A Million Years of Mammoth Mitogenome Evolution

The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.

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Publication Details

Journal
Molecular Biology and Evolution
Published
2025-04-01
DOI
https://doi.org/10.1093/molbev/msaf065
Citations
7
Primary Topic
Genomics and Phylogenetic Studies
Type
article
Field-Weighted Citation Impact
5.64

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article

A Million Years of Mammoth Mitogenome Evolution

Grant D. Zazula, Adrian M. Lister, Dick Mol, Kirstin Henneberger et al.
7 citations
Molecular Biology and Evolution
Genomics and Phylogenetic Studies
5.64
article

A Million Years of Mammoth Mitogenome Evolution

Grant D. Zazula, Adrian M. Lister, Dick Mol, Kirstin Henneberger, Anders Götherström, Chenyu Jin, Johanna L. A. Paijmans, Marianne Dehasque, Tom van der Valk, Michael V. Westbury, Kelsey Moreland, Love Dalén, Juan Camilo Chacón-Duque, Michael Hofreiter, David Díez‐del‐Molino, Sergey Vartanyan, Peter D. Heintzman, Patrícia Pečnerová, Elizabeth Hall, Mikhail Sablin, Jessica Thomas, Mietje Germonpré, Susan Hewitson, Axel Barlow, Pavel A. Nikolskiy, Ian Barnes, Flore Wijnands, Wenxi Li
article en
7 citations

Abstract

The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.

Molecular Biology and EvolutionVol. 42(4)
Uppsala University (SE), University of Copenhagen (DK), Russian Academy of Sciences (RU), Natural History Museum (GB), Bangor University (GB), Stockholm University (SE), University of Potsdam (DE), University of Cambridge (GB), Institute of Natural Sciences (BE), Zoological Institute (RU), Swedish Museum of Natural History (SE), Wellcome Sanger Institute (GB), Natural History Museum Rotterdam (NL), Evolutionary Genomics (United States) (US), Geological Institute (RU), Interdisciplinary Scientific Research (US), Centre for Palaeogenetics (SE)
European Commission, Knut och Alice Wallenbergs Stiftelse, Vetenskapsrådet, Science for Life Laboratory, Koninklijk Belgisch Instituut voor Natuurwetenschappen, HORIZON EUROPE Framework Programme, Natural Environment Research Council, Uppsala Multidisciplinary Center for Advanced Computational Science, H2020 Marie Skłodowska-Curie Actions
Life in Land
Openalex Percentile: Top 4%
Genomics and Phylogenetic Studies
5.64
DOIOpen Access PDFOpenAlex
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