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A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan

Kanzawa-Kiriyama, Hideaki, Kryukov, Kirill, Jinam, Timothy A, Hosomichi, Kazuyoshi, Saso, Aiko, Suwa, Gen, Ueda, Shintaroh, Yoneda, Minoru, Tajima, Atsushi, Shinoda, Ken-ichi, Inoue, Ituro, Saitou, Naruya·2017·Journal of Human Genetics
DOI 10.1038/jhg.2016.110PMC PMC5285490
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Figure 1 Principal component analysis with genome sequence data. (a) Sanganji Jomon and 1000 Genomes Project worldwide humans based on 68 542 SNPs with PB. (b) Sanganji Jomon and 1000 Genomes Project East Eurasians based on 46 158 SNPs with PB.
Figure 1 Principal component analysis with genome sequence data. (a) Sanganji Jomon and 1000 Genomes Project worldwide humans based on 68 542 SNPs with PB. (b) Sanganji Jomon and 1000 Genomes Project East Eurasians based on 46 158 SNPs with PB.CC BY-NC-SA · PubMed Central
Figure 2 Principal component analysis with genome-wide SNP data. (a) Sanganji Jomon and HGDP East Eurasians based on 6864 SNPs with PB. (b) Sanganji Jomon, individuals of three populations inhabiting the Japanese Archipelago (Ainu, mainland Japanese and Ryukyuan), and Chinese Beijing (CHB) based on 5392 SNP sites with PB.
Figure 2 Principal component analysis with genome-wide SNP data. (a) Sanganji Jomon and HGDP East Eurasians based on 6864 SNPs with PB. (b) Sanganji Jomon, individuals of three populations inhabiting the Japanese Archipelago (Ainu, mainland Japanese and Ryukyuan), and Chinese Beijing (CHB) based on 5392 SNP sites with PB.CC BY-NC-SA · PubMed Central
Figure 3 Allele sharing between Sanganji Jomon and modern humans. Vertical line indicates the frequency of having the same allele with the Sanganji Jomon. (a) Comparison with Japanese Archipelago populations and Chinese Beijing (CHB) based on 5392 SNP sites with PB, (b) comparison with HGDP East Eurasians, Sahulians and Native Americans based on 7081 SNP sites with PB. Colors blue, green, brown and violet indicate northern East Eurasians, southern East Eurasians, Sahulians and Native Americans, respectively.
Figure 3 Allele sharing between Sanganji Jomon and modern humans. Vertical line indicates the frequency of having the same allele with the Sanganji Jomon. (a) Comparison with Japanese Archipelago populations and Chinese Beijing (CHB) based on 5392 SNP sites with PB, (b) comparison with HGDP East Eurasians, Sahulians and Native Americans based on 7081 SNP sites with PB. Colors blue, green, brown and violet indicate northern East Eurasians, southern East Eurasians, Sahulians and Native Americans, respectively.CC BY-NC-SA · PubMed Central
Figure 4 Phylogenetic analysis I. TreeMix tree with gene flows. A comparison of Sanganji Jomon, 1000 Genomes Project worldwide populations, Papuan, Karitiana, Mal'ta MA1, Ust'-Ishim and Denisovan based on 43 310 all sites. Denisovan was used as the outgroup, and three gene flow events were estimated. The tree was drawn by using MEGA6.38 Red colored values (only those higher than 90% are shown) are bootstrap probabilities (%) for their adjacent internal branch. Arrows were manually added to this tree, and colors of migration weight (ratio of gene flow) follow TreeMix outputs. Values inside arrows are the ratio of gene flow. Bootstrap probabilities (%) of the gene flow from Sanganji Jomon to JPT, Karitiana to the root of European and Mal'ta MA1, and LWK to European, estimated out of 1000 bootstrap replicate TreeMix outputs, are 42%, 86% and 0.4%, respectively.
Figure 4 Phylogenetic analysis I. TreeMix tree with gene flows. A comparison of Sanganji Jomon, 1000 Genomes Project worldwide populations, Papuan, Karitiana, Mal'ta MA1, Ust'-Ishim and Denisovan based on 43 310 all sites. Denisovan was used as the outgroup, and three gene flow events were estimated. The tree was drawn by using MEGA6.38 Red colored values (only those higher than 90% are shown) are bootstrap probabilities (%) for their adjacent internal branch. Arrows were manually added to this tree, and colors of migration weight (ratio of gene flow) follow TreeMix outputs. Values inside arrows are the ratio of gene flow. Bootstrap probabilities (%) of the gene flow from Sanganji Jomon to JPT, Karitiana to the root of European and Mal'ta MA1, and LWK to European, estimated out of 1000 bootstrap replicate TreeMix outputs, are 42%, 86% and 0.4%, respectively.CC BY-NC-SA · PubMed Central
Figure 5 Phylogenetic analysis II. Distance-based. A total of 15 519 transversion sites were used for computing distances. (a) Neighbor-joining tree. (b) Neighbor-net network. Branches for populations starting with ‘∼' were shortened for clarity.
Figure 5 Phylogenetic analysis II. Distance-based. A total of 15 519 transversion sites were used for computing distances. (a) Neighbor-joining tree. (b) Neighbor-net network. Branches for populations starting with ‘∼' were shortened for clarity.CC BY-NC-SA · PubMed Central
Figure 6 D-statistic tests of Sanganji Jomon and worldwide humans. (a) Comparison of Sanganji Jomon, 1000 Genomes Project worldwide populations, Mal'ta MA1 and Ust'-Ishim based on 15 549 transversion sites. (b) Comparison with HGDP East Eurasians and Native Americans and SGVP Malay population based on 7439 SNPs.
Figure 6 D-statistic tests of Sanganji Jomon and worldwide humans. (a) Comparison of Sanganji Jomon, 1000 Genomes Project worldwide populations, Mal'ta MA1 and Ust'-Ishim based on 15 549 transversion sites. (b) Comparison with HGDP East Eurasians and Native Americans and SGVP Malay population based on 7439 SNPs.CC BY-NC-SA · PubMed Central

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Cites

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Cited by

Metadata

Authors
Kanzawa-Kiriyama, H., Kryukov, K., Jinam, T. A., Hosomichi, K., Saso, A., Suwa, G., Ueda, S., Yoneda, M., Tajima, A., Shinoda, K.-I., Inoue, I., & Saitou, N.
Venue
Journal of Human Genetics
Publisher
Springer Science and Business Media LLC
Published
2016-09-01
Volume
62
Issue
2
Pages
213-221
ISSN
  • 1434-5161
  • 1435-232X
DOI
10.1038/jhg.2016.110
PMC
PMC5285490
Cited by
72
References
9
Language
en
Licence
creativecommons.org/licenses/by-nc-sa/4.0 (tdm)

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