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发表于 2018-7-8 08:28 | 显示全部楼层 |阅读模式
本帖最后由 ChinaHistory 于 2018-7-8 08:34 编辑

http://science.sciencemag.org/content/361/6397/88.full

The prehistoric peopling of Southeast Asia

Science  06 Jul 2018:Vol. 361, Issue 6397, pp. 88-92          DOI: 10.1126/science.aat3628

The past movements and peopling of Southeast Asia have been poorly represented in ancient DNA studies (see the Perspective by Bellwood). Lipson et al. generated sequences from people inhabiting Southeast Asia from about 1700 to 4100 years ago. Screening of more than a hundred individuals from five sites yielded ancient DNA from 18 individuals. Comparisons with present-day populations suggest two waves of mixing between resident populations. The first mix was between local hunter-gatherers and incoming farmers associated with the Neolithic spreading from South China. A second event resulted in an additional pulse of genetic material from China to Southeast Asia associated with a Bronze Age migration. McColl et al. sequenced 26 ancient genomes from Southeast Asia and Japan spanning from the late Neolithic to the Iron Age. They found that present-day populations are the result of mixing among four ancient populations, including multiple waves of genetic material from more northern East Asian populations.

Abstract

The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the “two-layer” hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.

Anatomically modern humans expanded into Southeast Asia (SEA) at least 65 thousand years (ka) ago (1, 2), leading to the formation of the Hòabìnhian hunter-gatherer tradition first recognized by ~44 ka ago (3, 4). Though Hòabìnhian foragers are considered the ancestors of present-day hunter-gatherers from mainland Southeast Asia (MSEA) (5), the East Asian phenotypic affinities of the majority of present-day Southeast Asian populations suggest that diversity was influenced by later migrations involving rice and millet farmers from the north (4). These observations have generated two competing hypotheses: One states that the Hòabìnhian hunter-gatherers adopted agriculture without substantial external gene flow (6, 7), and the other (the “two-layer” hypothesis) states that farmers from East Asia (EA) replaced the indigenous Hòabìnhian inhabitants ~4 ka ago (8, 9). Studies of present-day populations have not resolved the extent to which migrations from EA affected the genetic makeup of SEA.

Obtaining ancient DNA evidence from SEA is challenging because of poor preservation conditions (10). We thus tested different whole-human-genome capture approaches and found that a modified version of MYbaits Enrichment performed best (11). We applied this method together with standard shotgun sequencing to DNA extracted from human skeletal material from Malaysia, Thailand, the Philippines, Vietnam, Indonesia, Laos, and Japan dating between 0.2 and 8 ka ago (11). We obtained 26 low-coverage ancient whole genomes, including those of a Japanese Ikawazu Jōmon individual and Hòabìnhian hunter-gatherers from Malaysia and Laos, as well as Late Neolithic, Bronze Age, and Iron Age farmers from across SEA (Fig. 1 and table S1) (11). We also sequenced mitochondrial DNA from 16 additional ancient individuals and high-coverage whole genomes from two present-day Jehai individuals from Northern Parak state, West Malaysia (table S3). All samples showed damage patterns typical of ancient DNA and minimal amounts of contamination (table S3) (11)


Fig. 1 Maps of ages and differential ancestry of ancient Southeast Asian genomes.

(A) Estimated mean sample ages for ancient individuals. (B to D) D statistics testing for differential affinity between (B) Papuans and Tiányuán (2240k dataset), (C) Önge and Tiányuán (2240k dataset), and (D) Mlabri and Hàn Chinese (Pan-Asia dataset).

We performed a principal component analysis (PCA) of worldwide present-day populations (12, 13) to find the strongest axes of genetic variation in our data and projected the ancient individuals onto the first two principal components. The two oldest samples—Hòabìnhians from Pha Faen, Laos [La368; 7950 with 7795 calendar years before the present (cal B.P.)] and Gua Cha, Malaysia (Ma911; 4415 to 4160 cal B.P.)—henceforth labeled “group 1,” cluster most closely with present-day Önge from the Andaman Islands and away from other East Asian and Southeast Asian populations (Fig. 2), a pattern that differentiates them from all other ancient samples. We used ADMIXTURE (14) and fastNGSadmix (15) to model ancient genomes as mixtures of latent ancestry components (11). Group 1 individuals differ from the other Southeast Asian ancient samples in containing components shared with the supposed descendants of the Hòabìnhians: the Önge and the Jehai (Peninsular Malaysia), along with groups from India and Papua New Guinea.

