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.
Gray seal RAD loci
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.
Hg_consensus_seq_all.fa
Harbor seal RAD loci
Catalog 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.fa
Gray seal SNPs
Catalog 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.csv
Harbor seal SNPs
Catalog 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.csv
Gray seal genotypes
A 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.txt
Harbor seal genotypes
A 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