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Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia

发表于 2018-3-9 10:36 | 显示全部楼层 |阅读模式
本帖最后由 cpan0256 于 2018-3-11 04:20 编辑

biorxiv 预印本:

Hugh McColl, Fernando Racimo, Lasse Vinner, Fabrice Demeter, Uffe Gram Wilken, J. Victor Moreno Mayar, Andaine Seguin-Orlando, Constanza de la Fuente Castro, Sally Wasef, Ana Prohaska, Ashot Margarayan, Peter de Barros Damgaard, Rasmi Shoocongdej, Viengkeo Souksavatdy, Thongsa Sayavongkhamdy, Mohd Mokhtar Saidin, Supannee Kaewsutthi, Patcharee Lertrit, Huong Mai Nguyen, Hsiao-chun Hung, Thi Minh Tran, Huu Nghia Truong, Shaiful Shahidan, Ketut Wiradnyana, Anne-Marie Bacon, Philippe Duringer, Jean-Luc Ponche, Laura Shackelford, Elise Patole-Edoumba, Anh Tuan Nguyen, Berenice Bellina-Pryce, Jean-Christophe Galipaud, Rebecca Kinaston, Hallie Buckley, Christophe Pottier, Simon Rasmussen, Tom Higham, Robert A. Foley, Marta Mirazon Lahr, Ludovic Orlando, Martin Sikora, Charles Higham, David M. Lambert, Eske Willerslev

Abstract: Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. We find that early genomes from Hoabinhian hunter-gatherer contexts in Laos and Malaysia have genetic affinities with the Onge hunter-gatherers from the Andaman Islands, while Southeast Asian Neolithic farmers have a distinct East Asian genomic ancestry related to present-day Austroasiatic-speaking populations. We also identify two further migratory events, consistent with the expansion of speakers of Austronesian languages into Island Southeast Asia ca. 4 kya, and the expansion by East Asians into northern Vietnam ca. 2 kya. These findings support the Two Layer model for the early peopling of Southeast Asia and highlight the complexities of dispersal patterns from East Asia.
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Ancient genomes document multiple waves of migration in Southeast Asian prehistory

Mark Lipson, Olivia Cheronet, Swapan Mallick, Nadin Rohland, Marc Oxenham, Michael Pietrusewsky, Thomas Oliver Pryce, Anna Willis, Hirofumi Matsumura, Hallie Buckley, Kate Domett, Giang Hai Nguyen, Hoang Hiep Trinh, Aung Aung Kyaw, Tin Tin Win, Baptiste Pradier, Nasreen Broomandkhoshbacht, Francesca Candilio, Piya Changmai, Daniel Fernandes, Matthew Ferry, Beatriz Gamarra, Eadaoin Harney, Jatupol Kampuansai, Wibhu Kutanan, Megan Michel, Mario Novak, Jonas Oppenheimer, Kendra Sirak, Kristin Stewardson, Zhao Zhang, Pavel Flegontov, Ron Pinhasi, David Reich

Abstract:  Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from thirteen Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100-1700 years ago). Early agriculturalists from Man Bac in Vietnam possessed a mixture of East Asian (southern Chinese farmer) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. In a striking parallel with Europe, later sites from across the region show closer connections to present-day majority groups, reflecting a second major influx of migrants by the time of the Bronze Age.





发表于 2019-1-9 22:50 | 显示全部楼层
本帖最后由 Yungsiyebu 于 2019-1-9 22:52 编辑
geoanth 发表于 2019-1-9 22:39


发表于 2019-1-10 15:16 | 显示全部楼层
发表于 2019-1-10 10:46 | 显示全部楼层
Yungsiyebu 发表于 2019-1-9 22:50
这叫推测不叫证据,就像复旦用ystr多态性估计M117等起源于东南亚一样,是推测不是证据。方法本身靠不靠 ...

