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Thread: Ancient genomes document multiple waves of migration in Southeast Asian prehistory (Lipson et al. 2018)280 days old

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    Default Ancient genomes document multiple waves of migration in Southeast Asian prehistory (Lipson et al. 2018)


    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.

    [...]

    Here we analyze samples from five ancient sites (Table 1; Figure 1A): Man Bac (Vietnam, Neolithic; 4100–3600 yBP), Nui Nap (Vietnam, Bronze Age; 2100–1900 yBP), Oakaie 1 (Myanmar, Late Neolithic/Bronze Age; 3200–2700 yBP [15]), Ban Chiang (Thailand, Bronze Age portion of site; 3000–2800 yBP [16]), and Vat Komnou (Cambodia, Iron Age; 1900–1700 yBP [17]).

    [...]

    To obtain a broad-scale overview of the data, we performed principal component analysis (PCA) with a set of diverse non-African populations (East and Southeast Asian, Australasian, Central American, and European [20–22]). When projected onto the first two axes, the ancient individuals fall close to present-day Chinese and Vietnamese, with Man Bac shifted slightly in the direction of Onge (Andaman Islanders) and Papuan (Figure S1). Next, we carried out a second PCA using a panel of 16 present-day populations from East and Southeast Asia [22, 23]. The populations fill a roughly triangular space in the first two dimensions (Figure 1B; compare [24]), with Han Chinese on the right, most Austroasiatic-speaking groups (Mlabri and Htin from Thailand, Nicobarese, and Cambodian, but not Kinh) toward the left, and aboriginal (Austronesian-speaking) Taiwanese at the top. Man Bac, Ban Chiang, and Vat Komnou cluster with Austroasiatic speakers, while Nui Nap projects close to present-day Vietnamese and Dai near the center, and Oakaie projects close to present-day Burmese and other Sino-Tibetan speakers (two samples, BC8 and OAI1/S29, have especially low coverage, so their exact positions should be interpreted with caution). Present-day Lao are intermediate between Austroasiatic speakers and Dai, and the Borneo and Semende populations from western Indonesia fall intermediate between Austroasiatic speakers and aboriginal Taiwanese.

    We measured levels of allele sharing between populations via outgroup f3-statistics and observed results consistent with those from PCA (Table S2). Nominally, the top sharing for each ancient population is provided by another ancient population, but this pattern is likely to be an artifact due to correlated genotype biases between different ancient samples (Supplementary Text). Restricting to present-day comparisons, Man Bac shares the most alleles with Austroasiatic-speaking groups (as Austroasiatic-speaking groups do with each other), Nui Nap with Austronesian speakers and Dai, Oakaie with Sino-Tibetan-speaking groups, and Vat Komnou with a range of different populations. We also investigated the relationships between the ancient individuals and archaic hominins (Neanderthal and Denisova). Using Han Chinese as a baseline, we observed nominal signals of excess archaic alleles in all populations (statistically significant for Man Bac and Nui Nap; all 1240k SNPs), but as above, these results appear to be driven by artifacts in the data, rather than reflecting actual excess archaic ancestry (Supplementary Text).

    [...]

    Using these observations as a starting point, we built admixture graph models to test the relationships between the Vietnam Neolithic samples and present-day Southeast Asians in a phylogenetic framework. We began with a scaffold model containing the Upper Paleolithic Siberian Ust’-Ishim individual as an outgroup and present-day Mixe, Onge, and Atayal. We then added Nicobarese and Mlabri, two present-day Austroasiaticspeaking populations that appear to have relatively simple admixture histories, as well as Man Bac. All three are inferred to have ancestry from a Southeast Asian farmer-related source (∼70%, forming a clade with Atayal) and a deeply diverging eastern Eurasian source (∼30%, sharing a small amount of drift with Onge; f-statistics indicate that this source is also not closely related to Papuan or South Asians). The allele sharing demonstrated by outgroup f3-statistics can be explained in the admixture graphs by shared genetic drift along the farmer lineage, along the deeply-splitting lineage, or both, but we are not able to determine the relative contributions without additional unadmixed reference populations (Supplementary Text). Given the closeness of the mixture proportions among the three groups, however, we found that the most parsimonious model (Figure 3; Figure S2) involved a shared ancestral admixture event (29% deep ancestry; 28% omitting VN29), followed by divergence of Man Bac from the present-day Austroasiatic speakers, and finally a second pulse of deep ancestry (5%) into Nicobarese. We did not fit full models for the more recent samples given their thinner coverage and likely more complex histories; however, we used f-statistics to probe the relationship between Nui Nap and present-day Southeast Asians more carefully. We found that the statistic f4(Nui Nap, X; Y , Z) is slightly but significantly different from 0 (|Z| > 2.3) for any combination of 1000 Genomes East Asian populations X, Y , and Z (Dai, Kinh, Han, or Japanese; all 1240k SNPs), pointing to small but measurable changes in ancestry between the Bronze Age period in Vietnam and today.

    [...]

