Ancient DNA reveals the maternal genetic history of East Asian domestic pigs

Ming Zhang; Yichen Liu; Zhipeng Li; Peng Lü; Jacob D. Gardner; Maolin Ye; Jihuai Wang; Miaomiao Yang; Jing Shao; Weilin Wang; Qingyan Dai; Peng Cao; Ruowei Yang; Feng Liu; Xiaotian Feng; Lizhao Zhang; Enwei Li; Yunzheng Shi; Zehui Chen; Shilun Zhu; Weiwei Zhai; Tao Deng; Ziyuan Duan; E. Andrew Bennett; Songmei Hu; Qiaomei Fu

doi:10.1016/j.jgg.2021.11.014

Volume 49 Issue 6

Jun. 2022

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Article Navigation > Journal of Genetics and Genomics > 2022 > 49(6): 537-546

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Ancient DNA reveals the maternal genetic history of East Asian domestic pigs

doi: 10.1016/j.jgg.2021.11.014

a. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
b. Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China;
c. Shanghai Qi Zhi Institute, Shanghai 200232, China;
d. Institute of Archaeology, Chinese Academy of Social Sciences, Beijing 100710, China;
e. School of History and Culture, Lanzhou University, Lanzhou, Gansu 730000, China;
f. Shaanxi Academy of Archaeology, Xi’an, Shaanxi 710054, China;
g. School of History and Culture, Shanxi University, Taiyuan, Shanxi 030006, China;
h. Xingtai Cultural Relics Administration, Xingtai, Hebei 054000, China;
i. Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing 100101, China;
j. University of Chinese Academy of Sciences, Beijing 100049, China

Funds:

We are grateful to the following people and institutions for providing samples, support, and advice: Jing Yuan (Institute of Archaeology, Chinese Academy of Social Science), Albert Min-Shan Ko (Department of Biomedical Sciences, Chang Gung University), and Xiaowei Mao (Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences). This work was supported by the Chinese Academy of Sciences (CAS, XDB26000000), the Ministry of Finance of the People’s Republic of China (YSBR-019), the National Natural Science Foundation of China (41925009), the Tencent Foundation (through the XPLORER PRIZE), the Howard Hughes Medical Institute (grant 55008731), and the Shanghai Qi Zhi Institute.

Received Date: 2021-07-28
Revised Date: 2021-11-30
Accepted Date: 2021-11-30
Publish Date: 2022-06-30

Abstract

Abstract

Zoo-archaeological and genetic evidence suggest that pigs were domesticated independently in Central China and Eastern Anatolia along with the development of agricultural communities and civilizations. However, the genetic history of domestic pigs, especially in China, has not been fully explored. In this study, we generate 42 complete mitochondrial DNA sequences from ~7500- to 2750-year-old individuals from the Yellow River basin. Our results show that the maternal genetic continuity of East Asian domestic pigs dates back to at least the Early to Middle Neolithic. In contrast, the Near Eastern ancestry in European domestic pigs saw a near-complete genomic replacement by the European wild boar. The majority of East Asian domestic pigs share close haplotypes, and the most recent common ancestor of most branches dates back to less than 20,000 years before present, inferred using new substitution rates of whole mitogenomes or combined protein-coding regions. Two major population expansion events of East Asian domestic pigs coincided with changes in climate, widespread adoption of introduced crops, and the development of agrarian societies. These findings add to our understanding of the maternal genetic composition and help to complete the picture of domestic pig evolutionary history in East Asia.
- Ancient mitogenomes,
- Sus scrofa,
- Pig domestication,
- Genetic history,
- East Asia

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