发表于 2019-1-10 12:04 | 显示全部楼层
 楼主| 发表于 2018-3-9 10:47 | 显示全部楼层
 楼主| 发表于 2018-3-9 11:04 | 显示全部楼层

Figure 1. (B) First two components of PCA of present-day and ancient individuals from mainland SEA, excluding Onge and the ancient Hoabinhians (Group 1), highlighting the differences in ancestry affinities among individuals from Groups 2-5.
发表于 2018-3-9 11:16 | 显示全部楼层
good! 再次印证我之前的多次迁徙混合推测~
发表于 2018-3-9 11:20 | 显示全部楼层
 楼主| 发表于 2018-3-9 11:20 | 显示全部楼层

Figure 1. Lower panel: fastNGSadmix plot at K=13, for all present-day samples, excluding SGDP genomes (see SOM5). We refer to the following present-day language speaking groups in relation to our ancient samples - Austroasiatic (Mlabri and Htin - bright green), Austronesian (Ami - pink) and Hmong (indigenous to the mountainous regions of China, Vietnam, Laos and Thailand - dark pink), along with a broad East Asian component (dark green).  (Hm=Hmong Mien, P.M.=Proto Malay, MN = Malaysian ‘Negrito’, PN = Philippines ‘Negrito’, P.N.G. = Papua New Guinea, And. Is. = Andaman Islands)
 楼主| 发表于 2018-3-9 11:42 | 显示全部楼层
Table 1. Meta-data for ancient samples, including IDs, radiocarbon dates and groups of similar ancestry into which they were placed for reference in the main text. A question mark denotes that a sample is of too low coverage to obtain information about genetic sex or haplogroup.

发表于 2018-3-9 12:00 | 显示全部楼层
还有很明显Mt N 从这个研究结果是更原始更老的

Mt M 才是后来扩张的
发表于 2018-3-9 12:05 | 显示全部楼层
imvivi001 发表于 2018-3-9 11:36


At K=2, we observe a blue component that is maximised in Yoruba, and a light pink component that is present in most EA and SEA populations, while Europe and South Asian (SA) populations are modeled as a mix of these two components. Certain SEA populations, like the Malay, Papuan ‘Negritos’, Onge, Jarawa and Melanesians are also a mix.
The Tianyuan and the Group 1 individuals show an unusually large blue component for the region. (这个不奇怪,本坛早就讨论过了,这种成分在早期欧洲人中也很普遍)

At K=4, a dark purple component is maximised in the Jehai and Melanesians. This component is also present at >50% frequency in many ISEA populations (including Group 5).
On the mainland, this component reaches ~50% frequency in the Mlabri, Htin(老挝泰国的一个少数民族,总人口约为7万人 and the Group 2
发表于 2018-3-9 12:09 | 显示全部楼层
本帖最后由 imvivi001 于 2018-3-9 12:16 编辑
Table 1. Meta-data for ancient samples, including IDs, radiocarbon dates and groups of similar ancestry into which they were placed for reference in the main text. A question mark denotes that a sampl ...
cpan0256 发表于 2018-3-9 11:42

发表于 2018-3-9 12:18 | 显示全部楼层
imvivi001 发表于 2018-3-9 12:09

发表于 2018-3-9 12:23 | 显示全部楼层
At K=5 the component that is dark purple in Melanesians and western Indonesian at K=4 now  becomes black, and is also seen in Group 6. The Onge and Group 1 samples now share a  blue+black+purple profile.

At K=6, a dark green East Asian component is maximised in the Ryukyuan and Japanese,  while a pink East Asian component is now maximised in the Ami. While the dark green component is present in almost all EA, SEA and some SA populations, it is absent in the Mlabri, the Jehai, and most ISEA individuals. When looking at the ancient samples, we also observe that it is absent in In662 (Group 5) and all Group 2 samples.

At K=7, the light green component is maximised in the Mlabri, followed by other Austroasiatic SEA populations and Group 2. This component is present in all  populations, and is at highest frequency in the populations lacking the dark green component at K=6.
发表于 2018-3-9 12:29 | 显示全部楼层

Figure 1. Lower panel: fastNGSadmix plot at K=13, for all present-day samples, excluding SGDP genomes (see SOM5). We refer to the following present-day language speaking groups in relation t ...
cpan0256 发表于 2018-3-9 11:20

发表于 2018-3-9 12:56 | 显示全部楼层

发表于 2018-3-9 13:48 | 显示全部楼层
本帖最后由 MNOPS 于 2018-3-9 13:51 编辑

12# imvivi001

发表于 2018-3-9 13:50 | 显示全部楼层
本帖最后由 MNOPS 于 2018-3-9 13:52 编辑

13# imvivi001

发表于 2018-3-9 13:53 | 显示全部楼层
12# imvivi001
发表于 2018-3-9 13:59 | 显示全部楼层
12# imvivi001

MNOPS 发表于 2018-3-9 13:48

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发表于 2018-3-9 14:04 | 显示全部楼层
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