March 07, 2010

Major East-West divide in Indonesian Y chromosomes

As usual I have my reservations about the time estimates in this paper, but it is very useful as a guide to genetic variation in Indonesia, an island nation of composite origins where the indigenous population forms part of the S/SE Asia/Oceania zone of "Australoids", probably reflecting early out-of-Africa humans taking the southern route, while this population has been influenced by movements from the north: Caucasoids into India, and Mongoloids or Mongoloid-influenced people into Indonesia.

Getting back to the ever-present time issue; the inferences on this paper are, of course, based on assumption about Y-STR diversity accumulation that I have criticized elsewhere and I will not repeat.

But, isn't it strange that the authors claim a Paleolithic gene pool, while, at the same time, discovering a sharp divide? Common sense dictates that genetic distinctions across a long time span would be blurred, and there would be no sharp divide.

Sharp divides are created by recent population movements and are maintained by insurmountable geographical barriers (e.g., the Sahara or the Pacific) that persist for a long-time.

Molecular Biology and Evolution, doi:10.1093/molbev/msq063

Major East-West Division Underlies Y Chromosome Stratification Across Indonesia

Tatiana M. Karafet et al.

Abstract

The early history of Island Southeast Asia is often characterized as the story of two major population dispersals: the initial Paleolithic colonization of Sahul 45 thousand years ago and the much later Neolithic expansion of Austronesian-speaking farmers 4,000 years ago. Here, in the largest survey of Indonesian Y chromosomes to date, we present evidence for multiple genetic strata that likely arose through a series of distinct migratory processes. We genotype an extensive battery of Y chromosome markers, including 85 SNPs/indels and 12 Y-STRs, in a sample of 1,917 men from 32 communities located across Indonesia. We find that the paternal gene pool is sharply subdivided between western and eastern locations, with a boundary running between the islands of Bali and Flores. Analysis of molecular variance reveals one of the highest levels of between-group variance yet reported for human Y chromosome data (e.g., ?ST = 0.47). Eastern Y chromosome haplogroups are closely related to Melanesian lineages (i.e., within the C, M and S subclades) and likely reflect the initial wave of colonization of the region, while the majority of western Y chromosomes (i.e., O-M119*, O-P203, and O-M95*) are related to haplogroups that may have entered Indonesia during the Paleolithic from mainland Asia. In addition, two novel markers (P201, P203) provide significantly enhanced phylogenetic resolution of two key haplogroups (O-M122, O-M119) that are often associated with the Austronesian expansion. This more refined picture leads us to put forward a four-phase colonization model in which Paleolithic migrations of hunter-gatherers shape the primary structure of current Indonesian Y chromosome diversity, and Neolithic incursions make only a minor impact on the paternal gene pool, despite the large cultural impact of the Austronesian expansion.

Link

202 comments:

  1. Dienekes asks: "But, isn't it strange that the authors claim a Paleolithic gene pool, while, at the same time, discovering a sharp divide?"

    The authors say: "We find that the paternal gene pool is sharply subdivided between western and eastern locations, with a boundary running between the islands of Bali and Flores".

    Which is exactly a major ecological divide: Wallace line. Such divide makes better sense if Paleolithic (when navigation was still technically limited) than if Neolithic and specially if caused by Austronesian expansion, which were the foremost open seas sailors of the Pacific and Indian oceans.

    So, while I don't have access to the whole paper and can't judge the detail, a Paleolithic divide across Wallace line makes total sense to me, while a Neolithic one is harder to support.

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  2. Someone please obtain the supplementary data (and perhaps the study itself might be a little interesting) and share it.

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  3. Maju - I was just going to mak ethe same point lol

    Heres a map showing the various eco dividing lines and ice age sea levels.

    http://en.wikipedia.org/wiki/File:Map_of_Sunda_and_Sahul.png

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  4. Matt: I just used that same map to illustrate my point at my blog. :)

    Seems a pre-sailing feature, not anything that Austronesian mariners would consider any obstacle.

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  5. This comment has been removed by the author.

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  6. Sorry - the end of the URL got lopped off. Add...

    .png on the end

    Maju, agreed.

    (I've just deleted my previous comment which was complete nonsense)

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  7. Like Maju, I hardly find it surprising that there would be a divide across the Wallace line. That is precisely where it should be.

    The surprise is mostly that the Paleolithic population wasn't wiped out by the Austronesians or Austroasiatic people during their expansions.

    Hunter-gathers almost always get wiped virtually entirely by invading agriculturalists. The survival of the Paleolithic gene package in Western Indonesia suggests that there may have been some sort of independent plant/animal domestication event prior to the Austronesian/Austroasiatic expansions that gave the locals staying power against agriculturalist invaders.

    Since the area is right around the likely initial domestication location for the dog (the first first of all of the domestications by thousands of years), it suggests that perhaps something like the Mississippian domestication event in the SE United States (where founder crops were domesticated and then entirely replaced by crops domeesticated elsewhere) may have happened in Western Indonesia and/or mainland SE Asia, probably sometime between 15kya and 4kya.

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  8. "The surprise is mostly that the Paleolithic population wasn't wiped out by the Austronesians or Austroasiatic people during their expansions".

    Austroasiatics expanded rather slowly and often we see them mixing with other peoples (Melanesians, Africans...)

    "Hunter-gathers almost always get wiped virtually entirely by invading agriculturalists".

    That's a belief rather than a scientifically proven reality. Anyhow, Austronesians were probably not the first farmers to arrive, at least to peninsular Malaysia: Austroasiatics were probably (but notice that Papuans also seem to have got a very old Neolithic - silviculture).

    "The survival of the Paleolithic gene package in Western Indonesia suggests that there may have been some sort of independent plant/animal domestication event prior to the Austronesian/Austroasiatic expansions that gave the locals staying power against agriculturalist invaders".

    Or that you are fundamentally wrong about your genocidal farmers hypothesis. After all early farming was only slightly more productive than foraging. Only when population densities increased, then foraging became comparatively unproductive and people took up farming and/or herding, imitating their more succesful neighbors. They still do nowadays where the last foragers remain.

    However both possibilities can be correct at the same time: farming might have arrived in various small waves and these have penetrated more or less gradually among local foragers, with more or less colonization, not from afar but from the neighboring "more developed" island or valley, diluting the agricultural blood as farming advanced, rather than just diluting to nothingness the forager blood, as you seem to expect.

    This process of localized colonization from the previous area (with randomized founder effects surely) along the wave, along with assimilation of local native foragers in most places, is exactly the process that is apparent in the spread of Cardium Pottery Neolithic in the middle and west Mediterranean.

    "Since the area is right around the likely initial domestication location for the dog"...

    Wait! The East Asian origin of domestic dog was strongly questioned when it was found that African street dogs have the same diversity as Asian ones and that the low diversity of European dogs is surely because of modern pedigree fashion with its inbreeding exaggerations. The oldest known fossil dog to date remains one from Belgian Aurignacian anyhow.

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  9. "we present evidence for multiple genetic strata that likely arose through a series of distinct migratory processes".