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预印版:http://www.ranhaer.com/thread-37785-1-1.html

Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia     发表于 2018-3-9 10:36

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 楼主| 发表于 2018-7-8 08:30 | 显示全部楼层


Fig. 2 Exploratory analyses of relationships of ancient Southeast Asian genomes to those of present-day populations.

Ancient samples are projected on the first two components of PCAs for (A) worldwide populations and (B) a subset of populations from EA and SEA. (C) fastNGSadmix plot at K = 13 (11). We refer to the following present-day language-speaking groups in relation to our ancient samples: Austroasiatic (bright green), Austronesian (pink), and Hmong-Mien (dark pink), along with a broad East Asian component (dark green). P.M., proto-Malay; M.N., Malaysian negrito; P.N., Philippines negrito; And. Is., Andaman Islands; NA, not applicable.

We also find a distinctive relationship between the group 1 samples and the Ikawazu Jōmon of Japan (IK002). Outgroup f3 statistics (11, 16) show that group 1 shares the most genetic drift with all ancient mainland samples and Jōmon (fig. S12 and table S4). All other ancient genomes share more drift with present-day East Asian and Southeast Asian populations than with Jōmon (figs. S13 to S19 and tables S4 to S11). This is apparent in the fastNGSadmix analysis when assuming six ancestral components (K = 6) (fig. S11), where the Jōmon sample contains East Asian components and components found in group 1. To detect populations with genetic affinities to Jōmon, relative to present-day Japanese, we computed D statistics of the form D(Japanese, Jōmon; X, Mbuti), setting X to be different present-day and ancient Southeast Asian individuals (table S22). The strongest signal is seen when X = Ma911 and La368 (group 1 individuals), showing a marginally nonsignificant affinity to Jōmon (11). This signal is not observed with X = Papuans or Önge, suggesting that the Jōmon and Hòabìnhians may share group 1 ancestry (11).

D-statistics of the form D(Papuan, Tiányuán; Y, Mbuti), where Y is a test population, are consistent with present-day East Asian populations and most populations of ancient and present-day SEA being more closely related to Tiányuán [a 40-ka-old East Asian individual (17)] than to Papuans (Fig. 1) (11, 18). However, this D statistic is not significantly different from 0 for Y = Jehai, Önge, Jarawa or group 1 (the ancient Hòabìnhians) (table S12). D statistics of the form D(Önge, Tiányuán; X, Mbuti), where X is Jarawa, Jehai, or group 1, show that these populations share more ancestry with Önge than with Tiányuán (Fig. 1) (11). Using TreeMix and qpGraph (16, 19) to explore admixture graphs that could potentially fit our data, we find that group 1 individuals are best modeled as a sister group to present-day Önge (Fig. 3, and figs. S21 to S23 and S35 to S37). Finally, the Jōmon individual is best-modeled as a mix between a population related to group 1/Önge and a population related to East Asians (Amis), whereas present-day Japanese can be modeled as a mixture of Jōmon and an additional East Asian component (Fig. 3 and fig. S29).
 楼主| 发表于 2018-7-8 08:31 | 显示全部楼层


Fig. 3 Admixture graphs fitting ancient Southeast Asian genomes.

TreeMix and qpGraph admixture graphs combining present-day populations and selected ancient samples with high single-nucleotide polymorphism coverage (11). (A) A graph including group 1 samples (Ma911 and La368) fits them as sister groups to present-day Önge. (B) A graph including the highest-coverage group 1 (La368) and group 2 (La364, Ma912) samples shows that group 2 receives ancestry from both group 1 and the East Asian branch. (C) Using qpGraph, we modeled present-day East Asians (represented by Amis) as a mixture of an Önge-like population and a population related to the Tiányuán individual. (D) The Jōmon individual is modeled as a mix of Hòabìnhian (La368) and East Asian ancestry.