    Our results provide strong genetic support for the hypothesis that agriculture was first practiced in Mainland Southeast Asia by (proto-) Austroasiatic-speaking migrants from southern China [4–6, 11–13]. We find that all seven of our sampled individuals from Man Bac are closely related to present-day Austroasiatic speakers, including a shared pattern of admixture, with one, VN29, showing significantly elevated indigenous ancestry. By comparison, studies of cranial and dental morphology have placed Man Bac either close to present-day East and Southeast Asians (“Neolithic”), intermediate between East Asians and a cluster containing more ancient hunter-gatherers from the region plus present-day Onge and Papuan (“indigenous”), or split between the two clusters [7,9,27]. The simplest explanation for our results is that the majority of our samples represent a homogeneous Neolithic cluster, with recent local contact between farmers and hunter-gatherers leading to additional hunter-gatherer ancestry in VN29 and perhaps VN40 [7, 9]. This model would imply that the incoming farmers had already acquired 25–30% hunter-gatherer ancestry, either in China or Southeast Asia, establishing the characteristic Austroasiatic-affiliated genetic profile seen in multiple populations today. The symmetric position with respect to Native Americans of (1) the majority East Asian ancestral lineage in Man Bac, and (2) aboriginal Taiwanese, points to an origin for the farming migration specifically in southern China (contrasting with f4(X, Atayal; Mixe, Dinka) > 0 for northern East Asians X = Han, Japanese, or Korean, Z > 4.5).

    Our findings also have implications for genetic transformations linked to later cultural and linguistic shifts in Southeast Asia and beyond. We observe substantial genetic turnover between the Neolithic period and Bronze Age in Vietnam, likely reflecting a new influx of migrants from China [28], although it is striking that present-day majority Vietnamese (Kinh), who are closely related to our Bronze Age samples from Nui Nap, still speak an Austroasiatic language. Late Neolithic/Bronze Age individuals from Oakaie also do not possess an Austroasiatic genetic signature, in their case being closer to populations speaking Sino-Tibetan languages (including present-day Burmese), pointing to an independent East Asian origin. Outside of Mainland Southeast Asia, we document admixture events involving derived Austroasiatic-related lineages in India (where Austroasiatic languages continue to be spoken) and western Indonesia (where all languages today are Austronesian), with the link between Borneo, Sumatra and Nicobarese supporting archaeological hints of an initial Austroasiatic-associated Neolithic settlement of western Indonesia [26]. Overall, Southeast Asia shares common themes with Europe, Oceania, and sub-Saharan Africa, where ancient DNA studies of farming expansions and language shifts have revealed similarly high levels of genetic turnover associated with archaeologically attested transitions in culture.


    Quote Originally Posted by MnM View Post
    Morocco is a western lapdog.
    Quote Originally Posted by NonFingo View Post
    Those Bronze Age samples are just red herrings to distract you from the actual arrivals of populations with Semitic ancestry. Don’t take the bait by focusing on the wrong samples, lol. He is passing off Bronze Age Levantines with no evidence of strong predynastic input, as “Semites“. This way, he can flip it around and say Proto-Semitic speakers and predynastics were more or less identical to the Bronze Age Levantines sampled so far.
    Quote Originally Posted by NonFingo View Post
    @Semitic Duwa

    Wonder what the resident Proto-Semite has to say about this. I thought unmixed Egyptians were supposed to be Abusir with less/zero Chl?

    In your view, does this prove you wrong, or is it just a coincidence () that M1 is absent in one of the three subsamples from Abusir, and rare overall?

    And don’t change your signature now, please. I’m looking forward to you looking more and more incompetent as more aDNA is published. Wish there was a way to speed this up. But the extra wait and seeing you with your pants down every day, kinda has its own appeal, too.

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    I2a in Neolithic Vietnam!? How is that possible????
    “The only true wisdom is in knowing you know nothing.”
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    Does anyone here have an explanation for that Neolithic Vietnamese I2a sample? Or would you guys say that it’s an error? What do you think, @Semitic Duwa ?
    Last edited by Power77; 2018-03-10 at 23:40.
    “The only true wisdom is in knowing you know nothing.”
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    Here's another preprint on the topic, also just released: https://www.biorxiv.org/content/early/2018/03/08/278374

    It's coming out just in time for David Reich's new book. I wonder if we'll finally see the legendary ancient Indian DNA paper before March 27, too.

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    Quote Originally Posted by VirginiaNumandale View Post
    Here's another preprint on the topic, also just released: https://www.biorxiv.org/content/early/2018/03/08/278374

    It's coming out just in time for David Reich's new book. I wonder if we'll finally see the legendary ancient Indian DNA paper before March 27, too.
    We already have a thread dealing with this pre-print.

    We can also expect Chalcolithic and Bronze Age data from Israel in the near future.
    Last edited by Semitic Duwa; 2018-03-11 at 05:20.


    Quote Originally Posted by MnM View Post
    Morocco is a western lapdog.
    Quote Originally Posted by NonFingo View Post
    Those Bronze Age samples are just red herrings to distract you from the actual arrivals of populations with Semitic ancestry. Don’t take the bait by focusing on the wrong samples, lol. He is passing off Bronze Age Levantines with no evidence of strong predynastic input, as “Semites“. This way, he can flip it around and say Proto-Semitic speakers and predynastics were more or less identical to the Bronze Age Levantines sampled so far.
    Quote Originally Posted by NonFingo View Post
    @Semitic Duwa

    Wonder what the resident Proto-Semite has to say about this. I thought unmixed Egyptians were supposed to be Abusir with less/zero Chl?

    In your view, does this prove you wrong, or is it just a coincidence () that M1 is absent in one of the three subsamples from Abusir, and rare overall?

    And don’t change your signature now, please. I’m looking forward to you looking more and more incompetent as more aDNA is published. Wish there was a way to speed this up. But the extra wait and seeing you with your pants down every day, kinda has its own appeal, too.

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    Quote Originally Posted by Semitic Duwa View Post
    We already have a thread dealing with this pre-print.

    We can also expect Chalcolithic and Bronze Age data from Israel in the near future.
    nice
    i expect plenty of j
    and maybe some E
    the killer look :)

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