    I've long been suspicious that the two migration theory was inadequate to explain the evidence.

    "the majority of western Y chromosomes (i.e., O-M119*, O-P203, and O-M95*) are related to haplogroups that may have entered Indonesia during the Paleolithic from mainland Asia".

    I doubt that the O Y-haps date back to the Paleolithic in Indonesia.

    "A Paleolithic divide across Wallace line makes total sense to me, while a Neolithic one is harder to support".

    But even during the Paleolithic Wallace's line was hardly impermeable. Melanesian haplogroups must have crossed it. Once the technology required to cross it had developed I'm sure it would also have moved back west and north. As would have any other improvements in the technology. Each improvement would have led to further expansion.

    "there may have been some sort of independent plant/animal domestication event prior to the Austronesian/Austroasiatic expansions that gave the locals staying power against agriculturalist invaders".

    There was. The Hoabinhian. In fact the Austronesian expansion included much of the Hoabinhian agriculture and was basically a hybrid between the Hoabinhian and the East Asian microlithic. As Maju said, 'Austroasiatics expanded rather slowly and often we see them mixing with other peoples (Melanesians, Africans...)'.

    "The oldest known fossil dog to date remains one from Belgian Aurignacian anyhow".

    I agree that the Austronesians were hardly the people who domesticated the dog they did have it. And the dingo arrived in Australia about the same time as the Austronesian expansion.

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  10. "I doubt that the O Y-haps date back to the Paleolithic in Indonesia".

    In West Indonesia, Sundaland, why not? It was not really apart from Indochina.

    "But even during the Paleolithic Wallace's line was hardly impermeable. Melanesian haplogroups must have crossed it".

    Evidence? I know of no Melanesian haplogroup west of Wallace line, at least at meaningful levels.

    Faith or fact, Terry?

    "In fact the Austronesian expansion included much of the Hoabinhian agriculture and was basically a hybrid between the Hoabinhian and the East Asian microlithic. As Maju said, 'Austroasiatics expanded rather slowly and often we see them mixing with other peoples (Melanesians, Africans...)'".

    Minor but important correction: here you have swapped Austroasiatics and Austronesians in their historical roles AFAIK (and in my words certainly). An error, I understand.

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  11. "In West Indonesia, Sundaland, why not?"

    Archeological and linguistic evidence suggests a major movement into SE Asia from further north.

    "Evidence? I know of no Melanesian haplogroup west of Wallace line, at least at meaningful levels".

    Don't be stupid. The Melanesian haplogroups must have crossed Wallace's Line to actually get to Melanesia. And it seems from this post they crossed several times. There would be no need for anyone to move back across the Line from as far east as Melanesia. They kept moving to uninhabited islands to the east. However you've claimed elsewhere that C moved east from Wallacea, and K1 seems most likely to have done so also.

    "here you have swapped Austroasiatics and Austronesians in their historical roles"

    Agreed. But the same probably holds for Austro-Asiatics.

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  12. "In West Indonesia, Sundaland, why not?"

    Archeological and linguistic evidence suggests a major movement into SE Asia from further north, presumably of Austro-Asiatic and Austronesian-speaking people. I'd guess they carried various Y-hap Os.

    "Evidence? I know of no Melanesian haplogroup west of Wallace line, at least at meaningful levels".

    Don't be stupid. The Melanesian haplogroups must have crossed Wallace's Line to actually get to Melanesia. And it seems from this post they crossed several times. There would be no need for anyone to move back across the Line from as far east as Melanesia. They kept moving progressively to uninhabited islands to the east. However you've claimed elsewhere that C moved east from Wallacea, and K1 seems most likely to have done so also.

    "here you have swapped Austroasiatics and Austronesians in their historical roles"

    Agreed. But the same probably holds for Austro-Asiatics.

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  13. ""Evidence? I know of no Melanesian haplogroup west of Wallace line, at least at meaningful levels".

    Don't be stupid. The Melanesian haplogroups must have crossed Wallace's Line to actually get to Melanesia".

    That doesn't mean they crossed it in East-West direction (at least inmaningful numbers), which is exactly my point.

    "However you've claimed elsewhere that C moved east from Wallacea"...

    I never said so. I have suggested a SE Asian origin for Y-DNA C but Wallacea was always beyond my idea. More like Thailand, Burma or Vietnam probably.

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  14. "Austroasiatics expanded rather slowly and often we see them mixing with other peoples (Melanesians, Africans...)"

    Austronesians (Philipines, island Indonesia, Oceania) expanded rather rapidly, in part because they were moving into virgin territory in Melanesia and Madagascar which had no prior human occupation of any kind.

    The time frame on Austroasiatic expansion (SE Asia and India) is not known with much certainty because they are the bottom layer of well defined extant language groups where they are found or were found. They preceded in those territories the Dravidians, Hmong-Mien, the Tai-Kendai, the Austronesians, and probably Sino-Tibetan speakers as well, but aren't likely to have been pre-Neolithic. SE Asia and South India are not optimal for preserving evidence useful in dating and their expansion started before written history did in Asia.

    "'Hunter-gathers almost always get wiped virtually entirely by invading agriculturalists.' That's a belief rather than a scientifically proven reality."

    See Bantu expansion, see agriculturalist expansion in India, note that small number of surviving Negritos in Malaysia and the Philipines (both of whom lost their language), see Europe, see the Americas, see Australia.

    There are exceptions, but they are exceptions that prove the rule. Pygmies managed to retreat to refugia in Congo rainforests (divided into two populations and losing their language). Highland Papuans were stone age agriculturalists and held their own until more than stone age agriculturalists came along (yes, a few hunter-gatherers managed in tropical swamps). Yes, a tiny pocket of Andamanese survived with government protection. Those who survived mostly converted rapidly to pastoralism which didn't take hold in Indonesia.

    "Anyhow, Austronesians were probably not the first farmers to arrive, at least to peninsular Malaysia: Austroasiatics were probably (but notice that Papuans also seem to have got a very old Neolithic - silviculture)."

    Austroasiatic expansion isn't dated well but is definitely after any domestication events in Asia, which happened when West Indonesia was no longer part of the mainland.

    "Or that you are fundamentally wrong about your genocidal farmers hypothesis."

    Farmers don't need to be genocidal (although farmers and herders routinely were on first contact with hunter-gatherers), they simply need to outnumber hunter-gatherers in population density. There aren't enough hunter-gatherers to convert and rule and no evidence that cultural adoption rather than demic expansion is ever the predomiant mode.

    Localized assimilation seems to only happen to peoples that are already agriculturalists. The evidence that local assimilation was the main character of Cardium Pottery Neolithic in the middle and west Mediterranean is increasingly disfavored by the genetic evidence coming in.

    "Since the area is right around the likely initial domestication location for the dog... The East Asian origin of domestic dog was strongly questioned when it was found that African street dogs have the same diversity as Asian ones."

    The evidence of dog domestication may support separate African and East Asian domestication events, but the dogs of Eurasia and the Americas are East Asian descendants. You need haloptype continuity, not just diverity measures.