The remaining ancient individuals are modeled in fastNGSadmix as containing East Asian and Southeast Asian components present in high proportions in present-day Austroasiatic, Austronesian, and Hmong-Mien speakers, along with a broad East Asian component. A PCA including only East Asian and Southeast Asian populations that did not show considerable Papuan or Önge-like ancestry (fig. S11) separates the present-day speakers of ancestral language families in the region: Trans-Himalayan (formerly Sino-Tibetan), Austroasiatic, and Austronesian/Kradai (20). The ancient individuals form five slightly differentiated clusters (groups 2 to 6) (Fig. 1B), in concordance with fastNGSadmix and f3 results (Fig. 2 and figs. S12 to S19) (11).

Group 2 contains late Neolithic and early Bronze Age individuals (4291 to 2184 cal B.P.), from Vietnam, Laos, and the Malay Peninsula who are closely related to present-day Austroasiatic language speakers such as the Mlabri and Htin (Fig. 1) (11). Compared with groups 3 to 6, group 2 individuals lack a broad East Asian ancestry component that is at its highest proportion in northern EA in fastNGSadmix. TreeMix analyses suggest that the two individuals with the highest coverage in group 2 (La364 and Ma912) form a clade resulting from admixture between the ancestors of East Asians and of La368 (Fig. 3 and figs. S24 to S27). This pattern of complex, localized admixture is also evident in the Jehai, fitted as an admixed population between group 2 (Ma912) and the branch leading to present-day Önge and La368 (fig. S28). Consistent with these results, La364 is best modeled as a mixture of a population ancestral to Amis and the group 1/Önge-like population (Fig. 3). The best model for present-day Dai populations is a mixture of group 2 individuals and a pulse of admixture from East Asians (fig. S39).

Group 6 individuals (1880 to 299 cal B.P.) originate from Malaysia and the Philippines and cluster with present-day Austronesians (11) (Fig. 2). Group 6 also contains Ma554, having the highest amounts of Denisovan-like ancestry relative to the other ancient samples, although we observe little variation in this archaic ancestry in our samples from MSEA (11).

Group 5 (2304 to 1818 cal B.P.) contains two individuals from Indonesia, modeled by fastNGSadmix as a mix of Austronesian- and Austroasiatic-like ancestry, similar to present-day western Indonesians, a finding consistent with their position in the PCA (Fig. 2) (11). Indeed, after Mlabri and Htin, the present-day populations sharing the most drift with group 2 are western Indonesian samples from Bali and Java previously identified as having mainland Southeast Asian ancestry (21) (fig. S13). Treemix models the group 5 individuals as an admixed population receiving ancestry related to group 2 (figs. S30 and S31) and Amis. Despite the clear relationship with the mainland group 2 seen in all analyses, the small ancestry components in group 5 related to Jehai and Papuans visible in fastNGSadmix may be remnants of ancient Sundaland ancestry. These results suggest that group 2 and group 5 are related to a mainland migration that expanded southward across MSEA by 4 ka ago and into island Southeast Asia (ISEA) by 2 ka ago (22–24). A similar pattern is detected for Ma555 (fig. S33) in Borneo (505 to 326 cal B.P., group 6), although this may be a result of recent gene flow.

Group 3 is composed of several ancient individuals from northern Vietnam (2378 to 2041 cal B.P.) and one individual from Long Long Rak (LLR), Thailand (1691 to 1537 cal B.P.). They cluster in the PCA with the Dai, Amis, and Kradai speakers from Thailand, consistent with an Austro-Tai linguistic phylum, comprising both the Kradai and Austronesian language families (20, 25). Group 4 contains the remaining ancient individuals from LLR in Thailand (1570 to 1815 cal B.P.), and Vt778 from inland Vietnam (2750 to 2500 cal B.P.). These samples cluster with present-day Austroasiatic speakers from Thailand and China, in support of a South China origin for LLR (26). The genetic distinction between Austroasiatic and Kradai speakers is discussed further in (11).

