DOI: 10.5068/d1zd4d
title: Sea otter sequence capture project data files

description: Extinction or severe population contractions are rarely uniform across an
 entire species. However, because of the rapid onset of the fur trade in
 the 18th and 19th centuries, sea otters (Enhydra lutris) were
 systematically hunted to near extinction across their entire Northern
 Pacific range. Many sea otter populations were driven fully extinct, and
 the populations that survived suffered a rapid decline from 10-20,000
 individuals per population to fewer than one hundred survivors. Each
 surviving remnant sea otter population represents a replicate of an
 extreme population bottleneck event impacting genetic diversity and
 fitness into the future. Here, we designed sequence capture probes of the
 sea otter exome and neutral regions to examine the population structure
 and demographic history of five surviving sea otter populations from
 throughout the species’ former range, including three ancient Californian
 samples from ~1500 and ~200 years ago. We show that southern sea otters in
 California are the last survivors of a divergent lineage that has been
 isolated from northern and Asian populations for thousands of years,
 highlighting the need for their separate conservation. We detect a signal
 of extreme population decline in every surviving sea otter population and
 use simulations to demonstrate that these contractions may have lowered
 the fitness of recovering populations. However, we also infer historically
 low effective population sizes prior to the fur trade bottleneck which
 paradoxically could have led to the purging of highly deleterious
 mutations and mitigated the effects of population decline on the burden of
 harmful genetic variants, countering the conventional wisdom that large
 populations are most robust to decline. Nonetheless, future bottlenecks
 caused by existing external threats may act to maintain the negative
 genetic impacts of the fur trade for hundreds of generations, illustrating
 how human exploitation can leave a species vulnerable long after its
 nominal recovery.
description: We carried out sequence capture on DNA from 122 sea otters,
 sampled in the 1970s-90s from the Kuril Islands, Commander Islands,
 Aleutian Islands, south central Alaska, California and Baja California. We
 designed the sequence capture based on the annotation of the southern sea
 otter genome.<i> </i>50Mb of sequence was captured, including
 all annotated exonic sequence passing custom filters (see <b>SI
 Methods</b>), 1kb regions upstream of genes, and 10Mb of neutral
 regions far from genes. All sequencing fastq files are available on the
 Sequence Read Archive (SRA), BioProject accession PRJNA629776, and sample
 information is available in modernSampleInfo.xlsx. We mapped
 reads to the domestic ferret reference genome (<i>Mustela putorius
 furo,</i> accession GCA_000215625.1)<i> </i>in order
 have an outgroup genome from all sea otter populations and to make use of
 the existing Ensembl Variant Effect Predictor (VEP) database. Read mapping
 was carried out using the PALEOMIX pipeline.<sup>
 </sup>Genotypes were called and filtered using GATK (v. 3.7). On
 average, each sequenced individual had 6.14 x 10<sup>7
 </sup>called genotypes (61.4 Mb). Approximately 60,000 SNPs were
 discovered. Details of read mapping, genotype calling, and
 genotype filtering are in the SI Methods of Beichman et al. SNPs in coding
 regions were annotated as synonymous or missense using VEP. We generated
 the neutral site frequency spectrum based on SNPs in putatively neutral
 regions far from genes (SI Methods) using hypergeometric projection to
 maximize the number of SNPs. In addition to these modern sea
 otter samples, we carried out sequence capture on three historical/ancient
 samples from shell middens in California (details in Beichman et al. and
 in aDNA.SampleInfo.xlsx). To enrich for endogenous content, the ancient
 samples were subject to two serial sequence captures. This led very high
 levels of clonality, but a successful 30-fold enrichment of target regions
 after PCR duplicates were removed. Adapter removal and read
 mapping to both the domestic ferret (Acc. GCA_000215625.1) and southern
 sea otter (Acc. GCA_006410715.1) reference genomes were carried out using
 the PALEOMIX pipeline. Mapdamage was used to detect DNA-damage profiles
 and to rescale the quality score of bases that are likely to be
 misincorporations. We found that the modern samples mapped
 well to both the domestic ferret and sea otter genomes, which validates
 our choice to do the majority of modern analyses mapped to the domestic
 ferret genomes. However, the ancient samples showed a mapping preference,
 with more reads mapping to the sea otter genome, likely due to lower
 coverage and read quality. We therefore carried out all ancient analyses
 mapped to both reference genomes, with similar qualitative results. We
 selected three modern samples from each population (California, Alaska,
 Aleutians, Commanders, Kurils) o be analyzed alongside the ancient
 samples. Genotype likelihoods, genotype posteriors and per-site depths
 were determined using ANGSD. Finally, to ensure that our choice
 of a diverged outgroup reference genome would not bias estimates of
 heterozygosity or demographic history, we also mapped all individuals to
 the southern sea otter reference genome (accession GCA_006410715.1),
 called variants as described in the SI Methods of Beichman et al. and
 generated neutral SFSs from putatively neutral regions in the southern sea
 otter genome. Note that the set of putatively neutral regions in the
 southern sea otter genome is not identical to the set of regions in the
 ferret genome due to different annotations (see Methods section of
 Beichman et al. for details on these regions).
description: Here we present (1) VCF genotype files mapped to the domestic
 ferret reference genome for the modern data that were used for PCA and
 structure analysis and to generate the site frequency spectrum, (2) the
 folded neutral site frequency spectrum for each population, as well as the
 folded joint SFS for California and Alaska, (3) bam and ANGSD output files
 for the ancient+modern comparison analyses (3 ancient samples paired with
 15 modern samples, 3 from each modern remnant population), (4) sets of VCF
 genotype files mapped to the southern sea otter reference genome for
 comparison of reference genomes, (5) site frequency spectra from sites
 mapped to the southern sea otter reference genome, for comparison of
 reference genomes. Population identifiers are California (CA), south
 central Alaska (AK), Aleutian Islands (AL), Commander Islands (COM), Kuril
 Islands (KUR). All sequencing fastq files are available
 on the Sequence Read Archive (SRA), BioProject accession PRJNA629776, and
 sample information is available in modern.SampleInfo.xlsx and
 aDNA.SampleInfo.xlsx. Details of methods are available in Beichman et
 al. Please see README.txt for more details.