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Genomics of adaptive evolution in the woolly mammoth

Díez-Del-Molino, David ; Dehasque, Marianne ; Chacón-Duque, J Camilo ; Pečnerová, Patrícia LU orcid ; Tikhonov, Alexei ; Protopopov, Albert ; Plotnikov, Valeri ; Kanellidou, Foteini ; Nikolskiy, Pavel and Mortensen, Peter , et al. (2023) In Current biology : CB 33(9). p.4-1764
Abstract

Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad... (More)

Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.

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publishing date
type
Contribution to journal
publication status
published
keywords
Animals, Mammoths/genetics, Sequence Analysis, DNA, Genomics/methods, Genome/genetics, Mutation, Fossils, Evolution, Molecular
in
Current biology : CB
volume
33
issue
9
pages
4 - 1764
publisher
Elsevier
external identifiers
  • scopus:85153039198
  • pmid:37030294
ISSN
1879-0445
DOI
10.1016/j.cub.2023.03.084
language
English
LU publication?
no
additional info
Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.
id
7dd4c051-ab3e-431f-8d4e-8ca66701d099
date added to LUP
2024-10-10 15:53:33
date last changed
2025-07-05 17:12:52
@article{7dd4c051-ab3e-431f-8d4e-8ca66701d099,
  abstract     = {{<p>Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.</p>}},
  author       = {{Díez-Del-Molino, David and Dehasque, Marianne and Chacón-Duque, J Camilo and Pečnerová, Patrícia and Tikhonov, Alexei and Protopopov, Albert and Plotnikov, Valeri and Kanellidou, Foteini and Nikolskiy, Pavel and Mortensen, Peter and Danilov, Gleb K and Vartanyan, Sergey and Gilbert, M Thomas P and Lister, Adrian M and Heintzman, Peter D and van der Valk, Tom and Dalén, Love}},
  issn         = {{1879-0445}},
  keywords     = {{Animals; Mammoths/genetics; Sequence Analysis, DNA; Genomics/methods; Genome/genetics; Mutation; Fossils; Evolution, Molecular}},
  language     = {{eng}},
  month        = {{05}},
  number       = {{9}},
  pages        = {{4--1764}},
  publisher    = {{Elsevier}},
  series       = {{Current biology : CB}},
  title        = {{Genomics of adaptive evolution in the woolly mammoth}},
  url          = {{http://dx.doi.org/10.1016/j.cub.2023.03.084}},
  doi          = {{10.1016/j.cub.2023.03.084}},
  volume       = {{33}},
  year         = {{2023}},
}