Present-day Southeast Asian populations derive ancestry from at least four ancient populations (Fig. 4). The oldest layer consists of mainland Hòabìnhians (group 1), who share ancestry with present-day Andamanese Önge, Malaysian Jehai, and the ancient Japanese Ikawazu Jōmon. Consistent with the two-layer hypothesis in MSEA, we observe a change in ancestry by ~4 ka ago, supporting a demographic expansion from EA into SEA during the Neolithic transition to farming. However, despite changes in genetic structure coinciding with this transition, evidence of admixture indicates that migrations from EA did not simply replace the previous occupants. Additionally, late Neolithic farmers share ancestry with present-day Austroasiatic-speaking hill tribes, in agreement with the hypotheses of an early Austroasiatic farmer expansion (20). By 2 ka ago, Southeast Asian individuals carried additional East Asian ancestry components absent in the late Neolithic samples, much like present-day populations. One component likely represents the introduction of ancestral Kradai languages in MSEA (11), and another the Austronesian expansion into ISEA reaching Indonesia by 2.1 ka ago and the Philippines by 1.8 ka ago. The evidence described here favors a complex model including a demographic transition in which the original Hòabìnhians admixed with multiple incoming waves of East Asian migration associated with the Austroasiatic, Kradai, and Austronesian language speakers.
 楼主| 发表于 2018-7-8 08:32 | 显示全部楼层


Fig. 4 Model for plausible migration routes into SEA.

This schematic is based on ancestry patterns observed in the ancient genomes. Because we do not have ancient samples to accurately resolve how the ancestors of Jōmon and Japanese populations entered the Japanese archipelago, these migrations are represented by dashed arrows. A mainland component in Indonesia is depicted by the dashed red-green line. Gr, group; Kra, Kradai.
发表于 2018-7-8 09:02 | 显示全部楼层
这不就是今年三四月份发表的那篇文章吗?说东南亚最早的原住民是类Onge人群,然后东亚人群大约在四千年前才开始大规模南下东南亚。至于线路图看看就好,毕竟只是推测。
发表于 2018-7-8 10:48 | 显示全部楼层
这不就是今年三四月份发表的那篇文章吗?说东南亚最早的原住民是类Onge人群,然后东亚人群大约在四千年前才开始大规模南下东南亚。至于线路图看看就好,毕竟只是推测。
MNOPS 发表于 2018-7-8 09:02
线路图看看就好,但是树是客观的。
发表于 2018-7-8 12:29 | 显示全部楼层
如此明确的迁徙路线推演图,估计对某些神经衰弱者的刺激太大,作者有义务在文中注明:神经衰弱者慎看~
发表于 2018-7-8 12:30 | 显示全部楼层
这张图很直观:
第一波是类昂哥的古亚洲人,其中产生了和平文化人;
第二波是“田园洞人”指代的新亚洲人的远古祖先,与第一拨人的一些分支混血形成古东亚人(Ancient EA);
到新石器时期产生了两路主要的南下扩散——南亚语人从南陆南下(又与南部古亚洲土著混血形成孟高棉族群)和南岛人从台湾渡海南下。

另外从3楼转贴的常染源流图看,台湾Ami族人的古亚洲人常染遗传比重高达76-79%。这可能还是说明了古亚洲人更早进入EA-SEA,所以产生了比新亚洲人更多的EA适应性常染基因。
发表于 2018-7-8 12:46 | 显示全部楼层
这张图很直观:
第一波是类昂哥的古亚洲人,其中产生了和平文化人;
第二波是“田园洞人”指代的新亚洲人的远古祖先,与第一拨人的一些分支混血形成古东亚人(Ancient EA);
到新石器时期产生了两路主要的南下扩 ...
baiyueren 发表于 2018-7-8 12:30
从图中看不出谁早谁晚,田园洞人四万年到北京也不算晚吧,除非你心里上强行要加这么个时间差。
发表于 2018-7-8 13:13 | 显示全部楼层
跟某些人没什么好说的,6楼和7楼我不予回复。

注意谱系树上标明东欧亚人群是94%的出非洲人群和6%的阿尔泰尼人混合而成的。那么究竟是走北线还是走南线更可能会发生这种混合呢?请各位看官自己判断。
发表于 2018-7-8 13:28 | 显示全部楼层
跟某些人没什么好说的,6楼和7楼我不予回复。

