SNP genotype data for assessing population structure among bearded seals in the Pacific Arctic

• Main Author: Aimee Lang
• Format: Dataset
• Language: unknown
• Published: Research Workspace
• Subjects: OCEAN > ARCTIC OCEAN > CHUKCHI SEA; OCEAN > PACIFIC OCEAN > NORTH PACIFIC OCEAN > BERING SEA; Erignathus; bearded seals; sea ice; Erignathus barbatus; population structure; high throughput sequencing; bearded seal; EARTH SCIENCE > AGRICULTURE > ANIMAL SCIENCE > ANIMAL BREEDING AND GENETICS; North Pacific Research Board; Arctic; Arctic Ocean; Bering Sea; Chukchi Sea; Pacific; Chukchi; Pacific Arctic; Sea ice
• Online Access: https://search.dataone.org/view/10.24431_rw1k45k_2020_6_19_202353

Data in this collection include genotypes (n= 240,560 loci) generated from samples collected from bearded seals (n=190) in the Pacific Arctic region, primarily the northern Bering and southeastern Chukchi Seas, between 1993 and 2015. Almost all of the samples were derived from harvested seals (n=179), while the remainder were collected from seals (n=3) killed by polar bears and from stranded animals (n=8). DNA was extracted from the seal samples at the Southwest Fisheries Science Center in La Jolla, CA, and then sent to the Genomic Diversity Facility (GDF) at Cornell University for library preparation and subsequent genotyping by sequencing (Elshire et al. 2011). The data provided consists of 1) ‘Data_NPRB1514_SampleInfo.csv’, which contains information on the source, sampling locality, and sampling date for all samples, and 2) a gzipped compressed vcf file ‘NPRB1514.all.vcf.gz’that contains the raw genotype data for all SNPs identified in the GDF pipeline, prior to applying any quality control filters. VCF is a format for holding SNP information that retains data on depth of coverage for each allele, allowing recalling of the genotypes as needed. This data set was subjected to quality control filtering (see final report for NPRB1514) prior to conducting population structure analyses. The FASTQ.gz files generated from the sequencing data can be provided upon request.