring ddRAD loci with at least one
SNPblueback_batch_1.faAlewife haplotypesAlewife haplotype calls from all
combinations of locus and
individual.alewife_batch_1.haplotypes.tsvBlueback herring
haplotypesBlueback herring haplotype calls from all combinations of locus
and individual.blueback_batch_1.haplotypes.tsvREADMEREADME file
Eastern North America
Northwest Atlantic Ocean