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  15. "Austroasiatics expanded rather slowly and often we see them mixing with other peoples (Melanesians, Africans...)"

    I meant Austronesians, obviously. As should be clear from the context. My bad anyhow.

    "The time frame on Austroasiatic expansion (SE Asia and India) is not known with much certainty"...

    But notice that the Senoi (not really Negritos) appear to be a genuine Austroasiatic people, maybe dating to c. 13,000 BP, when the Hoabinhian arrives to Malaysia. The whole issue seems in need of further research anyhow.

    "See Bantu expansion"...

    Bantu expansion is not "Neolithic" but Iron Age. Neolithic seems to have spread in Africa, as elsewhere, with low demic impacts (some anyhow but not massive replacement).

    Still, Bantus differ much between each other and Mozambicans in particular seem autosomally different from their more northeasternly relatives, and also hold loads of what seems pre-Bantu mtDNA. The Xhosa are almost more Khoi than Bantu, at least by phenotype. Khoi herders (who had acquired this Neolithic skill from pre-Bantu contacts with East Africans) persisted until European colonization of the Industrial Age.

    "Farmers don't need to be genocidal (although farmers and herders routinely were on first contact with hunter-gatherers)"...

    Evidence? A lot of data says the opposite in fact. Even Iron Age Bantus had an almost religious respect for the first inhabitants (at least in South Africa), even if they had the upper hand in numbers, technology and organization and often pushed them anyhow (but not without moral contradictions).

    "There aren't enough hunter-gatherers to convert and rule"...

    Rule what? We're talking tribal societies here. States only appear at a later stage, it seems, not early Neolithic.

    Numbers and dialectic relation between foragers and farmers varied a lot surely. But the lengthy transition times we know for most areas, clearly allow for gradual transition of at least some foragers into farming. And some foragers would still be more than a tiny agricultural colony.

    You and the others who claim Neolithic replacement as a matter of fact are misled by Industrial Age genocidal colonization in America and Australia, which is not comparable at all.

    "The evidence that local assimilation was the main character of Cardium Pottery Neolithic in the middle and west Mediterranean is increasingly disfavored by the genetic evidence coming in".

    Sorry:

    1. Archaeology rules: you can complement archaeology with genetics but you can't overrule it.

    2. Genetic evidence does NOT favor AT ALL any replacement scenario in the Mediterranean Neolithic. Spaniards are not massively E1b1b1 nor J2b, Valencians (a region of marked CP colonization) don't cluster too well with Greeks or Eastern Mediterraneans at autosomal level (Bauchet 07) but form a distinct cluster on their own that must be of Paleolithic origin, Portuguese epipaleolithics and neolithics look about the same by ancient mtDNA (Chandler 05), while the Riffians of Taforalt are like the Riffians of today (Kèfi 05).

    So, instead of making blank statements, I'd suggest you look at the facts.

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  16. Thanks Maju, for your statements, especially the statements below.

    "Numbers and dialectic relation between foragers and farmers varied a lot surely. But the lengthy transition times we know for most areas, clearly allow for gradual transition of at least some foragers into farming. And some foragers would still be more than a tiny agricultural colony.

    You and the others who claim Neolithic replacement as a matter of fact are misled by Industrial Age genocidal colonization in America and Australia, which is not comparable at all."

    If anyone actually read the paper on bushmen that was posted a week or so ago, it clearly postulates a gradual absorption of women from the bushmen tribes into the Bantu agriculturalist population. The authors state that they think the only reason that the absorption doesn't go the other way is that bushmen men don't hold property and hence cannot meet the property requirement for the customary Bantu present to the bride.

    Even in the supposed genocidal colonization in the Americas, even with the decimation of smallpox and other diseases, many North American "hunter gatherers" survived. My thesis supervisor's mother was a full blooded Ojibwe. He's obviously not dead. He's not out catching buffalo. He's in a lab designer high speed electronic circuits and antennas.

    I'm sorry that I don't have many SE Asian references for this. It is out of my experience, but certainly hunter gatherers encountered agriculturalists and either coexisted or occasionally intermarried.

    I once went to beautiful exibit of Northwest coast (North America) native masks. What really caught my eye is that different west coast peoples developed masks to describe foreigners. It wasn't fear that these masks describe. In fact, they regarded the "other" with a sense of humour. Their most typical response when encountering the "other" was to either paddle the other way, or attempt to trade. And yes, sometimes there was warfare.

    Here's the link for the "Down from the Shimmering sky exibit:"

    http://www.tfaoi.com/newsm1/n1m204.htm

    We continally make the mistake of thinking that all peoples responded to the "other" with antipathy.

    I think the answer would be, not always. We may not even understand the extent to which hunter gatherers and pastoralist/farmers intermarried, given the fact that a really successful intermarriage of the two groups would obliterate the record that there had been two separate groups.

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  17. Brilliant response by Maju to Andrew's statement that Neolithic replacement of hunter-gatherers is an established fact. I've always wondered why agriculture has had a disproportionate tendency to first appear in rather not favorable arid lands, such as the Middle East, the dry highlands of south Mexico (corn), or coastal Peru. I wonder if the original hunter-gatherer existence in those places was so marginal, that very primitive farming methods just barely managed to edge out hunting-gathering, so they took hold initially in the most marginal areas. Then, as agricultural technology improved, this allowed farming to gradually have an edge over hunting-gathering in other areas where our original lifestyle had better results. This would allow prolonged coexistence of farmers and hunter-gatherers, and the marginal advantage of farming as technology improved would permit that hunter-gatherers adopt the technology themselves instead of being swamped by a wave of millions of farmers. Like Maju said, no comparison with the massive onslaught of relatively modern Europeans and Bantus overwhelming southern Africa or Australia, and I would add that there's also no comparison with the European destruction of America, which had the exceptional factor of the battery of deadly Afro-Asian diseases that almost disintegrated Americans. If we go back 10,000 years, things were likely on a much, much more level playing field between farmers and hunter-gatherers.

    marnie said:

    If anyone actually read the paper on bushmen that was posted a week or so ago, it clearly postulates a gradual absorption of women from the bushmen tribes into the Bantu agriculturalist population.


    Are you talking about the study that sequenced the dna of several people, including Desmond Tutu? If so, then I don't understand, they would have had to have done an mtdna study to say something like that.

    I think what we really need here is a y-dna study of the Negritos people of the Philippines.

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  18. While we wait for someone to share with us the results of this 2010 study of Indonesia, we can look at the results of the 2009 study of Indonesia, by Lansing:

    Indonesia y-dna (Lansing, 2009) - SNPs only.xls

    Note that it appears there's a huge amount of Bali samples that are of historic Indian origin (R1a, R2, H, L, etc.). I would adjust their sample size downwards from 493 to something like 442.

    The Wallace divide is indeed very notable. Amongst western isles, Bali has 95% O, and Borneo and Java have 65% and 75%, and Nias has 100% but it's most likely due to genetic drift. Instead, the eastern isles, Sumba and Flores, have 16% and 17% O. In the case of eastern haplogroups [C, K, M, S], the eastern isles have 84% and 81%, while Bali has 4%, Java 0%, and Borneo 30% (Nias has 0% but it doesn't count because of genetic drift).

