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Thread: Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia (McColl et al. 2018)587 days old

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    Default Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia (McColl et al. 2018)








    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.

    [...]

    We obtained 25 low-coverage ancient genomes (Table 1), along with mtDNA and nuclear DNA from an additional set of individuals (Table S3), belonging to hunter-gatherers from the Hoabinhian culture, as well as Neolithic, Bronze Age and Iron Age farmers (SOM3). All samples showed damage patterns typical of ancient DNA (38) (Table S3).

    To address the genetic relationships among the ancient individuals, we performed a principal component analysis (PCA) with our Pan-Asia Panel (see Methods) using smartpca (39). We projected the ancient samples onto the first two principal components of a PCA constructed solely with present-day samples (40) (SOM4). We then used ADMIXTURE (41) to find reference latent ancestry components that could best fit our present-day data, and then used fastNGSadmix (42, 43) to model the low-coverage ancient samples as mixtures of these reference components (SOM5). Unlike all other ancient samples, the two Hoabinhian samples (which also happen to be the oldest samples in our study) - Pha Faen, Laos (La368 - 140 C 7,888 ± 40) and Gua Cha, Malaysia (Ma911 - C 4,319 ± 64) - designated as Group 1, cluster distantly from most East and Southeast Asians in the PCA and position closely to present-day Onge (Figure 1A). Group 1 individuals also contain a mixture of several different ancestral components in the fastNGSadmix plot, including components shared with Onge, the Pahari and Spiti from India, Papuans and Jehai (a Malaysian ‘Negrito’ group), which are markedly different from the other SEA ancient samples. This possibly results from our modeling of ancient populations as a mixture of components inferred in present-day populations, via fastNGSadmix (44), and from the fact the ancient samples are likely poorly represented by a single present-day group. The rest of the ancient samples are defined primarily by East and Southeast Asian components that are maximised in present-day Austroasiatic (Mlabri and Htin), Austronesian (Ami) and Hmong (indigenous to the mountainous regions of China, Vietnam, Laos and Thailand) populations, along with a broad East Asian component.

    [...]

    This is the first study to reconstruct the population history of SEA using ancient DNA. We find that the genetic diversity found in present day SEA populations derives from at least four prehistoric population movements by the Hoabinhians, an “Austroasiatic-like” population, the Austronesians and, finally, additional EA populations into MSEA. We further show that the ancient mainland Hoabinhians (Group 1) shared ancestry with present-day Onge of the Andaman Islands and the Jehai of peninsular Malaysia. These results, together with the absence of significant Denisovan ancestry in these populations, suggest that the Denisovan admixture observed in Papuans occurred after their ancestors split from the ancestors of the Onge, Jehai and the ancient Hoabinhians. This is also consistent with the presence of substantial Denisovan admixture in the Mamanwa from the Philippines, which are best modeled as resulting from an admixture between Austronesians and Papuans, not Onge (61).

    Consistent with the Two Layer model, we observe a dramatic change in ancestry by 4 kya (Group 2) which coincides with the introduction of farming, and thus supports models that posit a significant demographic expansion from EA into SEA during the Neolithic transition. Group 2 are the oldest samples with distinctive EA ancestry that we find. The most closely related present-day populations to Group 2 are the Mlabri and Htin - the Austroasiatic hill tribes of Thailand - which is in agreement with hypotheses of an early Austroasiatic farmer expansion into the region. They also share ancestry with the Temuan and Jehai of Peninsular Malaysia and populations of Western Indonesia, supporting an Austroasiatic (“Western Route”) expansion into ISEA (post-Hoabinhian, pre-Austronesian), as previously proposed based on linguistic and archaeological grounds (27, 49, 68). Furthermore, a recent study also identified populations of Bali and Java as the groups in ISEA with the highest frequency of mainland SEA ancestry (47), also reflected in the large amounts of shared drift between Group 2 and the Javanese that we observe (Figure S13). The extent and nature of this Austroasiatic expansion into western Indonesia prior to the Austronesian expansion could be resolved by sequencing ancient genomes from ISEA prior to the Austronesian expansion.

    By around 2 kya, all ancient mainland samples carry additional EA ancestry components that are absent in Group 2. Within the variation of these recent samples, we find two clusters of ancestry, possibly representing independent EA migrations into mainland SEA. Group 3 has affinities to the Hmong, the Dai from China, the Thai from Thailand and the Kinh from Vietnam, while Group 4 individuals - found only in inland regions - have affinities to Austroasiatic Thai and Chinese speakers. Finally, we also find evidence for the arrival of Austronesian ancestry into the Philippines by 1.8 kya (Group 6) and into Indonesia by 2.1 kya (Group 5). By 2 kya, the population structure in MSEA was very similar to that among present day individuals. Despite observing a clear change in genetic structure coinciding with the transition from the Hoabinhian hunter-gatherers to Neolithic farmers, we also see a degree of local continuity at all sites at different points in time, suggesting that incoming waves of migration did not completely replace the previous occupants in each area (Figure 4).