注意谱系树上标明东欧亚人群是94%的出非洲人群和6%的阿尔泰尼人混合而成的。那么究竟是走北线还是走南线更可能会发生这种混合呢?请各位看官自己判断。
MNOPS 发表于 2018-7-8 13:13
阿尔泰尼人只分布在阿尔泰山,北京猿人只分布在北京。
发表于 2018-7-8 13:37 | 显示全部楼层
11# wanhuatong

虽然确实没证据表明阿尔泰尼人只分布在阿尔泰山,但尼人这种适应寒冷地区生活的人科物种分布于北线的可能性还是要大于南线。
发表于 2018-7-8 14:07 | 显示全部楼层
周末简单逻辑测试题
约七万年前有一大波非洲人出非洲,请问,此时的南亚居住着什么人?
发表于 2018-7-8 14:55 | 显示全部楼层
本帖最后由 baiyueren 于 2018-7-8 14:56 编辑
从图中看不出谁早谁晚,田园洞人四万年到北京也不算晚吧,除非你心里上强行要加这么个时间差。
wanhuatong 发表于 2018-7-8 12:46

你先看清楚,我这里的措辞是:“田园洞人”指代的新亚洲人的远古祖先。
因为田园洞人不过是个绝灭的旁支,所以他根本不代表现代东亚人的某一祖先类群。
发表于 2018-7-8 14:57 | 显示全部楼层
你先看清楚,我这里的措辞是:“田园洞人”指代的新亚洲人的远古祖先。
因为田园洞人不过是个绝灭的旁支,所以他根本不代表现代东亚人的某一祖先类群。
baiyueren 发表于 2018-7-8 14:55
你认为此时东亚人的祖先在哪里呢?
发表于 2018-7-8 15:02 | 显示全部楼层
你认为此时东亚人的祖先在哪里呢?
wanhuatong 发表于 2018-7-8 14:57

如果要追溯东亚人的(新亚洲)祖先,那么我认为他们大约是以3.5万年前EDAR370a出现为标志的。这时我们可以这个常染来确定他们是我们的祖先,否则就不能确定是直系祖先还只是进化过程中的旁支。
换言之,4万年前根本没有东亚人这个遗传学意义上的种族存在。
发表于 2018-7-8 15:08 | 显示全部楼层
本帖最后由 baiyueren 于 2018-7-8 15:11 编辑

以3.6-3.8万年前的K14为例,当时的古人只有典型的赤道人种特征或者克罗马农(西欧亚)人种特征,或者两者的混血特征存在。从目前各种研究来看,蒙古人种特征只是比上述两者更晚近才出现的地方性变异而已。
发表于 2018-7-8 15:09 | 显示全部楼层
如果要追溯东亚人的(新亚洲)祖先,那么我认为他们大约是以3.5万年前EDAR370a出现为标志的。这时我们可以这个常染来确定他们是我们的祖先,否则就不能确定是直系祖先还只是进化过程中的旁支。
baiyueren 发表于 2018-7-8 15:02
一个基因位点定祖先,没有就无法判断,那这几万年的时间内东亚突变产生的基因位点多了去了。那付巧妹如何一口断定田园洞人不是现代东亚人群的祖先?那肯定是田园洞人有的基因在现在东亚人群中都没有,你指的新亚洲祖先此事在哪里?
发表于 2018-7-8 15:13 | 显示全部楼层
18# wanhuatong
这个很容易判断,田园洞人的母系是mt-B*,而东亚南部有大量的B4和B5,还有少量的B6。所以田园洞人无疑是东亚人的新亚洲祖先的近亲。
发表于 2018-7-8 21:56 | 显示全部楼层
本帖最后由 lll 于 2018-7-8 22:00 编辑

13# imvivi001 http://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.2003703.s002&type=supplementary你发过来的这个常染成分分析中onge人的成分很复杂,在k值低时以南亚成分、东亚成分、巴布亚成分为主,在k=13时才变成相对较为单一的成分。但为什么在3楼的那个演化树中onge却很少有其他族群的成分混入?难道是3楼的演化图太过粗略没有表现出来?
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