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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , |
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| Language: | English |
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eLife Sciences Publications Ltd
2022-05-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/73346 |
| _version_ | 1828108671957073920 |
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| author | Dawei Cai Siqi Zhu Mian Gong Naifan Zhang Jia Wen Qiyao Liang Weilu Sun Xinyue Shao Yaqi Guo Yudong Cai Zhuqing Zheng Wei Zhang Songmei Hu Xiaoyang Wang He Tian Youqian Li Wei Liu Miaomiao Yang Jian Yang Duo Wu Ludovic Orlando Yu Jiang |
| author_facet | Dawei Cai Siqi Zhu Mian Gong Naifan Zhang Jia Wen Qiyao Liang Weilu Sun Xinyue Shao Yaqi Guo Yudong Cai Zhuqing Zheng Wei Zhang Songmei Hu Xiaoyang Wang He Tian Youqian Li Wei Liu Miaomiao Yang Jian Yang Duo Wu Ludovic Orlando Yu Jiang |
| author_sort | Dawei Cai |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-11T10:49:24Z |
| format | Article |
| id | doaj.art-f901392976f54be9bee23318242d1891 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-11T10:49:24Z |
| publishDate | 2022-05-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-f901392976f54be9bee23318242d18912022-12-22T04:28:57ZengeLife Sciences Publications LtdeLife2050-084X2022-05-011110.7554/eLife.73346Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late HoloceneDawei Cai0https://orcid.org/0000-0001-6650-0217Siqi Zhu1https://orcid.org/0000-0001-6307-1189Mian Gong2https://orcid.org/0000-0002-1785-0621Naifan Zhang3Jia Wen4Qiyao Liang5Weilu Sun6Xinyue Shao7Yaqi Guo8Yudong Cai9Zhuqing Zheng10Wei Zhang11Songmei Hu12Xiaoyang Wang13He Tian14Youqian Li15Wei Liu16Miaomiao Yang17Jian Yang18Duo Wu19Ludovic Orlando20Yu Jiang21https://orcid.org/0000-0003-4821-3585Bioarchaeology Laboratory, Jilin University, Changchun, ChinaBioarchaeology Laboratory, Jilin University, Changchun, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, ChinaBioarchaeology Laboratory, Jilin University, Changchun, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, ChinaBioarchaeology Laboratory, Jilin University, Changchun, ChinaBioarchaeology Laboratory, Jilin University, Changchun, ChinaBioarchaeology Laboratory, Jilin University, Changchun, ChinaBioarchaeology Laboratory, Jilin University, Changchun, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, ChinaHeilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, ChinaShaanxi Provincial Institute of Archaeology, Xi’an, ChinaNingxia Institute of Cultural Relics and Archaeology, Yinchuan, ChinaHeilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, ChinaHeilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, ChinaHeilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, ChinaShaanxi Provincial Institute of Archaeology, Xi’an, ChinaNingxia Institute of Cultural Relics and Archaeology, Yinchuan, ChinaCollege of Earth and Environmental Sciences; MOE Key Laboratory of Western China's Environmental Systems, Lanzhou University, Lanzhou, ChinaCentre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France, Toulouse, FranceKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, ChinaThe 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.https://elifesciences.org/articles/73346equus ovodoviequidsancient DNAevolutionary genomicsextinction |
| spellingShingle | Dawei Cai Siqi Zhu Mian Gong Naifan Zhang Jia Wen Qiyao Liang Weilu Sun Xinyue Shao Yaqi Guo Yudong Cai Zhuqing Zheng Wei Zhang Songmei Hu Xiaoyang Wang He Tian Youqian Li Wei Liu Miaomiao Yang Jian Yang Duo Wu Ludovic Orlando Yu Jiang Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene eLife equus ovodovi equids ancient DNA evolutionary genomics extinction |
| 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 | equus ovodovi equids ancient DNA evolutionary genomics extinction |
| url | https://elifesciences.org/articles/73346 |
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