DOI: 10.5061/dryad.fg52075
title: Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds

description: Population increases over the past several decades provide natural
 settings in which to study the evolutionary processes that occur during
 bottleneck, growth, and spatial expansion. We used parallel natural
 experiments of historical decline and subsequent recovery in two sympatric
 pinniped species in the Northwest Atlantic, the gray seal (Halichoerus
 grypus atlantica) and harbor seal (Phoca vitulina vitulina), to study the
 impact of recent demographic change in genomic diversity. Using
 restriction site‐associated DNA sequencing, we assessed genomic diversity
 at over 8,700 polymorphic gray seal loci and 3,700 polymorphic harbor seal
 loci in samples from multiple cohorts collected throughout recovery over
 the past half‐century. Despite significant differences in the degree of
 genetic diversity assessed in the two species, we found signatures of
 historical bottlenecks in the contemporary genomes of both gray and harbor
 seals. We evaluated temporal trends in diversity across cohorts, as well
 as compared samples from sites at both the center and edge of a recent
 gray seal range expansion, but found no significant change in genomewide
 diversity following recovery. We did, however, find that the variance and
 degree of allele frequency change measured over the past several decades
 were significantly different from neutral expectations of drift under
 population growth. These two cases of well‐described demographic history
 provide opportunities for critical evaluation of current approaches to
 simulating and understanding the genetic effects of historical demographic
 change in natural populations.
description: Gray seal RAD
 lociCatalog 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.Hg_consensus_seq_all.faHarbor seal RAD lociCatalog of 195,906 RAD loci consensus sequences resulting from ddRAD sequencing of genomic DNA from 55 bycaught harbor seals sampled in the Northeast United States between 1992 and 2015. 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.Pv_consensus_seq_all.faGray seal SNPsCatalog of single nucleotide polymorphisms (SNPs) identified in ddRAD loci among 252 gray seals from the Northwest Atlantic. SNPs were identified and genotyped using a bounded maximum-likelihood model in Stacks v1.21 with no minimum minor allele frequency. LocusID refers to the locus ID in RAD loci catalog FASTA file; Column refers to the position of the variable nucleotide within the locus.Hg.catalog.snps.csvHarbor seal SNPsCatalog of single nucleotide polymorphisms (SNPs) identified in ddRAD loci among 55 harbor seals from the Northwest Atlantic. SNPs were identified and genotyped using a bounded maximum-likelihood model in Stacks v1.21 with no minimum minor allele frequency. LocusID refers to the locus ID in RAD loci catalog FASTA file; Column refers to the position of the variable nucleotide within the locus.Pv.catalog.snps.csvGray seal genotypesA genepop file containing ddRAD genotypes for 252 gray seals from the Northwest Atlantic. All including loci were genotyped in at least 80% of the individuals in each sample group. Gray seals samples represent three breeding colonies and up to five cohorts per colony. Locus names are composed of the LocusID that corresponds to the RAD loci catalog FASTA file and the position of the variable nucleotide within the locus.Hg_genepop_r80p8.gen.txtHarbor seal genotypesA genepop file containing ddRAD genotypes for 55 harbor seals from the Northeast US. All including loci were genotyped in at least 80% of the individuals in each sample group. Harbor seals samples represent three cohorts sampled since 1992. Locus names are composed of the LocusID that corresponds to the RAD loci catalog FASTA file and the position of the variable nucleotide within the locus.Pv_genepop_r80p3.gen.txt