Gray seal RAD loci

• Main Author: Cammen, Kristina
• Format: Dataset
• Language: unknown
• Published: Dryad Digital Repository 2018
• Subjects: gray seal; restriction site-associated DNA sequencing; Northwest Atlantic; Halichoerus grypus atlantica; Canada
• Online Access: https://dx.doi.org/10.5061/dryad.fg52075/1; https://datadryad.org/resource/doi:10.5061/dryad.fg52075/1

Catalog of 244,822 RAD loci consensus sequences resulting from ddRAD sequencing of genomic DNA from 56 gray seals sampled in the Northwest Atlantic. The gray seals selected to build the RAD catalog included 7 individuals from each of the following sampling locations and cohorts - Gulf of St Lawrence, Canada: 2015; Sable Island, NS, Canada: 1973-74, 1985, 1998, 2004, and 2015; Muskeget Island, MA, USA: 2002 and 2015-16. The details of the ddRAD protocol and bioinformatic processing are described in detail in the Methods section and Appendix S1 of Cammen et al. (2018). In brief, ddRAD was conducted with restriction enzymes SBfI-HF and MspI, size selection by 1.5x beads, and 50-bp single-end read Illumina Hiseq 2500 sequencing. Sequences were processed using Stacks v1.21 to build loci de novo using the following parameters, selected using the r80 optimization approach: m = 2, M = 2, and n = 2. File is in FASTA format and each sequence is identified by a numerical locus ID.