    For the Philippines I went to ysearch, where I found 35 Philippine samples, 27 being O, resulting in 77% O. They also had 5 C, resulting in 14% C, similar to neighboring Borneo (but not the other western isles).

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  19. hi aargiedude,

    Yes, i'm talking about the bushman paper that includes the dna of Desmond Tutu.

    The study includes an extensive autosomal dna analysis.

    The comments about Bantu/Bushman intermarriage are in the supplemental information (a pdf download).

    I'm cutting and pasting from that:

    "Impact of traditional life-style on gender-biased gene flow"

    "The reported limited male-mediated gene flow8 in southern African Bantu populations9 has
    resulted in a predominance of the E1b1a (M2) Y-chromosome haplogroup across the region.
    Lack of Y-chromosome divergence has been attributed to cultural practices of patrilocality
    (location of family with that of the male) and polygyny (multiple wives), resulting in a lower
    male migration rate and lower male effective size, respectively10. In contrast to their Bantu
    neighbors, the indigenous hunter-gatherers practice a culture of matrilocality and monogyny;
    thus we can assume a male-biased migration rate resulting in greater Y-chromosome over
    mtDNA diversity.
    Traditionally, due to a nomadic lifestyle, the hunter-gatherer people do not own
    possessions. This lack of ownership results in Bushmen men being ineligible to marry a Bantu
    woman, because they cannot pay the father-in-law a “lobola” (also known as lobolo or mahadi),
    a payment usually made in cattle for her hand in marriage. Male-contributed Bushmen-Bantu
    admixture is therefore assumed to be minimal to absent. Bantu men marrying hunter-gatherer
    women is however reported to have been quite common. A feeling of inferiority associated with
    the “Bushmen” or “San” ethnic classification meant that many Bushmen women tried to uplift
    their status via marriage to Bantu men. We therefore speculate the strong possibility of Bushmen
    contributions to the mitochondrial genome and X-chromosome in southern African Bantu
    populations."

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  20. Thanks for your compliments, Marnie and Argidude.

    Anyhow:

    "... and I would add that there's also no comparison with the European destruction of America, which had the exceptional factor of the battery of deadly Afro-Asian diseases that almost disintegrated Americans".

    Personally I'm not so sure of the impact that such diseases would have (or in fact got) when they were not coupled with exploitation (such as slavery or similar), war and general pressure for the land. It's known that diseases do not just take their toll because of themselves but also because of the condition of the hosts, so an exploited and impoverished people will generally suffer much more from them... and probably will have less chance of recovery too.

    Where or when colonization was slow and not brutal, admixture happened (many white North Americans with deep roots pride of native ancestry for example) and also most native tribes survived pretty well. But then the industrial revolution became consolidated and masses and masses of dispossessed ex-farmers migrated to the colonies in journeys that only lasted some weeks, and political measures of genocidal nature such as the displacement of natives beyond the Mississippi were implemented by force... then populations could barely stand and the masses of displaced colonists took their place easily.

    But this is a model that can't fit in pre-modern contexts. No state almost ever before had such masses of colonists at its disposition and such strong means as the railroad to move them across a whole continent in few decades, or forcibly remove whole nations of natives that were generally much less developed (even if they were often agriculturalists) than their colonialist rivals and masters.

    This is a very extreme industrial reality that can't be imagined happening in the remote past, much less without state organization.

    But most crucial is the archaeological and genetic evidence where available. Because one can imagine the past in many ways... but when you see almost everywhere such striking continuity of the local Epipaleoithic toolkits, which may have changed just a thousand years before Neolithic arrived but not at all at the arrival of pottery, sheep, lentils and cereals... then it becomes crystal clear that there was no replacement and just a very limited colonization.

    I'm talking again of the West Mediterranean but I understand that it was also, with localized variations, the case in other regions probably.

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  21. Thinking about this further, are we perhaps being misled by percentages here?

    Apparently there are very few Melanesians west of Wallaces Line. BUT those islands (esp Java) have a much higher population than the islands farther east.

    Even if only a small percentage of the 150,000,000 plus population of Java are of Melanesian origin, that could represent the same total number of people (in absolute numbers not percentages) as all the Melanesians in the eastern islands combined. Or even more.

    Which would change the picture completely in terms of past migrations.

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  22. The Austroasiatic language family dates to about 3000-4000 BC (Archaeology and Language: Correlating archaeological and linguistic hypotheses By R. Blench, Matthew Spriggs p. 107).

    They and their Austronesian contemporaries were both bronze age farmers.

    Neither farming nor hearding had reached anywhere in Asia at 13,000 BP when Hoabinhian arrives to Malaysia. So, Hoabinhian have to be hunter-gatherers, possibly with dogs. So far as I can discern, the Austronesians in Indonesia, and the Austroasiatic population in mainland SE Asia, are the first farming/herding population to arrive in SE Asia. Everybody before them was some manner or another of hunter-gatherer.

    We know where the language groups originated, and we no that no earlier than these language family prior languages survive (with the possible exception of Andaman, and of course in addition to New Guinea/Australia), so the language of the hunter-gathers is gone without a trace other than substrate influence in regional dialects. In Europe the pre-farming expansion wave may have left Sami and Siberian Paleo-Eskimo and Basque, or they may be more recent - but the first wave of farming was a demic expansion. In India, there are essentially no cognizable signs of pre-Austroasiatic or Dravidian languages (or crops outside the Indus Valley civilization); strong physical differences between "tribals" and other populations in India point to the original population being overwhelmed by newcomers around the time of first agriculture. In Africa, there is no sign of any pre-Bantu farming or herding in the Khoisan or Pygmie, the Pygmie in the jungle lost their language to Bantu anyway, and the Khoisan hung on in what amounts to a couple of desert revervations in small number (mostly by adopting herding) in a small portion of their previously inhabited area. The Bantu numbers are now about 400-1 Bantu to Pgymie/Khosian and the ratio was high very early on, despite starting at zero outside West Africa starting 3500 years ago.

    In places with predominantly hunter-gatherer societies (like the Americas, New Guinea, Australia) you don't get big, recent, comprehensive language groups, you get lots of little languages and language families with dim connections to each other. By the time the Austonesians arrive there is probably no less than one language family per island of the hunter-gatherers.

    West Indonesia separates from the mainland due to rising sea levels around 8,000 BP, and no significant numbers of people get in or out of Indonesia's islands due to lack of boats until the Austronesians arrive several t housand years later. Wallacia may have nobody on it at all, like Oceania, because the boats were never good enough to get there and the freak incidents that populated New Guinea and Australia pass them by, or fail to reach sufficient population to be sustainable (a la Tasmania).

    If there was a farming/herding population before the Austronesians in Indonesia (outside New Guinea) or in SE Asia before the Austroasiatic expansion, I don't know of it and would be interested to learn.

