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eLife2022; 11; e73346; doi: 10.7554/eLife.73346

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

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 lineage, while the subgenus is another remarkable 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 , a species representative of . We present the first high-quality complete genome of the lineage, which was sequenced to 13.4× depth of coverage. Radiocarbon dating demonstrates that this lineage survived until ~3500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the phylogenetic tree and found that 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.
© 2022, Cai, Zhu, Gong et al.
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Publication Date: 2022-05-11 PubMed ID: 35543411PubMed Central: PMC9142152DOI: 10.7554/eLife.73346Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research presents the first complete genome of the subgenus Equus Sussemionus, a previously extinct horse lineage that survived until about 3500 years ago. The study utilized sequencing of fossils and radiocarbon dating, revealing the lineage’s survival despite significant climatic and human activity challenges.

Research Methodology and Findings

  • The paper relies on the rich equid family fossil record, focusing mainly on the subgenus Equus Sussemionus. This horse lineage spanned from North America to Ethiopia during the Pleistocene period.
  • The researchers were able to sequence 26 archaeological specimens from Northern China dating from the Holocene period. The samples were both morphologically and genetically identified as belonging to the Equus Sussemionus species.
  • The successful sequencing created the first complete genome for this lineage, indicating a 13.4× depth coverage.
  • The team used radiocarbon dating methods to estimate that the Equus Sussemionus species survived until around 3500 years ago. This was despite significant climate challenges associated with the Last Glacial Maximum period and the rapid human expansion in East Asia.

Findings on Genetic Diversity & Inbreeding

  • The researchers further explored the lineage’s genetic development and evolution. They corroborated the Equus Sussemionus phylogenetic tree and found that this species detached from the ancestor of non-caballine equids between 2.3 and 2.7 million years ago.
  • Moreover, they observed that the species likely continued facing secondary gene flow effects post-divergence.
  • Contrary to some expectations, the study findings showed that the limited genetic diversity within Equus Sussemionus, rather than increased inbreeding, hampered the species’ chances of survival into modern times.

Broader Impacts of the Study

  • This paper contributes to increasingly robust research that uses ancient DNA to shed light on extinction dynamics and the persisting resilience of species existing in concealed population pockets.
  • The findings have potential implications for the understanding of genomic diversity, evolution, and survival strategies in broader animal species, including those currently endangered.
  • The innovative use of combined sequencing, radiocarbon dating, and morphological identification methods also offers a valuable model for future research in the area of paleogenomics.

Cite This Article

APA
Cai D, Zhu S, Gong M, Zhang N, Wen J, Liang Q, Sun W, Shao X, Guo Y, Cai Y, Zheng Z, Zhang W, Hu S, Wang X, Tian H, Li Y, Liu W, Yang M, Yang J, Wu D, Orlando L, Jiang Y. (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

Publication

eLife
ISSN: 2050-084X
NlmUniqueID: 101579614
Country: England
Language: English
Volume: 11
PII: e73346

Researcher Affiliations

Cai, Dawei
  • Bioarchaeology Laboratory, Jilin University, Changchun, China.
Zhu, Siqi
  • Bioarchaeology Laboratory, Jilin University, Changchun, China.
Gong, Mian
  • Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
Zhang, Naifan
  • Bioarchaeology Laboratory, Jilin University, Changchun, China.
Wen, Jia
  • Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
Liang, Qiyao
  • Bioarchaeology Laboratory, Jilin University, Changchun, China.
Sun, Weilu
  • Bioarchaeology Laboratory, Jilin University, Changchun, China.
Shao, Xinyue
  • Bioarchaeology Laboratory, Jilin University, Changchun, China.
Guo, Yaqi
  • Bioarchaeology Laboratory, Jilin University, Changchun, China.
Cai, Yudong
  • Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
Zheng, Zhuqing
  • Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
Zhang, Wei
  • Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China.
Hu, Songmei
  • Shaanxi Provincial Institute of Archaeology, Xi'an, China.
Wang, Xiaoyang
  • Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China.
Tian, He
  • Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China.
Li, Youqian
  • Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China.
Liu, Wei
  • Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China.
Yang, Miaomiao
  • Shaanxi Provincial Institute of Archaeology, Xi'an, China.
Yang, Jian
  • Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China.
Wu, Duo
  • College of Earth and Environmental Sciences; MOE Key Laboratory of Western China's Environmental Systems, Lanzhou University, Lanzhou, China.
Orlando, Ludovic
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France, Toulouse, France.
Jiang, Yu
  • Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.

MeSH Terms

  • Animals
  • DNA, Mitochondrial / genetics
  • Equidae / genetics
  • Fossils
  • Genome
  • Genomics
  • Horses / genetics
  • Phylogeny

Conflict of Interest Statement

DC, SZ, MG, NZ, JW, QL, WS, XS, YG, YC, ZZ, WZ, SH, XW, HT, YL, WL, MY, JY, DW, LO, YJ No competing interests declared

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