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

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...

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Autores principales: Cai, Dawei, Zhu, Siqi, Gong, Mian, Zhang, Naifan, Wen, Jia, Liang, Qiyao, Sun, Weilu, Shao, Xinyue, Guo, Yaqi, Cai, Yudong, Zheng, Zhuqing, Zhang, Wei, Hu, Songmei, Wang, Xiaoyang, Tian, He, Li, Youqian, Liu, Wei, Yang, Miaomiao, Yang, Jian, Wu, Duo, Orlando, Ludovic, Jiang, Yu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9142152/
https://www.ncbi.nlm.nih.gov/pubmed/35543411
http://dx.doi.org/10.7554/eLife.73346
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author Cai, Dawei
Zhu, Siqi
Gong, Mian
Zhang, Naifan
Wen, Jia
Liang, Qiyao
Sun, Weilu
Shao, Xinyue
Guo, Yaqi
Cai, Yudong
Zheng, Zhuqing
Zhang, Wei
Hu, Songmei
Wang, Xiaoyang
Tian, He
Li, Youqian
Liu, Wei
Yang, Miaomiao
Yang, Jian
Wu, Duo
Orlando, Ludovic
Jiang, Yu
author_facet Cai, Dawei
Zhu, Siqi
Gong, Mian
Zhang, Naifan
Wen, Jia
Liang, Qiyao
Sun, Weilu
Shao, Xinyue
Guo, Yaqi
Cai, Yudong
Zheng, Zhuqing
Zhang, Wei
Hu, Songmei
Wang, Xiaoyang
Tian, He
Li, Youqian
Liu, Wei
Yang, Miaomiao
Yang, Jian
Wu, Duo
Orlando, Ludovic
Jiang, Yu
author_sort Cai, Dawei
collection PubMed
description 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 ~3500 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.
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spelling pubmed-91421522022-05-28 Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene Cai, Dawei Zhu, Siqi Gong, Mian Zhang, Naifan Wen, Jia Liang, Qiyao Sun, Weilu Shao, Xinyue Guo, Yaqi Cai, Yudong Zheng, Zhuqing Zhang, Wei Hu, Songmei Wang, Xiaoyang Tian, He Li, Youqian Liu, Wei Yang, Miaomiao Yang, Jian Wu, Duo Orlando, Ludovic Jiang, Yu eLife Evolutionary Biology 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 ~3500 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. eLife Sciences Publications, Ltd 2022-05-11 /pmc/articles/PMC9142152/ /pubmed/35543411 http://dx.doi.org/10.7554/eLife.73346 Text en © 2022, Cai, Zhu, Gong et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Evolutionary Biology
Cai, Dawei
Zhu, Siqi
Gong, Mian
Zhang, Naifan
Wen, Jia
Liang, Qiyao
Sun, Weilu
Shao, Xinyue
Guo, Yaqi
Cai, Yudong
Zheng, Zhuqing
Zhang, Wei
Hu, Songmei
Wang, Xiaoyang
Tian, He
Li, Youqian
Liu, Wei
Yang, Miaomiao
Yang, Jian
Wu, Duo
Orlando, Ludovic
Jiang, Yu
Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene
title Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene
title_full Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene
title_fullStr Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene
title_full_unstemmed Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene
title_short Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene
title_sort radiocarbon and genomic evidence for the survival of equus sussemionus until the late holocene
topic Evolutionary Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9142152/
https://www.ncbi.nlm.nih.gov/pubmed/35543411
http://dx.doi.org/10.7554/eLife.73346
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