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Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia

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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: https://www.biorxiv.org/content/early/2018/03/08/278374

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.

编辑此帖时所加评论:等了很久,才见到了列为此帖标题的这篇研究亚洲古DNA的文章。不料短短几天之内,又见到了一篇内容接近的文章,现把它的链接和摘要也加在这帖里。在编辑时,此帖已有144楼。

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 楼主| 发表于 2018-3-9 10:47 | 显示全部楼层
f4.jpg
 楼主| 发表于 2018-3-9 11:04 | 显示全部楼层
f1b.jpg

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
很有意思,这个大嘴博士指导的研究团队包括不少安南人士,希望他们这次参与不是来打酱油的,呵呵
 楼主| 发表于 2018-3-9 11:20 | 显示全部楼层
f1l.jpg

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.

t1a.jpg
发表于 2018-3-9 12:00 | 显示全部楼层
中国人进入越南就是2000年前,和历史书上吻合完美。
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
这个K值图参考价值有限,因为没有k值递进演示或Fst值演示,很难看出各种成分之间的关系
...
imvivi001 发表于 2018-3-9 11:36

看到了,附件有一个文字说明,正在慢慢看...

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

七八千年前在老挝发现了y-C,这个倒是比较有意思,不知道是C1b还是C2南...?
说明现在aDNA提取技术又有了重大进步,好,祝贺!
发表于 2018-3-9 12:18 | 显示全部楼层
七八千年前在老挝发现了y-C,这个倒是比较有意思,不知道是C1b还是C2南...?
说明现在aDNA提取技术又有了重大进步,好,祝贺!
imvivi001 发表于 2018-3-9 12:09

四五千年年前在马来西亚发现了y-D,这个也蛮有意思的,说明当年y-D的扩张也是蛮不错的。会不会是安达曼人的祖先呢?
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
56458

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

这个大嘴博士率领的“北欧-安南东西亚欧联队”,居然把日韩人群列为‘阿尔泰语人群’,而琉球人群居然是最典型的‘阿尔泰’,可见这个联队的语言学知识是多么的令人呜呜呜...
发表于 2018-3-9 12:56 | 显示全部楼层
这次大嘴绘制的东亚欧人群的发育树,和以前相比似乎进步不大,依然还未能摆脱线性思维模式(可能北欧人还不适应矩阵思维模式)。不过其中有一点可以看出,与之前其他所有的研究团队的结果保持一致,那就是咱们东亚人(以汉土苗和台湾土著为代表)距离EE老祖宗的遗传距离最近。我的看法,是因为这些人群与‘外种系’混合最少(当然,并不是没有,只是极少)

大嘴-东亚欧-发育树-2018.png
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
哪里说了发现七八千年前的老挝Y-C了?能把原文贴出来吗?

另外我觉得C1的可能性要大于C2。
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
能把发现四五千年前马来西亚Y-D的原文也一并贴出来吗?

这个倒是不奇怪,因为毕竟临近的andaman群岛上就有Y-D
发表于 2018-3-9 13:53 | 显示全部楼层
12# imvivi001
刚看到不好意思,在8楼
发表于 2018-3-9 13:59 | 显示全部楼层
12# imvivi001
哪里说了发现七八千年前的老挝Y-C了?能把原文贴出来吗?

另外我觉得C1的可能性要大于C2。
MNOPS 发表于 2018-3-9 13:48

如果发现是C2,那你会不会从一楼的窗台上毅然决然地跳出去,或是找一个洗脚盆一头扎进去?
发表于 2018-3-9 13:59 | 显示全部楼层
不信的话拭目以待,我打赌老挝和平文化的那个C是C1。老永之前说过和平文化人群体质类澳美,澳洲土著是有C1的,且其配套的母系M5也是在南亚次大陆比较常见,而南亚同样有C1。
发表于 2018-3-9 14:04 | 显示全部楼层
F46在新石器末期已经出现在越南,有意思...
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