Ancient DNA indicates human population shifts and admixture in northern and southern China

Yang, Melinda A.; Fan, Xuejun; Sun, Bo; Chen, Chung‐Yu; Lang, Jianfeng; Ko, Ying‐Chin; Tsang, Cheng-hwa; Chiu, Hui-Ling; Wang, Tianyi; Bao, Qingchuan; Wu, Xiaohong; Hajdinjak, Mateja; Ko, Albert Min-Shan; Ding, Manyu; Cao, Peng; Yang, Ruowei; Liu, Feng; Nickel, Birgit; Dai, Qingyan; Feng, Xiaotian; Zhang, Lizhao; Sun, Chenguang; Ning, Chao; Zeng, Wen; Zhao, Yongsheng; Zhang, Ming; Gao, Xing; Cui, Yinqiu; Reich, David; Stoneking, Mark; Fu, Qiaomei

doi:10.1126/science.aba0909

Cited by 220 publications

(318 citation statements)

References 64 publications

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“…The early expansion of rice agriculture is significant because the migrations of rice farmers may have played a vital role in contributing to the genetic and linguistic diversity of southeastern Asia ( 1 – 4 ). Models based on archaeological evidence suggest that domesticated rice ( Oryza sativa subsp.…”

mentioning

confidence: 99%

“…Recent genetic research indicates complex patterns in the southward spread of early rice farming populations showing that migrating farmers did not simply replace groups of indigenous SEA hunter-gatherers. Rather, indigenous populations admixed with multiple waves of migrating farmers originating from the north ( 1 – 3 ). Similarly, ongoing archaeological research suggests that despite the introduction of rice by migrating farmers who settled among hunter-gatherer communities, agriculture remained a comparatively small component of subsistence strategies for 1,000 y or more ( 10 , 12 , 13 ).…”

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confidence: 99%

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Holocene coastal evolution preceded the expansion of paddy field rice farming

Rolett

Zheng

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Rice agriculture is the foundation of Asian civilizations south of the Yangtze River. Although rice history is well documented for its lower Yangtze homeland area, the early southward expansion of paddy rice farming is poorly known. Our study investigates this process using a compilation of paleoenvironmental proxies from coastal sediment cores from southeast China to Thailand and Island Southeast Asia. We propose that a shortage of land suitable for paddy fields, caused by marine transgression, constrained rice agriculture during the mid-Holocene. Rapid expansion of coastal plains, particularly in deltaic basins, over the past three millennia has coincided with increases in land suitable for rice cultivation. Our study also helps explain the past population movements of rice farmers.

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confidence: 99%

mentioning

confidence: 99%

Holocene coastal evolution preceded the expansion of paddy field rice farming

Rolett

Zheng

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…The most pronounced distinction is the north-to-south cline of genetic patterns among EA, i.e., the haplotype diversity is strongly correlated with latitude. This pattern is confirmed by studies on mtDNA, Y chromosome, and autosomal variations [3,6,8], and a recent study further proved that the south-to-north division could be traced back to Early Neolithic, more than 7500 ya [34]. Intuitively, it raises the question of whether the early migration route occurred in the north-to-south direction or the opposite?…”

Section: Relationship and Origin Of Ea Groupsmentioning

confidence: 60%

“…Based on mtDNA, NRY, whole-genome sequencing data and recent ancient DNA data, the common ancestor in EA is characterized as two layers of ancestry: pre-Neolithic hunter-gatherers as the first layer and northern East Asians since Early Neolithic as the second layer [6,18,34]. The two layers of ancestry admixture contribute to the basal genetic architecture of present-day EAs, while subsequent regional migration and admixture introduce additional genetic variations among the EA populations.…”

Section: Relationship and Origin Of Ea Groupsmentioning

confidence: 99%

Population genomics of East Asian ethnic groups

Pan

2020

Hereditas

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East Asia constitutes one-fifth of the global population and exhibits substantial genetic diversity. However, genetic investigations on populations in this region have been largely under-represented compared with European populations. Nonetheless, the last decade has seen considerable efforts and progress in genome-wide genotyping and whole-genome sequencing of the East-Asian ethnic groups. Here, we review the recent studies in terms of ancestral origin, population relationship, genetic differentiation, and admixture of major East- Asian groups, such as the Chinese, Korean, and Japanese populations. We mainly focus on insights from the whole-genome sequence data and also include the recent progress based on mitochondrial DNA (mtDNA) and Y chromosome data. We further discuss the evolutionary forces driving genetic diversity in East-Asian populations, and provide our perspectives for future directions on population genetics studies, particularly on underrepresented indigenous groups in East Asia.

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“…Asians have a complex demographic history and differentiated population structure [19,[22][23][24]41]. Thus, updated region-specific AISNP panels need to be developed.…”

Section: Evaluating the Efficacy Of Forensic Ancestry Inferencementioning

confidence: 99%

Massively parallel sequencing of 165 ancestry-informative SNPs and forensic biogeographical ancestry inference in three southern Chinese Sinitic/Tai-Kadai populations

Liu

Wang

et al. 2020

Preprint

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Ancestry informative markers (AIMs), which are distributed throughout the human genome, harbor significant allele frequency differences among diverse ethnic groups. The use of sets of AIMs to reconstruct population history and genetic relationships is attracting interest in the forensic community, because biogeographic ancestry information for a casework sample can potentially be predicted and used to guide the investigative process. However, subpopulation ancestry inference within East Asia remains in its infancy due to a lack of population reference data collection and incomplete validation work on newly developed or commercial AIM sets. In the present study, 316 Chinese persons, including 85 Sinitic-speaking Haikou Han, 120 Qiongzhong Hlai and 111 Daozhen Gelao individuals belonging to Tai-Kadai-speaking populations, were analyzed using the Precision ID Ancestry Panel (165 AISNPs). Combined with our previous 165-AISNP data (375 individuals from 6 populations), the 1000 Genomes Project and forensic literature, comprehensive population genetic comparisons and ancestry inference were further performed via ADMIXTURE, TreeMix, PCA, f-statistics and N-J tree. Although several nonpolymorphic loci were identified in the three southern Chinese populations, the forensic parameters of this ancestry inference panel were better than those for the 23 STR-based Huaxia Platinum System, which is suitable for use as a robust tool in forensic individual identification and parentage testing. The results based on the ancestry assignment and admixture proportion evaluation revealed that this panel could be used successfully to assign individuals at a continental scale but also possessed obvious limitations in discriminatory power in intercontinental individuals, especially for European-Asian admixed Uyghurs or in populations lacking reference databases. Population genetic analyses further revealed five continental population clusters and three East Asian-focused population subgroups, which is consistent with linguistic affiliations. Ancestry composition and multiple phylogenetic analysis further demonstrated that the geographically isolated Qiongzhong Hlai harbored a close phylogenetic relationship with Austronesian speakers and possessed a homogenous Tai-Kadai-dominant ancestry, which could be used as the ancestral source proxy in population history reconstruction of Tai-Kadai-speaking populations and as one of the representatives for forensic database establishment. In summary, more population-specific AIM sets focused on East Asian subpopulations, comprehensive algorithms and high-coverage population reference data should be developed and validated in the next step.

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Ancient DNA indicates human population shifts and admixture in northern and southern China

Cited by 220 publications

References 64 publications

Holocene coastal evolution preceded the expansion of paddy field rice farming

Holocene coastal evolution preceded the expansion of paddy field rice farming

Population genomics of East Asian ethnic groups

Massively parallel sequencing of 165 ancestry-informative SNPs and forensic biogeographical ancestry inference in three southern Chinese Sinitic/Tai-Kadai populations

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