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  23. Continued:

    My working hypothesis is essentially that farmers or herders of any kind kill/replace/overwhelm hunter-gatherers in numbers anywhere that they can produce food, that farmers/herders of similar technology level don't conquer or replace each other, and that more advanced farmers/herders either rule or replace/overwhelm less advanced farmers/herders.

    To be clear, I've been using the term "Neolithic" loosely to mean post-agricultural. In other words, waves of expansion of farmers and herders generally replace or dwarf hunter-gather populations.

    Trying to see where this view is off. Now, by my working theory, if there is proto-agriculture in Indoneisa then Austronesians rule them, rather than replace them. hence the genes we see.

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  24. And thanks Argiedude for the Lansing file. Very interesting.

    For example, we can reply to Matt, thanks to it: more than 50% C2 in Sumba, 0 west of Wallace line (excepting to a small degree Bali, that seems somewhat transitional).

    The lineages that seem strikingly restricted to the East of Wallace Line (with some minor presence in Bali) are: C2, M1 and S. Those that are rare East of the line are: O3 and O2a.

    Some lineages are original in their distribution though: O1a appears much more common East of WL but is also very common in Bali (almost 25%) and in the peripheral Sumatran island of Nias, so I wonder if it represents some sort of intermediate layer. Bali also has some presence of Indian lineages H and R2. There's some R1a1a, specially in Java.

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  25. "The Austroasiatic language family dates to about 3000-4000 BC (...) They and their Austronesian contemporaries were both bronze age farmers".

    I don't make sense of that. Why then Orang Asli (and the remote Nicobarese) speak Austroasiatic and not Austronesian? Why then is it thought that the Munda arrived to India with rice farming? (some claim they are absolute natives but I don't believe that). A Neolithic frame is more reasonable.

    And that's also probably the case for the earliest Austronesian expansion into Philippines (but not yet much farther).

    "So far as I can discern, the Austronesians in Indonesia, and the Austroasiatic population in mainland SE Asia, are the first farming/herding population to arrive in SE Asia".

    As far as I can discern that can't be the case for Austronesians in most of Indonesia: it's a later time frame. Also remember that Papuans seem to have a very old agricultural tradition, though its origins are a mystery.

    "We know where the language groups originated"...

    Do you know where Austroasiatic originated? I think that SE Asia but wouldn't be able to say exactly where.

    "and we no that no earlier than these language family prior languages survive (with the possible exception of Andaman, and of course in addition to New Guinea/Australia)".

    Actually there are some survivals in Maluku and Lesser Sunda islands. They are loosely considered withing the "Papuan" catch-all para-phylum and at least the language of Halmahera directly correlates with languages of New Guinea.

    But what was spoken West of Wallace Line we don't know, excepted Andamanese and Austroasiatic.

    "In Europe the pre-farming expansion wave may have left Sami and Siberian Paleo-Eskimo and Basque, or they may be more recent - but the first wave of farming was a demic expansion".

    No. I have already stated why and you don't bother refuting my evidence or even discussing it. Your attitude is religious, not scientific.

    Maybe there was replacement in Central Europe but that cannot be automatically extrapolated to all Europe and in other places the evidence is contrary.

    ReplyDelete
  26. "In India, there are essentially no cognizable signs of pre-Austroasiatic or Dravidian languages".

    Burushaski and Nahali. We don't know if Dravidian originated or expanded with Neolithic.

    "(or crops outside the Indus Valley civilization)"

    There is Neolithic outside IVC, many different cultures across the subcontinent which are normally paid no attention. Obviously IVC, which is not the first Neolithic but a civilization grown on some of it, is not all the South Asian Neolithic. By no means!

    "strong physical differences between "tribals" and other populations in India"

    Highly skeptic about such "strong differences".

    "In Africa, there is no sign of any pre-Bantu farming or herding in the Khoisan"...

    You have absolutely no idea! The Khoikhoi (Hottentots) were a cattle-herding people long before the arrival of Bantus. Circumstantial genetic evidence may suggest a limited contact with East African herders (Nilotes?) at that episode.

    I'm outraged by your verbose ignorance, really, Andrew!

    "In places with predominantly hunter-gatherer societies (like the Americas"...

    America was initiating the Bronze Age at the time of Columbus (which began if I'm correct in NW Mexico, not too far from where you live). Some peoples remained hunter-gatherer but most were already farmers and many had impressive civilizations (loosely comparable to what we see in Chalcolithic Europe: huge stone monuments, astronomy, long distance trade...)

    America (pre-Columbian America) is in fact a very good example of how farming spreads whithout smashing the pre-existent diversity. The lack of mounts may have limited the conquests somewhat. We did not have that luck here in Eurasia... but in any case these large homogenization processes (Indoeuropeans, Semites) seem to belong to a much later period than mere Neolithic. Even the Bantu expansion, which lacked mounts, belongs to the Iron Age and implied not just tribes but also rather complex polities (kingdoms particularly, not too different of how must have been the Euro-Mediterranean realms of late prehistory and even the nebulous proto-history).

    "... New Guinea"...

    New Guinea is also not hunter-gatherer at all.

    Very few hunter-gatherers reached modernity, some in the peripheries of America maybe (Patagonia, Tierra del Fuego, some parts of North America), some in Africa (Bushmen, Pygmies and Hadza and maybe some other East African tribes), Australian Aborigines and some Negritos (maybe one or two South Asian tribes too) and a scatter of North Asian peoples. That's it. Many still survive, though with difficulty.

    But the tribes of Papua, the Amazon or many others that we usually consider "primitive" are pretty much Neolithic. They do hunt but they also farm.

    The Cherokee or the Iroquois were farmers for example. Just that their agriculture was less intensive and hunting was still important for them.

    "My working hypothesis is essentially that farmers or herders of any kind kill/replace/overwhelm hunter-gatherers in numbers anywhere that they can produce food"...

    Your working hypothesis look pretty feeble, as much as your anthropological and prehistorical (and even historical) knowledge.

    ReplyDelete
  27. Maju said,

    "For example, we can reply to Matt, thanks to it: more than 50% C2 in Sumba, 0 west of Wallace line (excepting to a small degree Bali, that seems somewhat transitional).

    The lineages that seem strikingly restricted to the East of Wallace Line (with some minor presence in Bali) are: C2, M1 and S. Those that are rare East of the line are: O3 and O2a."

    If I had one Euro for every error that Maju has made in his posts, I would be a rich man! (Sorry, I'm just mimicking Maju's style.)

