Genomics of adaptive evolution in the woolly mammoth
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Genomics of adaptive evolution in the woolly mammoth. / Díez-del-Molino, David; Dehasque, Marianne; Chacón-Duque, J. Camilo; Pečnerová, Patrícia; Tikhonov, Alexei; Protopopov, Albert; Plotnikov, Valeri; Kanellidou, Foteini; Nikolskiy, Pavel; Mortensen, Peter; Danilov, Gleb K.; Vartanyan, Sergey; Gilbert, M. Thomas P.; Lister, Adrian M.; Heintzman, Peter D.; van der Valk, Tom; Dalén, Love.
In: Current Biology, Vol. 33, No. 9, 2023.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Genomics of adaptive evolution in the woolly mammoth
AU - Díez-del-Molino, David
AU - Dehasque, Marianne
AU - Chacón-Duque, J. Camilo
AU - Pečnerová, Patrícia
AU - Tikhonov, Alexei
AU - Protopopov, Albert
AU - Plotnikov, Valeri
AU - Kanellidou, Foteini
AU - Nikolskiy, Pavel
AU - Mortensen, Peter
AU - Danilov, Gleb K.
AU - Vartanyan, Sergey
AU - Gilbert, M. Thomas P.
AU - Lister, Adrian M.
AU - Heintzman, Peter D.
AU - van der Valk, Tom
AU - Dalén, Love
N1 - Publisher Copyright: © 2023 The Author(s)
PY - 2023
Y1 - 2023
N2 - 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.
AB - 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.
KW - adaptation
KW - genes
KW - genome
KW - Mammuthus primigenius
KW - non-synonymous mutations
KW - selection
U2 - 10.1016/j.cub.2023.03.084
DO - 10.1016/j.cub.2023.03.084
M3 - Journal article
C2 - 37030294
AN - SCOPUS:85153039198
VL - 33
JO - Current Biology
JF - Current Biology
SN - 0960-9822
IS - 9
ER -
ID: 345641673