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Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter. / Beichman, Annabel C.; Koepfli, Klaus-Peter ; Li, Gang; Murphy, William J.; Dobrynin, Pasha ; Kliver, Sergei ; Tinker, Martin T.; Murray, Michael J.; Johnson, Jeremy ; Lindblad-Toh, Kerstin; Karlsson, Elinor K.; Lohmueller, Kirk E. ; Wayne, Robert K.

в: Molecular Biology and Evolution, Том 36, № 12, 01.12.2019, стр. 2631-2655.

Результаты исследований: Научные публикации в периодических изданияхстатьяРецензирование

Harvard

Beichman, AC, Koepfli, K-P, Li, G, Murphy, WJ, Dobrynin, P, Kliver, S, Tinker, MT, Murray, MJ, Johnson, J, Lindblad-Toh, K, Karlsson, EK, Lohmueller, KE & Wayne, RK 2019, 'Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter', Molecular Biology and Evolution, Том. 36, № 12, стр. 2631-2655. https://doi.org/10.1093/molbev/msz101

APA

Beichman, A. C., Koepfli, K-P., Li, G., Murphy, W. J., Dobrynin, P., Kliver, S., Tinker, M. T., Murray, M. J., Johnson, J., Lindblad-Toh, K., Karlsson, E. K., Lohmueller, K. E., & Wayne, R. K. (2019). Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter. Molecular Biology and Evolution, 36(12), 2631-2655. https://doi.org/10.1093/molbev/msz101

Vancouver

Beichman AC, Koepfli K-P, Li G, Murphy WJ, Dobrynin P, Kliver S и пр. Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter. Molecular Biology and Evolution. 2019 Дек. 1;36(12):2631-2655. https://doi.org/10.1093/molbev/msz101

Author

Beichman, Annabel C. ; Koepfli, Klaus-Peter ; Li, Gang ; Murphy, William J. ; Dobrynin, Pasha ; Kliver, Sergei ; Tinker, Martin T. ; Murray, Michael J. ; Johnson, Jeremy ; Lindblad-Toh, Kerstin ; Karlsson, Elinor K. ; Lohmueller, Kirk E. ; Wayne, Robert K. / Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter. в: Molecular Biology and Evolution. 2019 ; Том 36, № 12. стр. 2631-2655.

BibTeX

@article{6695c7c268d5415e9e6a0eaafb92e2aa,
title = "Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter",
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 with the tropical freshwater-living giant otter (Pteronura brasiliensis) to assess common and divergent genomic trends between otter species, and with 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 may predate 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 = "Биоинформатика, sea otter, giant otter, genomics, population genetics, Adaptation, olfaction, Demography, deleterious variation, pseudogenes, demography, adaptation, DEMOGRAPHIC INFERENCE, PHYLOGENETIC ANALYSIS, MITOCHONDRIAL-DNA VARIATION, POPULATION-SIZE, MUTATION LOAD, LUTRA-LUTRA, SELECTIVE SWEEPS, DELETERIOUS GENETIC-VARIATION, SONIC-HEDGEHOG, RECEPTOR GENES",
author = "Beichman, {Annabel C.} and Klaus-Peter Koepfli and Gang Li and Murphy, {William J.} and Pasha Dobrynin and Sergei Kliver and Tinker, {Martin T.} and Murray, {Michael J.} and Jeremy Johnson and Kerstin Lindblad-Toh and Karlsson, {Elinor K.} and Lohmueller, {Kirk E.} and Wayne, {Robert K.}",
year = "2019",
month = dec,
day = "1",
doi = "10.1093/molbev/msz101",
language = "English",
volume = "36",
pages = "2631--2655",
journal = "Molecular Biology and Evolution",
issn = "0737-4038",
publisher = "Oxford University Press",
number = "12",

}

RIS

TY - JOUR

T1 - Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter

AU - Beichman, Annabel C.

AU - Koepfli, Klaus-Peter

AU - Li, Gang

AU - Murphy, William J.

AU - Dobrynin, Pasha

AU - Kliver, Sergei

AU - Tinker, Martin T.

AU - Murray, Michael J.

AU - Johnson, Jeremy

AU - Lindblad-Toh, Kerstin

AU - Karlsson, Elinor K.

AU - Lohmueller, Kirk E.

AU - Wayne, Robert K.

PY - 2019/12/1

Y1 - 2019/12/1

N2 - 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 with the tropical freshwater-living giant otter (Pteronura brasiliensis) to assess common and divergent genomic trends between otter species, and with 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 may predate 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.

AB - 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 with the tropical freshwater-living giant otter (Pteronura brasiliensis) to assess common and divergent genomic trends between otter species, and with 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 may predate 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.

KW - Биоинформатика

KW - sea otter

KW - giant otter

KW - genomics

KW - population genetics

KW - Adaptation

KW - olfaction

KW - Demography

KW - deleterious variation

KW - pseudogenes

KW - demography

KW - adaptation

KW - DEMOGRAPHIC INFERENCE

KW - PHYLOGENETIC ANALYSIS

KW - MITOCHONDRIAL-DNA VARIATION

KW - POPULATION-SIZE

KW - MUTATION LOAD

KW - LUTRA-LUTRA

KW - SELECTIVE SWEEPS

KW - DELETERIOUS GENETIC-VARIATION

KW - SONIC-HEDGEHOG

KW - RECEPTOR GENES

UR - http://www.scopus.com/inward/record.url?scp=85072304890&partnerID=8YFLogxK

UR - http://www.mendeley.com/research/aquatic-adaptation-depleted-diversity-deep-dive-genomes-sea-otter-giant-otter

U2 - 10.1093/molbev/msz101

DO - 10.1093/molbev/msz101

M3 - Article

VL - 36

SP - 2631

EP - 2655

JO - Molecular Biology and Evolution

JF - Molecular Biology and Evolution

SN - 0737-4038

IS - 12

ER -

ID: 49558170