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Cited by 106

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Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago

Siska, Veronika, Jones, Eppie Ruth, Jeon, Sungwon, Bhak, Youngjune, Kim, Hak-Min, Cho, Yun Sung, Kim, Hyunho, Lee, Kyusang, Veselovskaya, Elizaveta, Balueva, Tatiana, Gallego-Llorente, Marcos, Hofreiter, Michael, Bradley, Daniel G., Eriksson, Anders, Pinhasi, Ron, Bhak, Jong, Manica, Andrea·2017·Science Advances
DOI 10.1126/sciadv.1601877PMC PMC5287702
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Abstract

Early Neolithic (~7700-year-old) genetic data from the Russian Far East implies a high level of genetic continuity in this region.

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Fig. 1 Regional reference panel, PCA, and ADMIXTURE analysis. (A) Map of Asia showing the location of Devil’s Gate (black triangle) and of modern populations forming the regional panel of our analysis. (B) Plot of the first two principal components as defined by our regional panel of modern populations from East Asia and central Asia shown on (A), with the two samples from Devil’s Gate (black triangles) projected upon them (18). (C) ADMIXTURE analysis (19) performed on Devil’s Gate and our regional panel, for K = 5 (lowest cross-validation error) and K = 8 (appearance of Devil’s Gate–specific cluster).
Fig. 1 Regional reference panel, PCA, and ADMIXTURE analysis. (A) Map of Asia showing the location of Devil’s Gate (black triangle) and of modern populations forming the regional panel of our analysis. (B) Plot of the first two principal components as defined by our regional panel of modern populations from East Asia and central Asia shown on (A), with the two samples from Devil’s Gate (black triangles) projected upon them (18). (C) ADMIXTURE analysis (19) performed on Devil’s Gate and our regional panel, for K = 5 (lowest cross-validation error) and K = 8 (appearance of Devil’s Gate–specific cluster).CC BY-NC · PubMed Central
Fig. 2 Outgroup f3 statistics. Outgroup f3 measuring shared drift between Devil’s Gate (black triangle shows sampling location) and modern populations with respect to an African outgroup (Khomani). (A) Map of the whole world. (B) Fifteen populations with the highest shared drift with Devil’s Gate, color-coded by regions as in Fig. 1. Error bars represent 1 SE.
Fig. 2 Outgroup f3 statistics. Outgroup f3 measuring shared drift between Devil’s Gate (black triangle shows sampling location) and modern populations with respect to an African outgroup (Khomani). (A) Map of the whole world. (B) Fifteen populations with the highest shared drift with Devil’s Gate, color-coded by regions as in Fig. 1. Error bars represent 1 SE.CC BY-NC · PubMed Central
Fig. 3 Spatial pattern of outgroup f3 statistics. Relationship between outgroup f3(X, Devil’s Gate; Khomani) and distance on land from Devil’s Gate using DevilsGate1 and all single-nucleotide polymorphisms (SNPs). Populations up to 9000 km away from Devil’s Gate were considered when computing correlation. The highest distance considered was chosen to acquire the highest Pearson correlation in steps of 500 km. Best linear fit (r2 = 0.772, F1,108 = 368.4, P < 0.001) is shown as blue line, with 95% CI indicated by the shaded area.
Fig. 3 Spatial pattern of outgroup f3 statistics. Relationship between outgroup f3(X, Devil’s Gate; Khomani) and distance on land from Devil’s Gate using DevilsGate1 and all single-nucleotide polymorphisms (SNPs). Populations up to 9000 km away from Devil’s Gate were considered when computing correlation. The highest distance considered was chosen to acquire the highest Pearson correlation in steps of 500 km. Best linear fit (r2 = 0.772, F1,108 = 368.4, P < 0.001) is shown as blue line, with 95% CI indicated by the shaded area.CC BY-NC · PubMed Central
Fig. 4 Admixture f3 statistics. Admixture f3 representing modern Koreans and Japanese as a mixture of two populations, X and Y, color-coded by regions as in Fig. 1. (A) Thirty pairs with the lowest f3 score for the Koreans as the target, out of those giving a significant (z < −2) value. (B) All four pairs giving a significantly (z < −2) negative score for the Japanese as the target. Error bars represent 1 SE.
Fig. 4 Admixture f3 statistics. Admixture f3 representing modern Koreans and Japanese as a mixture of two populations, X and Y, color-coded by regions as in Fig. 1. (A) Thirty pairs with the lowest f3 score for the Koreans as the target, out of those giving a significant (z < −2) value. (B) All four pairs giving a significantly (z < −2) negative score for the Japanese as the target. Error bars represent 1 SE.CC BY-NC · PubMed Central

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Cited by

Metadata

Authors
Siska, V., Jones, E. R., Jeon, S., Bhak, Y., Kim, H.-M., Cho, Y. S., Kim, H., Lee, K., Veselovskaya, E., Balueva, T., Gallego-Llorente, M., Hofreiter, M., Bradley, D. G., Eriksson, A., Pinhasi, R., Bhak, J., & Manica, A.
Venue
Science Advances
Publisher
American Association for the Advancement of Science (AAAS)
Published
2017-02-03
Volume
3
Issue
2
ISSN
2375-2548
DOI
10.1126/sciadv.1601877
PMC
PMC5287702
Cited by
106
References
21
Language
en
Funders
  • Gates Cambridge Trust (ID0EDGAK13284)
  • European Research Council (ID0E1SAK13285, ADNABIOARC (263441), ID0EU4AK13286, GeneFlow (310763), ID0E6NCK13845, Consolidator Grant 647787 ‘LocalAdaptation’, ID0EHTCK13846)
  • Ulsan National Institute of Science and Technology (ID0ECJBK13287, Research Fund (1.140113.01))
  • Civil-Military Technology Cooperation Program (ID0EEWBK13288, Research Fund (14-BR-SS-03), ID0ENBCK13289)
  • Biotechnology and Biological Sciences Research Council (ID0EGGCK13290, DTP)

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