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Thread: The deep population history of northern East Asia from the Late Pleistocene to the

  1. #341
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    Quote Originally Posted by Ebizur View Post
    The source is Rumiko Suzuki et al. (2022), "Helicobacter pylori genomes reveal Paleolithic human migration to the east end of Asia."

    The analyzed samples are neither ancient nor human; they are samples of Helicobacter pylori bacteria obtained from the stomachs of present-day people.
    I think in this paper the hpOkinawa strain may originate from a mixture of hpHokkaido and hpRyuku, although the authors suggested divergence at about the time of the Jomon period in Japan.

  2. #342
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    Quote Originally Posted by Max_H View Post
    Is been a while since I posted but you said that in this scenario then Ustishim would be more of this Basal East Eurasian ancestry (likely haplogroup D and C for Y lineage and subclade of N and some early M for the mitochondrial lineage) and Tianyuan less so, but both admixed with it? In this case would Hoabinhian be a good proxy for basal East Eurasian or where that ancestry maximizes?
    The wholety of sampled East Eurasians (including Ust-Ishim, BachoKiro was not published at the time) all fell within the same ~50/50 post-admixture branch.
    Other than making Ust-Ishim firmly an East Eurasian, nothing downstream was different. The whole of the result was effectively shifting basal from West to East.
    I don't recall trying multiple edges to see if fit improved, at the time it wasn't necessary, maybe with new samples it would be.
    On the other hand, perhaps ZlatyKun could strike this whole idea dead in the water.
    Last edited by Kale; 08-11-2022 at 06:37 PM.
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  4. #343
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    Quote Originally Posted by Kale View Post
    'Population Y' is described as having elevated affinity to Australians/Papuans, Onge, Tianyuan, populations who really have nothing special in common.
    Bot15 and Bot17 if you were just looking at their uniparental and autosomal DNA without knowing where they were from, you'd say 'run-of-the-mill' Polynesian, case closed.
    They are almost certainly a case of mislabeling at the museum they were sourced from.
    Here's a link to the Botocudo paper.
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4370112/
    Thank you! Specifically Madagascar makes much more sense than the vague reference given in Columbo et al. 2022.

  5. #344
    Quote Originally Posted by anthrofennica View Post
    The identity of these "First Americans" or "Population Y" is fascinating to me. Autosomally I have seen them described as "Australasian" or "Australasian-like" in autosomal studies. In what sense exactly I do not know. Do they mean specifically the Australasians, to the exclusion of the South Asians, Andamanese, and East Asians (who were a quadfurcation)?

    When we exclude C2a-L1373 (TMRCA 16.2 kya) from the American Y-DNA record, there are still two samples from Brazil ~500 ya (Bot15 and Bot17) within C1b2a-M38 (formed 40.8 kya, YFull TMRCA 18.7 kya but it does not yet include these samples), a branch found at frequency in Melanesia. Columbo et al. 2022 dismissed it as the result of European maritime exchange, but that does not seem very plausible to me, leaving only two possibilities. (1) They discovered an extremely rare Amerind lineage that only managed to survive in a single individual. (2) They discovered a Population Y relict lineage. If the latter is the case, then we ought to pay special attention to C-M38.

    Scheinfeldt et al. 2006 gave C1b2a-M38 a TMRCA [42-]49.6[-61] kya, but noted it was rather rare, found in Austronesian speakers of Bougainville although that could have hypothetically come from the Austronesians of New Ireland as it had not yet been found among Papuan speakers (keep in mind however transmission of Austronesian itself in that area was largely matrilineal). They also gave a popular subclade C1b2a1-M208 a TMRCA [39-]46.2[-57] kya.

