DOI: 10.5061/dryad.djh9w0vxz
title: Archaeological mitogenomes illuminate the historical ecology of sea otters (Enhydra lutris) and the viability of reintroduction

description: Genetic analyses are an important contribution to wildlife
 reintroductions, particularly in the modern context of extirpations and
 ecological destruction. To address the complex historical ecology of the
 sea otter (Enhydra lutris) and its failed 1970s reintroduction to coastal
 Oregon, we compared mitochondrial genomes of pre-extirpation Oregon sea
 otters to extant and historical populations across the range. We sequenced
 the first complete ancient mitogenomes from archaeological Oregon sea
 otter dentine and historical sea otter dental calculus. Archaeological
 Oregon sea otters (N=20) represent ten haplotypes, which cluster with
 haplotypes from Alaska, Washington, and British Columbia, and exhibit a
 clear division from California haplotypes. Our results suggest that extant
 northern populations are appropriate for future reintroduction efforts.
 This project demonstrates the feasibility of mitogenome capture and
 sequencing from non-human dental calculus and the diverse applications of
 ancient DNA analyses to pressing ecological and conservation topics and
 the management of at-risk/extirpated species.
description: Archaeological tooth dentine was sampled at the Laboratories of
 Molecular Anthropology and Microbiome Research (LMAMR) at the University
 of Oklahoma, Norman, in the dedicated sample preparation area following
 standard ancient DNA contamination protocols. Dental calculus was sampled
 in the Department of Mammals at the Smithsonian Institution National
 Museum of Natural History and Santa Barbara Museum of Natural History
 following a calculus-specific sampling protocol designed to reduce
 contamination. Ancient and historical DNA extraction and library
 construction was performed in the LMAMR Ancient DNA Laboratory, a
 dedicated, six-room ISO-6 class clean room custom-built for ancient DNA
 and microbiome research. DNA was extracted from dental calculus and
 dentine using a protocol described in Morales et al. (2017). DNA extracts
 were converted into dual indexed Illumina sequencing libraries and
 captured using a custom in-solution biotinylated RNA bait set (Arbor
 Biosciences). Captured libraries were sequenced on an Illumina MiSeq with
 2 x 150 bp chemistry. The raw fastq files were quality filtered using the
 program Adapter Removal2 (2.1.7) and mapped using bwa (0.7.17) with
 ancient DNA parameters to the published modern sea otter mitogenome
 (Yonezawa et al. 2007). DNA authenticity was assessed using the program
 MapDamage2 and fragment length plots. Consensus sequences were called from
 rescaled bam files in Geneious (11.1.4) and aligned with MAFFT
 (7.308).
description: The consensus sequences (ConsensusAlignment_Dryad.fa) contain
 edits, specifically the addition of "N"s at the ends of the
 ancient sequences due to low coverage in this region and for ambiguous
 base calls. We have uploaded the complete consensus sequences. The edited
 alignment file (ModAlign.fa) used for downstream analysis is also included
 here. Raw sequence data is publicly available through SRA NCBI
 (PRJNA550086).