10.5061/DRYAD.DJH9W0VXZ
Wellman, Hannah
0000-0002-6761-2787
University of Oregon
Austin, Rita
University of Oklahoma
Dagtas, Nihan
University of Oklahoma
Moss, Madonna
0000-0003-1703-9422
University of Oregon
Rick, Torben
National Museum of Natural History
Hofman, Courtney
University of Oklahoma
Archaeological mitogenomes illuminate the historical ecology of sea otters
(Enhydra lutris) and the viability of reintroduction
Dryad
dataset
2020
Mitochondrial genomes
sea otters
applied zooarchaeology
Reintroductions
FOS: Biological sciences
University of Oklahoma
https://ror.org/02aqsxs83
University of Oregon Department of Anthropology
University of Oregon Graduate School
2020-12-22T00:00:00Z
2020-12-22T00:00:00Z
en
https://doi.org/10.1098/rspb.2020.2343
1855464 bytes
8
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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).
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).