Archaeological mitogenomes illuminate the historical ecology of sea otters ( Enhydra lutris ) and the viability of reintroduction

Abstract

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, to our knowledge, the first complete ancient mitogenomes from archaeological Oregon sea otter dentine and historical sea otter dental calculus. Archaeological Oregon sea otters ( n = 20) represent 10 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.

Genomic analyses reveal range‐wide devastation of sea otter populations

“…Since the intermediate populations between Alaska and California are now extinct, we cannot easily differentiate between a demographic model of long‐term isolation of northern and southern sea otter populations, or isolation by distance with low dispersal between populations, both of which are consistent with our results. Ancient mitochondrial DNA and morphological characteristics of extinct Oregon sea otters analysed in Valentine et al (2008) suggest they were more similar to California sea otters, but recent ancient mitogenome haplotype analyses in Wellman et al (2020) show clustering between northern sea otters and ancient Oregon sea otters, possibly indicating that the southern sea otters in California and Mexico may have been genetically distinct from Oregon populations, and/or that Oregon was a location in which northern and southern sea otters mixed (Larson et al, 2012; Lee Lyman, 1988). The genetic legacy of the southern sea otter lineage would have entirely been lost if not for the preservation of the last relict population in California.…”

“…Ancient mitochondrial DNA and morphological characteristics of extinct Oregon sea otters analysed in Valentine et al (2008) suggest they were more similar to California sea otters, but recent ancient mitogenome haplotype analyses in Wellman et al (2020) show clustering between northern sea otters and ancient Oregon sea otters, possibly indicating that the southern sea otters in California and Mexico may have been genetically distinct from Oregon populations, and/or that Oregon was a location in which northern and southern sea otters mixed (Larson et al, 2012;Lee Lyman, 1988).…”

Earliest evidence of primate captivity and translocation supports gift diplomacy between Teotihuacan and the Maya

“…DNA was extracted from a maxillary second left molar and libraries prepared from the extract using published protocols ( 95 ). The sample and negatives were dual-indexed and sequenced on a 2 × 150 NextSeq run.…”

Historical Ecology: A Robust Bridge between Archaeology and Ecology

“…Thus, sites containing the remains of kills and catches enter the archaeological record and allow deep knowledge of both prey and their environments. Particularly important in wildlife introductions and species history, genetic analysis can be undertaken with material from archaeological sites and collections [83]. These sites are time capsules for land and water species' histories, ecosystems, water quality, and the resource management and culinary practices of the searchers.…”