Journal of Archaeological Science: Reports 53 (2024) 104333 Available online 6 December 2023 2352-409X/© 2023 Elsevier Ltd. All rights reserved. Ancient genome analyses shed light on the origin and kinship among humans of a cliff tomb from southwestern China Fan Zhang a, b , Luhong Zheng c , Hongliang Lv a, b , Chen Duan d , Pengcheng Ma e, f , Zhiyan Liu c , Kehua Zhou c , Fei Tang c, * , Chao Ning d, g, * , Yan Zhang c, * a School of Archaeology and Museology, Sichuan University, Chengdu 610207, China b Center for Archaeological Science, Sichuan University, Chengdu 610207, China c Sichuan Province Institute of Cultural Relics and Archaeology, Chengdu China d School of Archaeology and Museology, Peking University, Beijing 100871, China e Institues of Biomedical Sciences, Inner Mongolia University, Hohhot 010010, China f School of Life Sciences, Jilin University, Changchun 130012, China g Key Laboratory of Archaeological Science (Peking University), Ministry of Education, Beijing 100871, China A R T I C L E INFO Keywords: Ancient DNA Cliff tomb Family burial Eastern Han Dynasty Kinship ABSTRACT The cliff tomb was a distinctive regional burial form that lasted for centuries in the southwestern region of China. However, the origin of cliff tombs and the genetic relatedness among the co-buried individuals remain elusive. Here, we successfully identifed four individuals from the scatted bone fragments in a single cliff tomb in the Sichuan Basin by using ancient DNA and physical anthropology analyses, and retrieved genomic data for the four individuals, to our best knowledge, the frst ancient genomic data from the region. Our fndings provide direct evidence supporting the Central Plains of China hypothesis for the people who practiced cliff tombs and further suggest that cliff tombs burial practices may also originate from the Central Plains of China, as supported by ancient DNA, archaeological and historical attestations. We successfully reconstructed the family tree of the four individuals and provided concrete evidence that individuals buried in the same cliff tomb are from a nuclear family rather than the long-hypothesized extended family, suggesting that genetic kinship plays a signifcant role for burial customs in the Sichuan Basin. 1. Introduction The burial practice using cliff tombs was widespread throughout past societies in southwestern China (SWChina) including Sichuan, Chongqing, Guizhou, and Yunnan provinces, starting from the Western Han period (206 BCE-8 AD) and continuing to the Ming Dynasty (1368 CE-1644 CE) (Erhu, 1988; Difei, 2018; Kaiyu, 2008). Although widely distributed, the cliff tombs were predominantly located along the Yangtze River and its major tributaries, such as the Min (岷), Fu (涪), Tuo (沱), and Jialing (嘉陵) River area (Erhu, 1988; Difei, 2018; Chen, 2015), particularly in the Sichuan Basin, a signifcant number of cliff tombs have been discovered in the middle and lower regions of the Min River, with the main concentration dating back to the Eastern Han Dy- nasty (25 AD  220 CE) (Chen, 2015; Yucheng and Ping, 2001; Ruiqin, 2016; Erickson, 2003). The origins of cliff tombs have been a subject of considerable controversy. Local residents referred to these tombs as “Manzidong” (蛮子洞) and believed that they were used for burying aboriginal people who inhabited the area in earlier times (Erhu, 1988; Chen, 2015). Most archaeologists speculate that cliff tombs evolved from rock-cut tombs found in the Central Plains of China, supported by signifcant similarities in architectural features, burial practices, and grave goods (Erhu, 1988; Chen, 2015; Changshou, 1987). Whereas, some researchers suggested that cliff tombs may have served as burial sites for the ancient Baiyue tribes, who inhabited regions such as Guangxi, Guangdong, Fujian, Borneo, Sulawesi, and the Philippine ar- chipelago during the pre-Qin period (prior to 221 BCE) (Zhifan, 1989). Additionally, there are even proposals suggesting that the origin of cliff tombs could be traced back to West Asia or Egypt (Erhu, 1988). As a result, the origins of the cliff tomb burial tradition and the identities of those buried in these tombs continue to be unresolved questions. * Corresponding authors at: Sichuan Province Institute of Cultural Relics and Archaeology, Chengdu China (F. Tang and Y. Zhang); School of Archaeology and Museology, Peking University, Beijing 100871, China (C. Ning). E-mail addresses: 348672999@qq.com (F. Tang), cning@pku.edu.cn (C. Ning), zhangyan201@foxmail.com (Y. Zhang). Contents lists available at ScienceDirect Journal of Archaeological Science: Reports journal homepage: www.elsevier.com/locate/jasrep https://doi.org/10.1016/j.jasrep.2023.104333 Received 10 July 2023; Received in revised form 22 October 2023; Accepted 28 November 2023