    Mona et al. 2007 focused on the spread of TNG, and found that C-M38 in the Bird's Head region reflected earlier local Y-DNA diversity rather than an intrusion following TNG expansion. In this study we see C-M38 very well-entrenched among Papuan speakers, so I highly doubt it is intrusive in Sahul. In fact it cannot possibly be a recent intrusion, as the C-M38 diversity in the Bird's Head Peninsula area alone reached [6.0-]12.3[-21.3] kya; in Southwest Papua it reached [1.8-]8.0[-16.9] kya. Keep in mind this was still one of the earliest detailed Y-DNA studies of Papuans. This included the domination among the Maybrat (16/24 were C-M38), the Tehit (< West Bird's Head; 5/5 C-M38), Baham (< West Bomberai < TNG; 15/24 C-M38). And a significant presence among the Moi (< West Bird's Head; 2/8 C-M38), Karon (7/22 C-M38, 1/22 specifically C-M208), Moskona=Meninggo (<Mantion-Meax; 5/10 C-M38). There was also 1/24 Ekari (Paniai Lakes < TNG) belonging specifically to C-M208. I cannot remember if it was still this study, but C-M38 was also found in a few Citak (< Asmat-Kamrau < TNG), a few Asmat (< Asmat-Kamrau < TNG), a few Aghu (< Asmat-Kamrau < TNG), and a few Muyu (< Ok < TNG); and specifically C-M208 was found in ~19/20 Dani (< Dani < TNG).

    Kayser et al. 2008 looked at Melanesian Y-DNA in the Admiralties, and determined that C-M38>M208 was present at 15%.

    Karafet et al. 2010 analysed the Y-DNA of Wallacea, the Philippines, and Sunda. Here they found a very strong presence, but they found it to be strongly associated with Papuan ancestry even on the islands of Wallacea (where they associate it with evidently bidirectional geneflow between Wallacea and Papua), in contrast to some other subclades. They found it in 12/27 Non-Austronesian samples from Alor (< TAP), and in 10/25 Non-Austronesian samples from the Moluccas.

    Delfin et al. 2011 focused on the Solomon Islands, including Papuan groups speaking Papuan languages Bilua, Lavukaleve, and Savosavo. They found that including subclades outside the Solomons the haplogroup C-M38 had a TMRCA ~17 kya. They found it specifically in 4/32 Lavokaleve and 1/30 Savosavo; they found the specific subclade C-M208 in 1/44 Bilua. Not very frequent on the Solomons apparently so. To borrow from other studies, we note that the nearest other instance of C-M38 is among the Kuot (2/32), and specifically C-M208 among the Anêm (1/34), and no other instances on the Bismarck Archipelago. So it is only barely found on the Bismarck Archipelago and at low frequency on the Solomons.

    Karmin et al. 2015 sampled the Madang at Koinambe/Koinanbe, all 3 of which belonged to a line C-MY1104 (TMRCA ~1 kya, diverged from the Boiken lines).

    Bergström et al. 2017 or 2018 (the date got lost from our group's notes) identified a single C-M38 subclade responsible for all Gende (< Madang), of TMRCA [0.8-]0.9[-1.1] kya. This was the same that Malaspinas et al. 2016 detailed, giving them all together a TMRCA of under ~2kya and perhaps closer to ~1 kya (C-MY1096, C-MY1097, C-MY1098, C-MY1099, C-MY1100). In fact this was calculated to be the deepest diverging subclade yet known within C-Y25191 with a TMRCA ~21 kya. So the Gende are a very homogenous Madang group, but still you can see C-M38 must have been on Papua for a very very long time.

    Brucato et al. 2021 conducted detailed phylogenetic work on C-M38, finding I believe that it was entirely restricted to Sahul-Wallacea. The Boiken (< East Sepik) belonged half to the branch C-Y25191 (which diverged ~11 kya from its brother clade C-MY1580), half to C-MY1108 (which diverged ~12 kya from its nearest relatives). I think there is even more data on the Boiken from this year, all C-M38 (and at least 2/2 in one group specifically C-M208).

    Karmin et al. 2022 studied Y-DNA throughout Oceania. It found the rapid diversification of C-M130 likely to reflect the first settlement of the Sunda and Sahul regions, calculating I think so the split off of most NEA lines except some of the Yaponesian ones at ~51 kya, then ~50 kya for C1-M8 of Japan, then ~49 kya the major breakup. This major breakup was practically a pentfurcation: C8-F725 of {Sunda, Philippines, Flores, Mentawi}, C5-M356 of [mainly West] India, C7-B67 of {Sunda, Flores, Lembata}, C9-B68 of Sunda (specifically Borneo), and the C2-C4 clade. This C2-C4 clade split ~46 kya into C2-M38 of Wallacea and "North Sahul" (TMRCA ~24 kya), and C4-MY1088 of Australia.