    According to that spreadsheet, only haplogroup C-M216(xC2-M38), and not C2-M38, has been found in Bali (9/493 = 1.8%) and Borneo (14/60 = 23.3%). However, Kayser et al. (2008) have reported finding only 2/40 = 5.0% C-M130 in a sample from southern Borneo, with one of these (1/40 = 2.5%) being C3-M217 and the other being C2-M38(xC2a-M208). The discrepancy between these two studies' samples from Borneo is incredible; besides haplogroup C, their results for haplogroup O1 (6/40 = 15.0% in southern Borneo according to Kayser et al.; 2/60 = 3.3% in Long Soluy and Long Gi, eastern Borneo according to Lansing et al.) and haplogroup O3 (7/40 = 17.5% according to Kayser et al.; 27/60 = 45.0% according to Lansing et al.) are also strikingly different. Based on these data, there appears to be a sharp genetic division between populations of eastern Borneo (probably Dayaks in this case) and populations of southern Borneo in terms of Y-DNA. Would anyone seriously claim that genetic differentiation between Austronesian-speaking populations on the island of Borneo dates back to the Palaeolithic era?

    By the way, the Malagasy of Madagascar, whose language supposedly derives from that spoken by ancient inhabitants of the vicinity of the Barito River in southern Borneo, do not have any C-M130 or O3-M122 Y-DNA according to the results of the study by Hurles et al. (2005). This means that the 17.5% O3-M122 (among other haplogroups) that Kayser et al. have found in southern Borneo has either been lost in the proto-Malagasy population in transit to Madagascar or else it has been introduced into southern Borneo after the departure of the proto-Malagasy. These populations (and the composition of their Y-DNA pools) have not been static.

    ReplyDelete
  28. "probably reflecting early out-of-Africa humans taking the southern route, while this population has been influenced by movements from the north: Caucasoids into India, and Mongoloids or Mongoloid-influenced people into Indonesia.“

    It seems that the typical Mongoloid groups immigrated to ES Asia during neolithic or bronze period. the related papers:

    Morphometric affinity of the late Neolithic human remains from Man Bac, Ninh Binh Province, Vietnam: key skeletons with which to debate the ‘two layer’ hypothesis, 2007

    PREHISTORIC PEOPLE FROM BAN CHIANG, NE THAILANDA PHYSICAL ANTHROPOLOGY PERSPECTIVEON A SOUTHEAST ASIAN AGRARIAN POPULATION

    The ancient inhabitants of Ban Chiang


    I believe that the original groups marked by Haplotype O should be anthropologically similar to the Australoid groups rather than Mongoloid ones.

    ReplyDelete
  29. "Personally I'm not so sure of the impact that such diseases would have (or in fact got) when they were not coupled with exploitation (such as slavery or similar), war and general pressure for the land. It's known that diseases do not just take their toll because of themselves but also because of the condition of the hosts, so an exploited and impoverished people will generally suffer much more from them... and probably will have less chance of recovery too."

    Sorry all, for diverting the discussion from the SE Asia paper.

    Maju, I'm not trying to say that there weren't intentional attempts to obliterate native peoples in North America. However, it is important to remember that smallpox and tuberculosis did play a large part in the decimation of native peoples. Here, I quote from a history on the Haida people, who were not weakened by a lack of food or intentional attempts to exterminate them.

    "Contact with Europeans, beginning in the late 1700s had a devastating impact on the Haida population. Several epidemics of smallpox ravaged the Haida villages. The most severe of these was recorded in 1862.

    "It is estimated that approximately 95 percent of the Haida population was wiped out by disease. A census conducted by the Hudson's Bay Company in 1885 counted only 800 Haida. By 1915, the population had dropped further to 588."

    Here's the website:
    http://www.virtualmuseum.ca/
    Exhibitions/Haida/java/english/c+o/co2a.html

    In this discussion, I'd also add that I believe that genetics must have played a part in the degree to which various native peoples were affected by European diseases. For instance, the Ojibwe seem to have been less affected by smallpox than the Haida.

    Back to the interesting Wallace line discussion . . .

    ReplyDelete
  30. "It seems that the typical Mongoloid groups immigrated to ES Asia during neolithic or bronze period".

    That used to be the accepted scenario, and probably still is. That would mean that most (if not all) Y-hap O in SE Asia is Neolithic.

    "Actually there are some survivals in Maluku and Lesser Sunda islands".

    But I tend to agree that the evidence suggests many islands south of Taiwan were uninhabited at the time of the Austronesian expansion. That's why it was so rapid.

    "Do you know where Austroasiatic originated? I think that SE Asia but wouldn't be able to say exactly where".

    I strongly suspect a little to the north of there. Thais have legends about coming from the north as do (I think) the Kmer. So South China seems the most likely place of origin for Austro-Asiatic.

    "Apparently there are very few Melanesians west of Wallaces Line".

    However the Hoabinhian people seem to have been much the same as Melanesians, so it's quite likely their haplogroups have been drifted out with the arrival of later more advance Neolithic Mongoloid-type people (and their O Y-haps).

    "I believe that the original groups marked by Haplotype O should be anthropologically similar to the Australoid groups rather than Mongoloid ones".

    I agree 'that the original groups ... should be anthropologically similar to the Australoid groups' but the Haplotype O people are Mogoloid.

    ReplyDelete
  31. "If I had one Euro for every error that Maju has made in his posts, I would be a rich man!"

    Meh, you'd have four or five euros. That's about it.

    But keep on it. I do welcome good criticisms.

    "According to that spreadsheet, only haplogroup C-M216(xC2-M38), and not C2-M38, has been found in Bali (9/493 = 1.8%) and Borneo (14/60 = 23.3%)".

    Yap, you're right. I was surely confused by the presence of M and S in Bali, which is real.

    "Based on these data, there appears to be a sharp genetic division between populations of eastern Borneo (probably Dayaks in this case) and populations of southern Borneo in terms of Y-DNA".

    Makes sense.

    "Would anyone seriously claim that genetic differentiation between Austronesian-speaking populations on the island of Borneo dates back to the Palaeolithic era?"

    I don't know. The Dayaks are a very peculiar people.

    Borneo is also a very large island whose main characteristic used to be to be mostly thick jungle, which allows for relatively high isolation of the inhabitants. But we know of no pre-Austronesian peoples, unlike in Peninsular Malaysia or Philippines. Don't you think that some of the most deeply rooted and "savage" peoples like the Dayaks could be at least partly pre-Austronesian?

    Anyhow that is what Karafet claims. As I said before, it makes good sense that Wallace Line would be absolutely no barrier for the Austronesian expansion, hence why that divide? A reasonable explanation is that the genetic divide is pre-Austronesian. Considering that Austroasiatics reached as far as Nicobar, they also must have known how to sail and hence it should also be a pre-Austroasiatic divide.

    How can you explain a sharp sea-caused divide in an Austronesian oceangoing context? I just cannot make any sense... unless the real barriers that demic (not cultural or linguistic) Austronesian expansion faced were the presence of native peoples, whom they absorbed in many cases. These peoples anyhow were probably already farmers in many cases (otherwise how did farming arrive to New Guinea? Was an independent local invention?)

    I'm guessing that Karafet's reasoning must go along these lines. However I don't know the full details.

    She mentions four waves: one must be the "Melanesian" wave, a second one at least should also be Paleolithic "normal" flow from nearby SE Asia, which essentially stopped at Wallace Line.

    "the 17.5% O3-M122 (among other haplogroups) that Kayser et al. have found in southern Borneo has either been lost in the proto-Malagasy population in transit to Madagascar or else it has been introduced into southern Borneo after the departure of the proto-Malagasy".

