Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene
- Jilin University, China
- Northwest A&F University, China
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, China
- Shaanxi Provincial Institute of Archaeology, China
- Ningxia Institute of Cultural Relics and Archaeology, China
- Lanzhou University, China
- Université Paul Sabatier, CNRS UMR 5288, France
Abstract
The exceptionally-rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4× depth-of-coverage. Radiocarbon dating demonstrates that this lineage survived until ~3,500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree, and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3-2.7 Million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species' chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.
Data availability
Sequencing data have been deposited in the European Nucleotide Archive under the accession number PRJEB44527.
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This study aims at improving the genome reference of the domestic donkey using the Chicago/HiRiSe technologyEuropean Nucleotide Archive, PRJEB24845.
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Speciation with gene flow in equids despite extensive chromosomal plasticityEuropean Nucleotide Archive, PRJEB7446.
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Sample from Equus caballusNCBI, SAMN02953672.
Article and author information
Author details
Funding
Major Program of National Fund of Philosophy and Social Science of China (17ZDA221)
- Dawei Cai
H2020 European Research Council (681605)
- Ludovic Orlando
National Natural Science Foundation of China (31822052)
- Yu Jiang
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- George H Perry, Pennsylvania State University, United States
Version history
- Received: August 25, 2021
- Preprint posted: September 16, 2021 (view preprint)
- Accepted: May 11, 2022
- Accepted Manuscript published: May 11, 2022 (version 1)
- Version of Record published: May 27, 2022 (version 2)
Copyright
© 2022, Cai et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene
eLife 11:e73346.
https://doi.org/10.7554/eLife.73346
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