Title
Aquatic adaptation and depleted diversity: a deep dive into the genomes of the sea otter and giant otter
UMMS Affiliation
Department of Bioinformatics and Integrative Biology
Publication Date
2019-06-18
Document Type
Article
Disciplines
Bioinformatics | Computational Biology | Ecology and Evolutionary Biology | Genetic Phenomena | Genomics | Population Biology
Abstract
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.
Keywords
Sea otter, adaptation, deleterious variation, demography, genomics, giant otter, olfaction, population genetics, pseudogenes
DOI of Published Version
10.1093/molbev/msz101
Source
Mol Biol Evol. 2019 Jun 18. pii: msz101. doi: 10.1093/molbev/msz101. [Epub ahead of print] Link to article on publisher's site
Journal/Book/Conference Title
Molecular biology and evolution
Related Resources
PubMed ID
31212313
Repository Citation
Beichman, Annabel C.; Koepfli, Klaus-Peter; Li, Gang; Murphy, William; Dobrynin, Pasha; Kilver, Sergei; Tinker, M. Tim; Murray, Michael J.; Johnson, Jeremy; Lindblad-Toh, Kerstin; Karlsson, Elinor K.; Lohmueller, Kirk E.; and Wayne, Robert K., "Aquatic adaptation and depleted diversity: a deep dive into the genomes of the sea otter and giant otter" (2019). Program in Bioinformatics and Integrative Biology Publications and Presentations. 157.
https://escholarship.umassmed.edu/bioinformatics_pubs/157