    A founder effect in such a long distance colonization can perfectly explain it. How many people did found the Malagasy population? Does anyone know?

    Which is the mtDNA pool of those people of Southern Borneo, because the Malagasy look basically B4a1a1a plus African lineages. Some other minor Asian lineages do exist (E1a1a, M7c3, M*, F3b, M46 and M23) but are rarer or non-existent among the Merina, who are the reference Malagasy group. This suggests a very strong founder effect among the Malagassy, with clear sharp reduction of diversity of the Asian lineages (unless someone tells me that their ancestors from Borneo also have such reduced mtDNA diversity, which I find unlikely).

    ReplyDelete
  32. "I was surely confused by the presence of M and S in Bali, which is real".

    Hang on. What are they doing west of Wallace's Line?

    "mostly thick jungle, which allows for relatively high isolation of the inhabitants".

    I'm pleased to note you finally accept that.

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  33. @Yungsiyebu:

    Found and read your reference (link). I notice that the supposedly "Australoid" individual C29 clusters with the Jomon (i.e. Ainu), not directly Australian Aborigines (cf. fig. 5). And it makes me think of how slight admixture has changed the phenotype of Japanese, while they still keep a good deal of the pre-Yayoi genetics, including about 50% Y-DNA D (probably even more in the mtDNA side).

    It's really difficult to judge on craniometry alone, which seems highly plastic. It'd be interesting to know about their DNA instead.

    ReplyDelete
  34. Dear Maju, there're two clusters among human skulls during time of neolithic Jomon culture, one was clustered with mainlanders from Manchuria, another was anthropologically similar to oceanic groups, that suggests a racial mixture between the neolithic migrants from mainland and the native paleolithic inhabitants of Japan, and also may explain that the ainu, descendants of Jomon inhabitants, is categorized to a blend racial type of Mongoloid and Australoid.

    the related papers:

    The Ancestors of the Jomon People Were Not Like Minatogawa I But Like Keilor?

    日本人种论, a Paper in chinese, a comparation between Japan's human skulls and China(Manchuria)'s.

    ReplyDelete
  35. This comment has been removed by the author.

    ReplyDelete
  36. "I agree 'that the original groups ... should be anthropologically similar to the Australoid groups' but the Haplotype O people are Mogoloid."

    It's hard to categorized the original halpogroup O to one of the Mongoloid groups if they originated from one of archaic groups in south China or ES Asia at 30,000-35,000 BP, because there're no typical Mongoloid skulls found there yet.

    ReplyDelete
  37. yungsiyebu,

    Any comments on the next paper regarding genome wide typing of Japanese, Chinese, Koreans and other groups?

    It seems obvious the Koreans form this bridge, but it would be nice to hear your thoughts, especially if you live in or are from that part of the world.

    ReplyDelete
  38. "I agree 'that the original groups ... should be anthropologically similar to the Australoid groups' but the
    "For instance, the Ojibwe seem to have been less affected by smallpox than the Haida".

    Also their overall numbers: you are talking of what seems to be a very small nation. 800 people are much more easily killed than 80,000. The Ojibwa are the largest native nation north of the Mexican border.

    It would be relatively easy to kill all the people of Andorra but quite hard to wipe out the French.

    "However the Hoabinhian people seem to have been much the same as Melanesians".

    Really? Where are they? Where are their genetic remnants? Even that craniometric paper suggests that one of several Man Bac people, maybe 10%, was of that stock, where are their descendants?

    "Haplotype O people are Mogoloid".

    That claim is inconsistent with the evidence pointing to south to north migration, not just of Y-DNA O but of most of the genetic pool of East Asia in general.

    Obviously this flow should be pre-Neolithic and there may have been some Neolithic back-flow from South China since Neolithic times. Maybe O3?

    "Dear Maju, there're two clusters among human skulls during time of neolithic Jomon culture, one was clustered with mainlanders from Manchuria, another was anthropologically similar to oceanic groups, that suggests a racial mixture between the neolithic migrants from mainland and the native paleolithic inhabitants of Japan, and also may explain that the ainu, descendants of Jomon inhabitants, is categorized to a blend racial type of Mongoloid and Australoid".

    Maybe but that's what Bac Man 29 clusters with. Man Bac 29 was also "a blend of Mongoloid and Australoid". I can't say because craniometry is not my strong point.

    ReplyDelete
  39. Sorry about the messy syntaxis of the previous post.

    Logically, the first quote should be along the third one in the single sentence that originally was. Like this:

    "I agree 'that the original groups ... should be anthropologically similar to the Australoid groups' but the haplotype O people are Mogoloid".

    Also I mispelled Man Bac as Bac Man once. Hope it's not any insult in Vietnamese... :P

    And this sentence was meant as a question:

    "Man Bac 29 was also "a blend of Mongoloid and Australoid"?"

    ... but forgot the question mark.

    ReplyDelete
  40. "For instance, the Ojibwe seem to have been less affected by smallpox than the Haida".

    Well, I'm talking percentages.

    95% of the Haida were wiped out by smallpox. Nothing else. If you check their original population, it is estimated to have been 30,000.

    And here, another devastating smallpox epidemic, this time on the East Coast amongst the Huron nation:

    http://www3.sympatico.ca/goweezer/
    canada/z16huron1.htm

    Quoting from Bray, R. S.. Armies of Pestilence-The Impact of Disease on History. Barnes & Nobel Inc., New York, 1994.

    "Smallpox and the Plains Indians:"

    "A smallpox outbreak in 1780-82 followed the distribution and trade route of the Indian horse (Haines). The outbreak in 1800-02 spreads from the Plains Indians to the Indians along the Pacific coast. Despite heavy losses during these periods, the most devastating outbreak of smallpox was yet to come.

    "In 1832, the first steamboat, a small side-wheeler named, Yellow Stone, reached Fort Union at the mouth of the Yellowstone River. The use of steamboats on the Missouri allowed large quantities of trade goods to move up and down the river. The buffalo hide trade now become more important than the trade in furs. Remote Indian villages brought their buffalo hides to the American Fur Company posts. This set the stage for ensuing disaster.

    "In June of 1837, the St. Peter arrived at Fort Clark, sixty miles north of present day Bismarck, North Dakota. Knowing there were men aboard the boat with smallpox, F. A. Chardon and others of the American Fur Company tried to keep the Mandans away from the boat, but to no avail. The two Mandan villages that had provided aid to Lewis and Clark during the winter of 1804-05 were devastated. Thirty-one Mandans out of a population of sixteen hundred survived the epidemic...these figures vary, but needless to say it was devastating to the Mandans.

    "The 1837 smallpox outbreaks were initially confined to the Indian tribes that lived by, or had come to trade at, the upper Missouri River trading posts. The Mandan, Blackfeet, and the Assiniboine nations suffered the highest number of deaths. The 1837-40 smallpox outbreaks were said to have a ninety-eight percent death rate among those infected."

