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