    It is fascinating to me that a specifically Papuan clade should be found in South America. Even among Australians, so long as the phylogeny they used still holds up (I have not checked ISOGG 2019-2020), studies like Nagle et al. 2016 only found its sister clade C-M347 in Australia, besides basal C. They explained it as a single group of males carrying C-M130 entering Papua, while other related C-M130 descendants migrated further south into Australia (while still part of Sahul). But the situation gets very complicated, both within that paper and in/between others.

    For sure today C-M38 is at its highest diversity today on the east side of Papua, but it is still widely distributed, and its deep internal divergences prevent us from fearing it might be a "recent" migration to Sahul-Wallacea. It is imperative to place the samples from Brazil on the C-M38 tree. And in general reconstructing the migrations associated with C are important to the population history of Eurasia and the Americas.
    More precisely, population Y is a sister branch of Onge, as can be read for example in the article "Deep genetic affinity between coastal Pacific and Amazonian natives evidenced by Australasian ancestry". Due to the Papuans and Australian Aboriginals being the most notorious of the cluster to which the Onge belong, the name Australasians is one of those given to the cluster. You can also call them Basal Asians or Asian Africans (Afrasians as opposed to Eurasians). The name Afrasians lends itself to confusion with linguistics.

    All the other skulls of the Botocudo group to which these two 100% Polynesian belong, are 100% Amerindian. The Brazilian museum that has them, received from New Zealand, a long time ago, 2 skulls of Polynesians from the Chatham Islands. Those 2 skulls disappeared. It must be those 100% Polynesians mixed in the Botocudos collection. This was in the New Zealand newspapers a few years ago. It's not that it's not possible, Polynesian boats were more maneuverable than Europeans in the 1500s, https://en.m.wikipedia.org/wiki/Crab_claw_sail , and Polynesian legends tell of voyages to the Antarctic Ocean. Long before reached Antarctica the Polynesians could use the Roaring Forties, https://en.m.wikipedia.org/wiki/Roaring_Forties , for in a few weeks arrive in the south of the Chilean coast, Strait of Magellan and even circumnavigate the planet in a few months, but there is no proof of this and the objects obtained from museological contexts when they go against all other evidence, are set aside.

    The Sumidouro5 sample I talked about is ~10,000 years old.

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  7. #345
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    Quote Originally Posted by Kale View Post
    The wholety of sampled East Eurasians (including Ust-Ishim, BachoKiro was not published at the time) all fell within the same ~50/50 post-admixture branch.
    Other than making Ust-Ishim firmly an East Eurasian, nothing downstream was different. The whole of the result was effectively shifting basal from West to East.
    I don't recall trying multiple edges to see if fit improved, at the time it wasn't necessary, maybe with new samples it would be.
    On the other hand, perhaps ZlatyKun could strike this whole idea dead in the water.
    Thank you for elaborating!

    There is another scenario you proposed where Tianyuan=Goyet+X where X is something generic Eurasian I recall. But later East Asians pick up more "basal" admixture that looks more Ustishim-like and that can also explain the affinities with Iran_N/AHG/CHG and so on. Or is this a confusion of two different models?

    Interestingly, in the stats you have posted and other I have seen, Iran_N showing the most basal ancestry also shows the most ENA affinity, however in qpGraph the ENA part appears close to the ENA part of ANE, but without the basal in ANE. Still, Sikora et al (2019) in the paper "The population history of northeastern Siberia since the Pleistocene" suggested that MA1 is part CHG-admixed, thereby having some low Basal-like admixture, however it is likely that result was only due to ANE admixture in CHG.

  8. #346
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    I've run so many over the years, perhaps your memory is better than mine
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

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  10. #347
    Quote Originally Posted by jose luis View Post
    More precisely, population Y is a sister branch of Onge, as can be read for example in the article "Deep genetic affinity between coastal Pacific and Amazonian natives evidenced by Australasian ancestry". Due to the Papuans and Australian Aboriginals being the most notorious of the cluster to which the Onge belong, the name Australasians is one of those given to the cluster. You can also call them Basal Asians or Asian Africans (Afrasians as opposed to Eurasians). The name Afrasians lends itself to confusion with linguistics.

