Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Aug 25;3(1):437.
doi: 10.1038/s42003-020-01162-2.

Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

Takashi Gakuhari #  1   2   3 , Shigeki Nakagome #  4 , Simon Rasmussen  5 , Morten E Allentoft  5   6 , Takehiro Sato  7 , Thorfinn Korneliussen  5 , Blánaid Ní Chuinneagáin  4 , Hiromi Matsumae  3 , Kae Koganebuchi  3 , Ryan Schmidt  3 , Souichiro Mizushima  8 , Osamu Kondo  9 , Nobuo Shigehara  10 , Minoru Yoneda  11 , Ryosuke Kimura  12 , Hajime Ishida  12 , Tadayuki Masuyama  13 , Yasuhiro Yamada  14 , Atsushi Tajima  7 , Hiroki Shibata  15 , Atsushi Toyoda  16 , Toshiyuki Tsurumoto  17 , Tetsuaki Wakebe  17 , Hiromi Shitara  18 , Tsunehiko Hanihara  3 , Eske Willerslev  5   19   20 , Martin Sikora  21 , Hiroki Oota  22   23
Affiliations

Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

Takashi Gakuhari et al. Commun Biol. .

Abstract

Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1. Genetic structure of present-day and ancient Eurasian and Ikawazu Jomon.
a Principal component analysis (PCA) of ancient and present-day individuals from worldwide populations after the out-of-Africa expansion. Gray labels represent population codes showing coordinates for individuals. Colored circles indicate ancient individuals. b ADMIXTURE ancestry components (K = 15) for ancient and selected contemporary individuals. The color of light blue represents the component of IK002, which is shared with the present-day Japanese and Ulchi. c Maximum-likelihood phylogenetic tree (TreeMix) with bootstrap support of 100% unless indicated otherwise. The tree shows phylogenetic relationship among present-day Southeast/East Asians, Northeast Siberians, Native Americans, and ancient East Eurasians. Mbuti are the present-day Africans; Ust’Ishim is an Upper-Paleolithic individual (45 kya) from Western Siberia; Mal′ta (MA-1) and Sunghir is Upper-Paleolithic individuals (24 kya and 34 kya), and Loschbour is a Mesolithic individual from West Eurasia; La368 is a pre-Neolithic Hòabìnhian hunter-gatherer (8.0 kya) in Laos and Önge is the present-day hunter-gatherers in the Andaman island, both of who are from Southeast Asia; Tiányuán is an Upper-Paleolithic individual (40 kya) in Beijing, China; Kusunda are the present-day minority people in Nepal; Chokhopani is an Iron-age individual (3.0–2.4 kya) and Sherpa are the present-day minority people, both of who are in Tibet; Han, Ami and main-island Japanese are the present-day East Asians; Devils Gate Cave is a Neolithic individual (8.0 kya) in the Primorye region of Northeast Siberia, and Shamanka and Lokomotive are Early-Neolithic individuals (8.0 kya) from Central Siberia, respectively; USR1 and Clovis are late-Paleolithic individuals (11.5 kya and 12.6 kya) in Alaska and Montana, respectively,. Colored arrows represent the migration pathways and signals of admixture among all datasets. The migration weight represents the fraction of ancestry derived from the migration edge.
Fig. 2
Fig. 2. Exploring genetic affinities of IK002 within Northeast Siberians and Southeast/East Asians, respectively.
Three different D values are plotted with different colors; D(Mbuti, MA-1; X, Ami) in red, D(Mbuti, X; MA-1, Ami) in cyan, and D(Mbuti, Ami; X, MA-1) in green. Error bars show three standard deviation, and the vertical dotted and dashed lines indicate D = 0 and D = −0.2, −0.1, 0.1, and 0.2.
Fig. 3
Fig. 3. Heatmap of f4-statistics comparing Eurasian populations to the Ikawazu Individual.
Heatmaps of f4(Mbuti, IK002;X, Chokhopani), where X are the present-day East Eurasian populations. The color and size represents the value of f4-statistics. The shape represents statistical significances of genetic affinities based on Z-score. Triangle label means statistical significance with |Z| > 3 (P < 0.01), inverted triangle means weak significance with |Z| = 2–3 and circle means non-significance with |Z| < 2 (P > 0.05).
Fig. 4
Fig. 4. Schematic of peopling history in Southeast and East Asians, Northeast Asian/East Siberians and Native Americans.
The basal East Eurasians (bEE) are an ancient population that had no divergence among the ancestors of East Asians, Northeast Asians/East Siberian, and Native Americans. NA-ES-NA presents another ancient population that had no split between the ancestors of Northeast Asians/East Siberian and Native Americans.
See this image and copyright information in PMC

References

    1. Bae CJ, Douka k, Petraglia MD. On the origin of modern humans: Asian perspectives. Science. 2017;358:1–7. - PubMed
    1. Shang H, Tong H, Zhang S, Chen F, Trinkaus E. An early modern human from Tianyuan Cave, Zhoukoudian, China. Proc. Natl. Acad. Sci. USA. 2007;104:6573–6578. - PMC - PubMed
    1. Pope KO, Terrell JE. Environmental setting of human migrations in the circum-Pacific region. J. Biogeogr. 2008;35:1–21.
    1. Kaifu, Y., Izuho, M. & Goebel, T. Modern human dispersal and behavior in Paleolithic Asia. in Emergence and diversity of modern human behavior in Paleolithic Asia (eds Kaifu, Y., Izuho, M., Goebel, T., Sato, H., & Ono, A.) 535–566 (Texas A & M University Press College Station, 2015).
    1. Reyes-Centeno H, Hubbe M, Hanihara T, Stringer C, Harvati K. Testing modern human out-of-Africa dispersal models and implications for modern human origins. J. Hum. Evol. 2015;87:95–106. - PubMed

Publication types

LinkOut - more resources