Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene

  1. Dawei Cai  Is a corresponding author
  2. Siqi Zhu
  3. Mian Gong
  4. Naifan Zhang
  5. Jia Wen
  6. Qiyao Liang
  7. Weilu Sun
  8. Xinyue Shao
  9. Yaqi Guo
  10. Yudong Cai
  11. Zhuqing Zheng
  12. Wei Zhang
  13. Songmei Hu
  14. Xiaoyang Wang
  15. He Tian
  16. Youqian Li
  17. Wei Liu
  18. Miaomiao Yang
  19. Jian Yang
  20. Duo Wu
  21. Ludovic Orlando  Is a corresponding author
  22. Yu Jiang  Is a corresponding author
  1. Jilin University, China
  2. Northwest A&F University, China
  3. Heilongjiang Provincial Institute of Cultural Relics and Archaeology, China
  4. Shaanxi Provincial Institute of Archaeology, China
  5. Ningxia Institute of Cultural Relics and Archaeology, China
  6. Lanzhou University, China
  7. 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.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Dawei Cai

    Bioarchaeology Laboratory, Jilin University, Changchun, China
    For correspondence
    caidw@jlu.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
  2. Siqi Zhu

    Bioarchaeology Laboratory, Jilin University, Changchun, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6307-1189
  3. Mian Gong

    College of Animal Science and Technology, Northwest A&F University, Yangling, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1785-0621
  4. Naifan Zhang

    Bioarchaeology Laboratory, Jilin University, Changchuin, China
    Competing interests
    The authors declare that no competing interests exist.
  5. Jia Wen

    College of Animal Science and Technology, Northwest A&F University, Yangling, China
    Competing interests
    The authors declare that no competing interests exist.
  6. Qiyao Liang

    Bioarchaeology Laboratory, Jilin University, Changchun, China
    Competing interests
    The authors declare that no competing interests exist.
  7. Weilu Sun

    Bioarchaeology Laboratory, Jilin University, Changchun, China
    Competing interests
    The authors declare that no competing interests exist.
  8. Xinyue Shao

    Bioarchaeology Laboratory, Jilin University, Changchun, China
    Competing interests
    The authors declare that no competing interests exist.
  9. Yaqi Guo

    Bioarchaeology Laboratory, Jilin University, Changchun, China
    Competing interests
    The authors declare that no competing interests exist.
  10. Yudong Cai

    College of Animal Science and Technology, Northwest A&F University, Yangling, China
    Competing interests
    The authors declare that no competing interests exist.
  11. Zhuqing Zheng

    College of Animal Science and Technology, Northwest A&F University, Yangling, China
    Competing interests
    The authors declare that no competing interests exist.
  12. Wei Zhang

    Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
    Competing interests
    The authors declare that no competing interests exist.
  13. Songmei Hu

    Shaanxi Provincial Institute of Archaeology, Xi'an, China
    Competing interests
    The authors declare that no competing interests exist.
  14. Xiaoyang Wang

    Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China
    Competing interests
    The authors declare that no competing interests exist.
  15. He Tian

    Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
    Competing interests
    The authors declare that no competing interests exist.
  16. Youqian Li

    Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
    Competing interests
    The authors declare that no competing interests exist.
  17. Wei Liu

    Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
    Competing interests
    The authors declare that no competing interests exist.
  18. Miaomiao Yang

    Shaanxi Provincial Institute of Archaeology, Xi'an, China
    Competing interests
    The authors declare that no competing interests exist.
  19. Jian Yang

    Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China
    Competing interests
    The authors declare that no competing interests exist.
  20. Duo Wu

    College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  21. Ludovic Orlando

    7Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, CNRS UMR 5288, Toulouse, France
    For correspondence
    ludovic.orlando@univ-tlse3.fr
    Competing interests
    The authors declare that no competing interests exist.
  22. Yu Jiang

    College of Animal Science and Technology, Northwest A&F University, Yangling, China
    For correspondence
    yu.jiang@nwafu.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4821-3585

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

  1. George H Perry, Pennsylvania State University, United States

Version history

  1. Received: August 25, 2021
  2. Preprint posted: September 16, 2021 (view preprint)
  3. Accepted: May 11, 2022
  4. Accepted Manuscript published: May 11, 2022 (version 1)
  5. 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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  1. Dawei Cai
  2. Siqi Zhu
  3. Mian Gong
  4. Naifan Zhang
  5. Jia Wen
  6. Qiyao Liang
  7. Weilu Sun
  8. Xinyue Shao
  9. Yaqi Guo
  10. Yudong Cai
  11. Zhuqing Zheng
  12. Wei Zhang
  13. Songmei Hu
  14. Xiaoyang Wang
  15. He Tian
  16. Youqian Li
  17. Wei Liu
  18. Miaomiao Yang
  19. Jian Yang
  20. Duo Wu
  21. Ludovic Orlando
  22. Yu Jiang
(2022)
Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene
eLife 11:e73346.
https://doi.org/10.7554/eLife.73346

Share this article

https://doi.org/10.7554/eLife.73346

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