Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Marie Louis (), Petra Korlević, Milaja Nykänen, Frederick Archer, Simon Berrow, Andrew Brownlow, Eline D. Lorenzen, Joanne O’Brien, Klaas Post, Fernando Racimo, Emer Rogan, Patricia E. Rosel, Mikkel-Holger S. Sinding, Henry Es, Nathan Wales, Michael C. Fontaine, Oscar E. Gaggiotti and Andrew D. Foote ()
Additional contact information
Marie Louis: University of St Andrews
Petra Korlević: Max Planck Institute for Evolutionary Anthropology
Milaja Nykänen: Department of Environmental and Biological Sciences
Frederick Archer: Southwest Fisheries Science Center, NOAA
Simon Berrow: Irish Whale and Dolphin Group
Andrew Brownlow: University of Glasgow
Eline D. Lorenzen: University of Copenhagen
Joanne O’Brien: Irish Whale and Dolphin Group
Klaas Post: Natural History Museum Rotterdam
Fernando Racimo: University of Copenhagen
Emer Rogan: University College Cork, North Mall
Patricia E. Rosel: Southeast Fisheries Science Center, NOAA
Mikkel-Holger S. Sinding: University of Copenhagen
Henry Es: Natural History Museum Rotterdam
Nathan Wales: University of York, BioArCh, Environment Building, Wentworth Way
Michael C. Fontaine: University of Groningen
Oscar E. Gaggiotti: University of St Andrews
Andrew D. Foote: Norwegian University of Science and Technology (NTNU)

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: Abstract 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.

Date: 2023
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DOI: 10.1038/s41467-023-39532-z

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