DOI: 10.5061/dryad.f8g6mg8
title: Data from: Aquatic adaptation and depleted diversity: a deep dive into the genomes of the sea otter and giant otter

description: Despite its recent invasion into the marine realm, the sea otter (Enhydra
 lutris) has evolved a suite of adaptations for life in cold coastal
 waters, including limb modifications and dense insulating fur. This
 uniquely dense coat led to the near-extinction of sea otters during the
 18th-20th century fur trade and an extreme population bottleneck. We used
 the de novo genome of the southern sea otter (E. l. nereis) to reconstruct
 its evolutionary history, identify genes influencing aquatic adaptation,
 and detect signals of population bottlenecks. We compared the genome of
 the southern sea otter to the tropical freshwater-living giant otter
 (Pteronura brasiliensis) to assess common and divergent genomic trends
 between otter species, and to the closely related northern sea otter (E.
 l. kenyoni) to uncover population-level trends. We found signals of
 positive selection in genes related to aquatic adaptations, particularly
 limb development and polygenic selection on genes related to hair follicle
 development. We found extensive pseudogenization of olfactory receptor
 genes in both the sea otter and giant otter lineages, consistent with
 patterns of sensory gene loss in other aquatic mammals. At the population
 level, the southern sea otter and the northern sea otter showed extremely
 low genomic diversity, signals of recent inbreeding, and demographic
 histories marked by population declines. These declines pre-date the fur
 trade and appear to have resulted in an increase in putatively deleterious
 variants that could impact the future recovery of the sea otter.
description: Southern sea otter
 genome annotationThis gff file is the
 annotation of the southern sea otter (Enhydra lutris nereis) genome,
 generated using MAKER2 based on evidence from RNA-Seq of sea otter whole
 blood and protein data from domestic ferret, domestic cat and domestic
 dog. Gene models were predicted by AUGUSTUS after three rounds of
 training. Protein and domain information from the Swissprot/Uniprot
 database (accessed in 2016) and Interproscan 5.19-58 are included in the
 annotations. See details in SI Methods of Beichman et al.
 (2019).final_sea_otter_23May2016_bS9RH.round5.AED1.0.blast1e-06.renamed.rmDupScaffs.20171118.gff.gzSouthern sea otter genome annotation protein sequencesThis fasta file contains the sequences of proteins from the southern sea otter (Enhydra lutris nereis) genome, generated using MAKER2 and AUGUSTUS. See details in SI Methods of Beichman et al. (2019).final_sea_otter_23May2016_bS9RH_proteins.round5.AED1.0.blast1e-06.renamed.rmDupScaffs.20171118.fasta.gzSouthern sea otter genome annotation transcript sequences (without UTRs)This fasta file contains the sequences of transcripts from the southern sea otter (Enhydra lutris nereis) genome, generated using MAKER2 and AUGUSTUS. UTR regions have been removed. See details in SI Methods of Beichman et al. (2019).sea_otter_23May2016_bS9RH.all.maker.transcripts.round5.AED1.0.renamed.NOUTRS.rmDupScaffs.20171118.fasta.gzSouthern sea otter genotypesThis directory contains the filtered genotypes from southern sea otter (Enhydra lutris nereis) sequencing reads (Project number: PRJNA472597, Acc. SRR8597300) mapped to the domestic ferret reference genome (GCF_000215625.1). The files are in vcf format, and the genome was split into 323 chunks to reduce file sizes. Each of the first 1-224 .vcf files contain a single scaffold, and the remaining 225-323 vcf files each contain groups of 76 smaller scaffolds. The directory ferret_genome_interval_bedfiles.tar.gz contains the bed files that give the scaffold coordinates of each .vcf file (e.g. interval_244.bed gives the coordinates of the scaffolds contained in the vcf file labeled as 244: *.raw_variants.244.*.HQsites.Only.rmDotGenotypes.rmBadVars.vcf.gz). The reads were mapped, genotypes were called and filtered as described in the README and SI Methods in Beichman et al. 2019.southern_sea_otter.vcfFiles.tar.gzNorthern sea otter genotypesThese vcf files contain filtered genotypes from the northern sea otter (Enhydra lutris kenyoni) sequencing reads (SRA: SRX2967283, from Jones et al. (2018)) mapped to the domestic ferret reference genome (GCF_000215625.1). When gVCF files were generated, the genome was split into 323 chunks to parallelize processing and reduce filesize. Each of the first 1-224 .vcf files each contain a single scaffold, and the remaining 225-323 .vcf files each contain groups of 76 smaller scaffolds. The directory ferret_genome_interval_bedfiles.tar.gz contains the bed files that give the scaffold coordinates of each .vcf file (e.g. interval_244.bed gives the coordinates of the scaffolds contained in the vcf file labeled as 244: *.raw_variants.244.*.HQsites.Only.rmDotGenotypes.rmBadVars.vcf.gz).northern_sea_otter.vcfFiles.tar.gzFerret genome intervals used to split vcf filesThe vcf files of each otter were split into intervals to reduce filesize. This directory (ferret_genome_interval_bedfiles.tar.gz) contains bed files that give the scaffold coordinates of each each interval. For example interval_244.bed gives the coordinates of the scaffolds contained in the vcf file labeled 244: *.raw_variants.244.*.HQsites.Only.rmDotGenotypes.rmBadVars.vcf.gz).ferret_genome_interval_bedfiles.tar.gzGiant otter genotypesThese vcf files contain filtered genotypes from the giant otter (Pteronura brasiliensis) sequencing reads (Project number: PRJNA399365) mapped to the domestic ferret reference genome (GCF_000215625.1). When gVCF files were generated, the genome was split into 323 chunks to parallelize processing and reduce filesize. Each of the first 1-224 .vcf files each contain a single scaffold, and the remaining 225-323 .vcf files each contain groups of 76 smaller scaffolds. The directory ferret_genome_interval_bedfiles.tar.gz contains the bed files that give the scaffold coordinates of each .vcf file (e.g. interval_244.bed gives the coordinates of the scaffolds contained in the vcf file labeled as 244: *.raw_variants.244.*.HQsites.Only.rmDotGenotypes.rmBadVars.vcf.gz).giant_otter.vcfFiles.tar.gz