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Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions,...

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Autores principales: Louis, Marie, Korlević, Petra, Nykänen, Milaja, Archer, Frederick, Berrow, Simon, Brownlow, Andrew, Lorenzen, Eline D., O’Brien, Joanne, Post, Klaas, Racimo, Fernando, Rogan, Emer, Rosel, Patricia E., Sinding, Mikkel-Holger S., van der Es, Henry, Wales, Nathan, Fontaine, Michael C., Gaggiotti, Oscar E., Foote, Andrew D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10354069/
https://www.ncbi.nlm.nih.gov/pubmed/37463880
http://dx.doi.org/10.1038/s41467-023-39532-z
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author Louis, Marie
Korlević, Petra
Nykänen, Milaja
Archer, Frederick
Berrow, Simon
Brownlow, Andrew
Lorenzen, Eline D.
O’Brien, Joanne
Post, Klaas
Racimo, Fernando
Rogan, Emer
Rosel, Patricia E.
Sinding, Mikkel-Holger S.
van der Es, Henry
Wales, Nathan
Fontaine, Michael C.
Gaggiotti, Oscar E.
Foote, Andrew D.
author_facet Louis, Marie
Korlević, Petra
Nykänen, Milaja
Archer, Frederick
Berrow, Simon
Brownlow, Andrew
Lorenzen, Eline D.
O’Brien, Joanne
Post, Klaas
Racimo, Fernando
Rogan, Emer
Rosel, Patricia E.
Sinding, Mikkel-Holger S.
van der Es, Henry
Wales, Nathan
Fontaine, Michael C.
Gaggiotti, Oscar E.
Foote, Andrew D.
author_sort Louis, Marie
collection PubMed
description Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.
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spelling pubmed-103540692023-07-20 Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Louis, Marie Korlević, Petra Nykänen, Milaja Archer, Frederick Berrow, Simon Brownlow, Andrew Lorenzen, Eline D. O’Brien, Joanne Post, Klaas Racimo, Fernando Rogan, Emer Rosel, Patricia E. Sinding, Mikkel-Holger S. van der Es, Henry Wales, Nathan Fontaine, Michael C. Gaggiotti, Oscar E. Foote, Andrew D. Nat Commun Article Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats. Nature Publishing Group UK 2023-07-18 /pmc/articles/PMC10354069/ /pubmed/37463880 http://dx.doi.org/10.1038/s41467-023-39532-z Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Louis, Marie
Korlević, Petra
Nykänen, Milaja
Archer, Frederick
Berrow, Simon
Brownlow, Andrew
Lorenzen, Eline D.
O’Brien, Joanne
Post, Klaas
Racimo, Fernando
Rogan, Emer
Rosel, Patricia E.
Sinding, Mikkel-Holger S.
van der Es, Henry
Wales, Nathan
Fontaine, Michael C.
Gaggiotti, Oscar E.
Foote, Andrew D.
Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
title Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
title_full Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
title_fullStr Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
title_full_unstemmed Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
title_short Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
title_sort ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10354069/
https://www.ncbi.nlm.nih.gov/pubmed/37463880
http://dx.doi.org/10.1038/s41467-023-39532-z
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