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Ancient genomes from northern China suggest links between subsistence changes and human migration

Ning, Chao, Li, Tianjiao, Wang, Ke, Zhang, Fan, Li, Tao, Wu, Xiyan, Gao, Shizhu, Zhang, Quanchao, Zhang, Hai, Hudson, Mark J., Dong, Guanghui, Wu, Sihao, Fang, Yanming, Liu, Chen, Feng, Chunyan, Li, Wei, Han, Tao, Li, Ruo, Wei, Jian, Zhu, Yonggang, Zhou, Yawei, Wang, Chuan-Chao, Fan, Shengying, Xiong, Zenglong, Sun, Zhouyong, Ye, Maolin, Sun, Lei, Wu, Xiaohong, Liang, Fawei, Cao, Yanpeng, Wei, Xingtao, Zhu, Hong, Zhou, Hui, Krause, Johannes, Robbeets, Martine, Jeong, Choongwon, Cui, Yinqiu·2020·Nature Communications
DOI 10.1038/s41467-020-16557-2PMC PMC7264253
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Abstract

Northern China harbored the world’s earliest complex societies based on millet farming, in two major centers in the Yellow (YR) and West Liao (WLR) River basins. Until now, their genetic histories have remained largely unknown. Here we present 55 ancient genomes dating to 7500-1700 BP from the YR, WLR, and Amur River (AR) regions. Contrary to the genetic stability in the AR, the YR and WLR genetic profiles substantially changed over time. The YR populations show a monotonic increase over time in their genetic affinity with present-day southern Chinese and Southeast Asians. In the WLR, intensification of farming in the Late Neolithic is correlated with increased YR affinity while the inclusion of a pastoral economy in the Bronze Age was correlated with increased AR affinity. Our results suggest a link between changes in subsistence strategy and human migration, and fuel the debate about archaeolinguistic signatures of past human migration.