    This study demonstrates that whole-genome capture is an efficient supplementary approach for retrieving whole genomes from the fossil skeletal and dental remains found in the tropics. As target enrichment inevitably results in subsampling library fragments, it is most useful for (combined) libraries with high underlying complexity. We found a median 7.5 fold enrichment, reducing the sequencing costs proportionally. By enriching the human DNA content, we were able to acquire whole-genome data from selected samples in which the low proportion of endogenous DNA would have been previously prohibitive. The whole genome approach which we have employed here combines shotgun sequencing and capture in order to maximise the potential of ancient samples.

    The clear genetic distinction between the Onge-like Hoabinhian and EA Neolithic demonstrated by this study provides an overwhelming support for the Two Layer model and indicates that in SEA, like in Europe, the onset of agriculture was accompanied by a demographic transition. However, on a more local level, our results point toward admixture events in northern Laos and Peninsula Malaysia between the two dispersal layers. We also show that the Hoabinhians of the first dispersal contributed a degree of ancestry to the incoming EA populations, which may have also resulted in the passing on of some phenotypic characteristics detected by proponents of the Continuity model. Finally, our results reveal that the appearance of these Austroasiatic farmers at around 4 kya was followed by multiple migrations of distinct EA ancestry. These subsequent migrations made significant contributions to the diversity of human populations in present-day SEA.
    Last edited by Semitic Duwa; 2018-03-09 at 01:28.


    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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    La368 carried Y-DNA haplogroup C and mtDNA haplogroup M5 while Ma911 carried Y-DNA haplogroup D and mtDNA haplogroup M21b1a. The later samples are either O1b or O2a.


    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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    Also interesting:

    The Jehai are best fitted as an admixed population between Group 2 (Ma912) and the branch leading to present day Onge and La368 (Figure 3C, S28). ISEA ancient samples from Indonesia (Group 5) and Borneo (Group 6) are best modelled as an admixed population carrying the signature of Group 2 (Figure 3D, Figures S29-33), supporting a previously reported mainland component in ISEA complementary to the well-documented Austronesian expansion (47). For the ISEA samples (Group 5 - In662 and Group 6 - Ma554), when a more basal migration event occurs, it originates from the Papuan branch, rather than the Onge branch as seen in MSEA.


    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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    Group 3 is made up of remnants from the Dong Son culture, these samples are close to present-day Thais ("TaiKadai_Thailand") and Vietnamese. This is interesting as Proto-Vietnamese is thought to have arrived in the Red River delta region during the 1st millennium BCE, which would coincide with the Dong Son culture.

    Unfortunately, no Y-DNA has been recovered for the samples from Group 3.
    Last edited by Semitic Duwa; 2018-03-09 at 02:30.


    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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    Now I'm quite sure that NG6 / Solo Man from Java was a Denisovan, not a Homo Erectus (and most likely this population was the source of archaic Denisovan admixture in Sahulians - Papuans and Australians):

    https://en.wikipedia.org/wiki/NG_6

    https://en.wikipedia.org/wiki/Solo_Man

    I suggested this before. Hoabinhian HG from mainland SEA lacking Denisovan admixture seem to confirm this. It was quite obvious that Denisovan DNA had to be absorbed on the way from Sundaland to Sahul:



    Last edited by Litvin; 2018-03-09 at 04:11.

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    Quote Originally Posted by Semitic Duwa View Post
    La368 carried Y-DNA haplogroup C and mtDNA haplogroup M5 while Ma911 carried Y-DNA haplogroup D and mtDNA haplogroup M21b1a. The later samples are either O1b or O2a.
    The former samples likely spoke language isolates related to Andamanese and/or Vedda, while the latter ones would have spoken something akin to either Proto-Austronesian or Proto-Austro-Asiatic (of course, Proto-Tai-Kadai is a possibility as well).

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    Quote Originally Posted by Power77 View Post
    The former samples likely spoke language isolates related to Andamanese and/or Vedda, while the latter ones would have spoken something akin to either Proto-Austronesian or Proto-Austro-Asiatic (of course, Proto-Tai-Kadai is a possibility as well).
    The samples that fall in Group 2 are bound to closely resemble the Proto-Austroasiatic speech community, the Lua/Htin, Mlabri and Khmu are the most similar to this set of ancient samples. The Khmer also seem to owe well over 50% of their ancestry to a source close to Group 2.