    All the other skulls of the Botocudo group to which these two 100% Polynesian belong, are 100% Amerindian. The Brazilian museum that has them, received from New Zealand, a long time ago, 2 skulls of Polynesians from the Chatham Islands. Those 2 skulls disappeared. It must be those 100% Polynesians mixed in the Botocudos collection. This was in the New Zealand newspapers a few years ago. It's not that it's not possible, Polynesian boats were more maneuverable than Europeans in the 1500s, https://en.m.wikipedia.org/wiki/Crab_claw_sail , and Polynesian legends tell of voyages to the Antarctic Ocean. Long before reached Antarctica the Polynesians could use the Roaring Forties, https://en.m.wikipedia.org/wiki/Roaring_Forties , for in a few weeks arrive in the south of the Chilean coast, Strait of Magellan and even circumnavigate the planet in a few months, but there is no proof of this and the objects obtained from museological contexts when they go against all other evidence, are set aside.

    The Sumidouro5 sample I talked about is ~10,000 years old.
    In fact, there are several proofs of relations between Polynesians and Amerindians: https://en.m.wikipedia.org/wiki/Pre-...ntact_theories

    The hypothesis that these Botocudos were slaves brought from Madagascar, despite presenting many difficulties, I think it was the best before knowing about the New Zealand skulls.
    Difficulties of the Madagascar hypothesis:
    1) Most slaves in Brazil came from the African Atlantic coast, some came from Mozambique, from Madagascar if there were any they would be rare.
    2) I think that the Polynesians of Madagascar would have African mix, and they came from northwest Indonésia, or a restricted area of southern Borneo, where this Polynesian Y chromosome will have a low frequency.

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  12. #348
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    Quote Originally Posted by jose luis View Post
    In fact, there are several proofs of relations between Polynesians and Amerindians: https://en.m.wikipedia.org/wiki/Pre-...ntact_theories

    The hypothesis that these Botocudos were slaves brought from Madagascar, despite presenting many difficulties, I think it was the best before knowing about the New Zealand skulls.
    Difficulties of the Madagascar hypothesis:
    1) Most slaves in Brazil came from the African Atlantic coast, some came from Mozambique, from Madagascar if there were any they would be rare.
    2) I think that the Polynesians of Madagascar would have African mix, and they came from northwest Indonésia, or a restricted area of southern Borneo, where this Polynesian Y chromosome will have a low frequency.
    Thank you!

    I will add that the C-M38 is a Papuan haplogroup, so even if autosomally they clustered with Borneans on their PCA, the Y-DNA points towards Melanesia (and Polynesia).

  13. #349
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    Last edited by Gentica277282; 08-12-2022 at 08:35 PM.
    Target: Me
    Distance: 1.4392% / 0.01439195
    36.0 TUR_Tepecik_Ciftlik_N
    22.2 Iberomaurusian
    22.0 SYR_Tell_Qarassa_Early_Antiquity
    13.4 COG_Kindoki_230BP
    5.8 Steppe_Pastoralist
    0.6 Iran_Neolithic

    Target: Me
    Distance: 1.5117% / 0.01511723
    41.8 MAR_LN
    24.6 SYR_Tell_Qarassa_Early_Antiquity
    13.8 COG_Kindoki_230BP
    10.8 Iberomaurusian
    5.0 Caucasus_Hunter-gatherer
    4.0 Steppe_Pastoralist

    R11109 MALE 1 CE 1749.5 400 CE ARCHAEOLOGY Isola_Sacra Y-DNA: J-Y15222 mtDNA: X2m'n

  14. #350
    Quote Originally Posted by Gentica277282 View Post
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    "the bASN [=Papuans and the like]-specific alleles share a deep root with the Africans ."

    Genetic connections and convergent evolution of tropical indigenous peoples in Asia,
    https://doi.org/10.1093/molbev/msab361

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