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Fig. 1 Geographic location and dates of ancient individuals. a Location of the 19 archeological sites covering 55 ancient individuals in this study. Each symbol corresponds to a site from a specific region: circle (AR); square (WLR); triangle (YR); diamond (sites from Inner Mongolia or Shaanxi) (see Table 1 for details). The published Early Neolithic genomes from the Russian Far East (“Devil’s Gate_EN”)57,58 are also indicated. The three major river basins in northern China are indicated in different color shades, namely Amur River Basin in light green, West Liao River Basin in pink, and Yellow River Basin in light blue. The base map was prepared from the ArcGIS “World Terrain Base” included in the ArcGIS desktop standard v. 9.2. ArcGIS user license was purchased by, and authorized to, the Max Planck Institute for the Science of Human History (MPI-SHH, Jena, Germany). b Calibrated radiocarbon dates and relative dating of ancient samples in this study. The archeological sites are ordered according to their locations. SX and IM refer to Shaanxi province and the Inner Mongolia Autonomous region of China, respectively. Their geographic locations are intermediate between the WLR and YR. Colors correspond to samples of different time periods: EN Early Neolithic, MN Middle Neolithic, LN Late Neolithic, BA Bronze Age, LBIA Late Bronze and Iron Age, IA Iron Age.
Fig. 1 Geographic location and dates of ancient individuals. a Location of the 19 archeological sites covering 55 ancient individuals in this study. Each symbol corresponds to a site from a specific region: circle (AR); square (WLR); triangle (YR); diamond (sites from Inner Mongolia or Shaanxi) (see Table 1 for details). The published Early Neolithic genomes from the Russian Far East (“Devil’s Gate_EN”)57,58 are also indicated. The three major river basins in northern China are indicated in different color shades, namely Amur River Basin in light green, West Liao River Basin in pink, and Yellow River Basin in light blue. The base map was prepared from the ArcGIS “World Terrain Base” included in the ArcGIS desktop standard v. 9.2. ArcGIS user license was purchased by, and authorized to, the Max Planck Institute for the Science of Human History (MPI-SHH, Jena, Germany). b Calibrated radiocarbon dates and relative dating of ancient samples in this study. The archeological sites are ordered according to their locations. SX and IM refer to Shaanxi province and the Inner Mongolia Autonomous region of China, respectively. Their geographic locations are intermediate between the WLR and YR. Colors correspond to samples of different time periods: EN Early Neolithic, MN Middle Neolithic, LN Late Neolithic, BA Bronze Age, LBIA Late Bronze and Iron Age, IA Iron Age.CC BY · PubMed Central
Fig. 2 A summary of the genetic profiles of the ancient and present-day East Asian populations. a The first two principal components constructed from 2077 present-day Eurasians; the ancient individuals are projected onto the first two PCs. Color-filled shapes represent ancient individuals, with the color-shape combinations as used in Fig. 1. Opaque circles represent the present-day individuals used for calculating PCs. Tungusic-speaking populations and Han Chinese are marked by green and purple shades, respectively. Individuals from other populations are marked by gray shades. The population labels of present-day individuals are provided in Supplementary Fig. 4. b A zoom-in visualization of the WLR and YR clusters in a. c The first two principal components calculated from present-day individuals from nine East Asian populations in the “1240k-Illumina” dataset. Present-day individuals are marked by their corresponding population names. d ADMIXTURE results for the “1240k-Illumina” dataset at K = 5. Only the East Asian populations are plotted. Present-day populations are sorted and colored according to their linguistic families.
Fig. 2 A summary of the genetic profiles of the ancient and present-day East Asian populations. a The first two principal components constructed from 2077 present-day Eurasians; the ancient individuals are projected onto the first two PCs. Color-filled shapes represent ancient individuals, with the color-shape combinations as used in Fig. 1. Opaque circles represent the present-day individuals used for calculating PCs. Tungusic-speaking populations and Han Chinese are marked by green and purple shades, respectively. Individuals from other populations are marked by gray shades. The population labels of present-day individuals are provided in Supplementary Fig. 4. b A zoom-in visualization of the WLR and YR clusters in a. c The first two principal components calculated from present-day individuals from nine East Asian populations in the “1240k-Illumina” dataset. Present-day individuals are marked by their corresponding population names. d ADMIXTURE results for the “1240k-Illumina” dataset at K = 5. Only the East Asian populations are plotted. Present-day populations are sorted and colored according to their linguistic families.CC BY · PubMed Central
Fig. 3 qpAdm modeling of the ancient populations in Northern China. Modeling ancient populations as a mixture of YR_MN and AR_EN. a Middle Neolithic populations in this study. X-axis shows the great circle distance from the YR_MN sites and y-axis shows estimates of AR-related ancestry proportion (represented by AR_EN). b WLR populations from Middle Neolithic to Bronze Age. Black squares represent the point estimates. Vertical bars represent ± 1 s.e.m. range, estimated by 5 cM block jackknifing.
Fig. 3 qpAdm modeling of the ancient populations in Northern China. Modeling ancient populations as a mixture of YR_MN and AR_EN. a Middle Neolithic populations in this study. X-axis shows the great circle distance from the YR_MN sites and y-axis shows estimates of AR-related ancestry proportion (represented by AR_EN). b WLR populations from Middle Neolithic to Bronze Age. Black squares represent the point estimates. Vertical bars represent ± 1 s.e.m. range, estimated by 5 cM block jackknifing.CC BY · PubMed Central

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Cited by

Metadata

Authors
Ning, C., Li, T., Wang, K., Zhang, F., Li, T., Wu, X., Gao, S., Zhang, Q., Zhang, H., Hudson, M. J., Dong, G., Wu, S., Fang, Y., Liu, C., Feng, C., Li, W., Han, T., Li, R., Wei, J., Zhu, Y., Zhou, Y., Wang, C.-C., Fan, S., Xiong, Z., Sun, Z., Ye, M., Sun, L., Wu, X., Liang, F., Cao, Y., Wei, X., Zhu, H., Zhou, H., Krause, J., Robbeets, M., Jeong, C., & Cui, Y.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2020-06-01
Volume
11
Issue
1
ISSN
2041-1723
DOI
10.1038/s41467-020-16557-2
PMC
PMC7264253
Cited by
305
References
13
Language
en
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