    In the supplementary material, the authors state that:

    Groups 3 and 4 show the most shared drift with each other. The closest present-day population for both is Ami, but there are notable differences among ancient groups (Figures S14, S15, Tables S6, S7). Group 3 has affinities to Tai-Kadai speakers, the Hmong Mien and Han, whereas Group 4 has affinities to Austroasiatic groups instead. When looking only at groups 3.1 and 4.1 (Figures S16, S17, Tables S8, S9), we observe that the Hmong Miao and the Austroasiatic Mlabri are the closest present-day populations to each of them, respectively.

    The present-day populations that share the most drift with Group 5 are the Austroasiatic Htin and the Austronesian Ami, followed by present-day Indonesian populations (Figure S18, Table S10). Similarly, the highest two f3-statistics for ancient samples are Group 6 (Austronesian affinities), and Group 2 (Austroasiatic affinities). Group 6 clearly shares the most drift with Austronesian Taiwanese and Filipino populations (Figure S19, Table S11).

    We can therefore ascertain that there is a strong association between:
    a) Group 1 and Jehai
    b) Group 2 and the Mlabri and Austroasiatic Populations
    c) Group 6 and the Austronesian populations.

    Despite a close relation between Groups 3 and 4, differential affinities to the Hmong and Austroasiatic populations are apparent in these two groups. Group 5 appears to have both Austronesian and Austroasiatic affinities, supporting theories of a mainland Austroasiatic migration prior to the Austronesian expansion.


    Group 3 could probably be modeled as a mixture of Group 4 (later Austroasiatic) and Group 6 (Austronesian). This is interesting since a genetic relationship between Tai-Kadai and Austronesian has often been put forth, this is the case in virtually every high-level hypothesis such as Austro-Tai, Austric and Sino-Austronesian (Laurent Sagart even views Tai-Kadai as a branch of Austronesian on the same level as Malayo-Polynesian). We also know that the southern varieties of Chinese (such as Min) have a non-Sino-Tibetan substratum, some linguists claim this is Austroasiatic, others claim it is Hmong-Mien or Tai-Kadai (Alexander Vovin also claims that Old Chinese had an Austronesian substratum).

    Regardless of the soundness of these different claims, the Proto-Tai-Kadai speakers are likely to have emerged right next to the earliest Austronesian-speaking communities in SE China and therefore probably weren't too dissimilar from Group 6. This could explain the position of Group 3 (as well as that of present-day Thais), right in between Groups 4 and 6. The fact that Austroasiatic (Waic) speakers from China cluster firmly with Group 4 (alongside some Sino-Tibetan groups from Taiwan and Southern China) also gives credence to the Austroasiatic nature of the substratum in Min Chinese.
    Last edited by Semitic Duwa; 2018-03-09 at 16:20.


    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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    @Semitic Duwa , how do you think the Proto-Malayo-Polynesians got their C2 Y-DNA haplogroup(s)? Also, do you believe that the Proto-Sino-Tibetans came from Northern China (or perhaps even the Himalayas for that matter)?

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    Quote Originally Posted by Power77 View Post
    @Semitic Duwa , how do you think the Proto-Malayo-Polynesians got their C2 Y-DNA haplogroup(s)? Also, do you believe that the Proto-Sino-Tibetans came from Northern China (or perhaps even the Himalayas for that matter)?
    I think the presence of C-Z31885 among the Proto-Malayo-Polynesians is related to the "basal migration" event in ISEA the authors mentioned:

    For the ISEA samples (Group 5 - In662 and Group 6 - Ma554), when a more basal migration event occurs, it originates from the Papuan branch, rather than the Onge branch as seen in MSEA.

    As far as the Proto-Sino-Tibetans go, I think the eastern parts of Tibet might be the best contender for the PST homeland, though keep in mind that our comprehension of the Sino-Tibetan family relies largely on our knowledge of Old Chinese, Old Tibetan and Old Burmese, and so the phylogeny of Sino-Tibetan remains uncertain.


    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
    I think the presence of C-Z31885 among the Proto-Malayo-Polynesians is related to the "basal migration" event in ISEA the authors mentioned:

    For the ISEA samples (Group 5 - In662 and Group 6 - Ma554), when a more basal migration event occurs, it originates from the Papuan branch, rather than the Onge branch as seen in MSEA.
    It looks like C-Z31885 “infiltrated” Austronesian speakers (which created the Proto-Malayo-Polynesians) in a similar way to J1-P58 and J2b1-M205 (both of whom “infiltrated” Afro-Asiatic speakers, which in turn created the Proto-Semites).

    Quote Originally Posted by Semitic Duwa View Post
    As far as the Proto-Sino-Tibetans go, I think the eastern parts of Tibet might be the best contender for the PST homeland, though keep in mind that our comprehension of the Sino-Tibetan family relies largely on our knowledge of Old Chinese, Old Tibetan and Old Burmese, and so the phylogeny of Sino-Tibetan remains uncertain.
    Are you saying that the Sino-Tibetan family might not be valid?

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    Semitic Duwa (2018-03-09)

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