    I'd also point out that native peoples that had collaborative trading relationships with the companies such as the Hudson's Bay Company and the Northwest Trading Company were devastated in great number. I don't see why these companies would have gone out of their way to kill their employees and their bottom line.

    Sure, plains Natives groups got into a fight with farmers over land. But I don't think that genocide accounts for the great losses.

    ReplyDelete
  41. What I mean, Marnie, is that two main factors, additionally of the novelty of the epidemics seem to have caused such disasters,: one you do mention passing by is the huge mobility provided by technology (steam boat) and in general the conditions of the industrial age but another is the size (and geographical concentration) of the affected populations.

    I knew of the Mandan disaster by the diary of George Catlin (a very interesting read), who lived among them. The Mandans had only one village, so a local calamity was a national disaster. That could neve happened to their Lakota neighbours, a much larger nation.

    Also Catlin says that he believes it was a careless temerity on the side of the steamer to trade with the village knowing they had smallpox in the ship.

    This reminds me that direct exposure to trade routes may help disease expansion, while relative isolation surely prevents it (another factor).

    The other day, discussing Basque fishing in East Canada, someone mentioned that no tribe is known to have been stroke by epidemics because of such seasonal arrivals. I'm not sure why, except that Basques and Bretons were there just to fish, not to colonize or trade. Though occasional trade happened too, I think, there was no exploitation as in the Caribbean, nor intensive trade as in the fur routes. The French traded with lots of natives through all North America and I'm not aware of any (and certainly not many) demographic disasters because of such trade.

    There must be other factors added to mere contact. I think that these can be synthesized as: exploitation, size of the potential victim (no major nation was ever destroyed by any epidemic), intensity of foreign exposure and guess that luck also may play a role.

    As said no major nation was ever wiped by any epidemic. These were destroyed and dumped into reservations by military means essentially.

    ReplyDelete
  42. I suppose that the bearers of the Hoabinhian technocomplex may have belonged to some subclade of K-M9 that is now rare in continental Southeast Asia.

    Bing Su, Li Jin, Peter Underhill et al., "Polynesian origins: Insights from the Y chromosome," PNAS, vol. 97, no. 15, 8225-8228 (July 18, 2000):

    Orang Asli
    4/17 = 23.5% H5 (=K-M9(xM1-M5, O1a-M119, O2a-M95, O3-M122, P-M45))
    1/17 = 5.9% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    1/17 = 5.9% H7 (=O3a3b-M7)
    11/17 = 64.7% H11(=O2a-M95(xO2a1-M88/M111))

    Tatiana M. Karafet, J. S. Lansing, Alan J. Redd et al., "Balinese Y-Chromosome Perspective on the Peopling of Indonesia: Genetic Contributions from Pre-Neolithic Hunter-Gatherers, Austronesian Farmers, and Indian Traders," Human Biology, v. 77, no. 1, pp. 93-114 (Feb. 2005):

    West Indonesians
    1/21 = 4.8% C-RPS4Y711
    1/21 = 4.8% F-P14(xG-M201, H-M69, I-P19, J-p12f2, K-M9)
    1/21 = 4.8% K-M9(xL-M20, M1-M5, N1-LLY22g, O1a-M119, O2-P31, O3-M122, P-P27, S-M230)
    3/21 = 14.3% O3-M122(xM134, LINE)
    2/21 = 9.5% O3a3c-M134
    4/21 = 19.0% O3-LINE
    4/21 = 19.0% O1a-M119
    3/21 = 14.3% O2a-M95
    1/21 = 4.8% R-M207(xR1-M173)
    1/21 = 4.8% R1-M173

    Taiwanese aboriginals
    1/48 = 2.1% C-RPS4Y711
    3/48 = 6.3% O3-M122(xM134, LINE)
    43/48 = 89.6% O1a-M119
    1/48 = 2.1% O2a-M95

    Philippinos[sic]
    1/48 = 2.1% C-RPS4Y711
    23/48 = 47.9% K-M9(xL-M20, M1-M5, N1-LLY22g, O1a-M119, O2-P31, O3-M122, P-P27, S-M230)
    12/48 = 25.0% O3-M122(xM134, LINE)
    2/48 = 4.2% O3a3c-M134
    3/48 = 6.3% O3-LINE
    5/48 = 10.4% O1a-M119
    2/48 = 4.2% O2a-M95

    Vietnamese
    3/70 = 4.3% C-RPS4Y711
    2/70 = 2.9% DE-YAP
    2/70 = 2.9% J-p12f2
    2/70 = 2.9% N1-LLY22g
    7/70 = 10.0% O3-M122(xM134, LINE)
    11/70 = 15.7% O3a3c-M134
    10/70 = 14.3% O3-LINE
    4/70 = 5.7% O1a-M119
    4/70 = 5.7% O2-P31(xO2a-M95)
    19/70 = 27.1% O2a-M95
    5/70 = 7.1% Q1-P36
    1/70 = 1.4% R1-M173

    Malaysians
    1/32 = 3.1% C-RPS4Y711
    1/32 = 3.1% DE-YAP
    2/32 = 6.3% G-M201
    2/32 = 6.3% K-M9(xL-M20, M1-M5, N1-LLY22g, O1a-M119, O2-P31, O3-M122, P-P27, S-M230)
    1/32 = 3.1% M1-M5(xM1a-P34)
    5/32 = 15.6% O3-M122(xM134, LINE)
    3/32 = 9.4% O3a3c-M134
    3/32 = 9.4% O3-LINE
    2/32 = 6.3% O1a-M119
    11/32 = 34.4% O2a-M95
    1/32 = 3.1% R1-M173

    I'd like to see the haplogroup C-M216(xC2-M38) individuals that Lansing et al. have found in their samples from eastern Borneo (14/60 = 23.3%), Flores (54/284 = 19.0%), Bali (9/493 = 1.8%), and Sumba (1/350 = 0.3%) typed for all known subclades of haplogroup C. Also note the finding of F-P14(xH-M69, J-12f2, K-M9) in eastern Borneo (2/60 = 3.3%) and Flores (6/284 = 2.1%); it would be nice to have these typed for markers of haplogroup G and haplogroup I.

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  43. "Sure, plains Natives groups got into a fight with farmers over land. But I don't think that genocide accounts for the great losses".

    It's not just plains natives. Think of the Cherokee: a proud thriving nation who were in full process of assimilation into Euro-American society, even to the point of having many black slaves, as was usual in that part of the States. They were, together with many other nations, deported to Oklahoma by state decree. That's genocide and certainly helped to make their numbers dwindle. Not in vain the whole tragic episode is called the Trail of Tears.

    ReplyDelete
  44. Maju, it's always a pleasure to talk with you. I didn't say that there weren't any cases of "rounding up the indians" so the "settlers" could get their land. To the "Trail of Tears" you can add the Louis Riel Rebellion, the California Goldrush, and the evil deads of some of the Puritans.

    However, it is an extremely complex picture. To even get to the start of it, you'd have to do an analysis state by state, province by province.


    I do know that even in areas where Europeans tried to negotiate and collaborate with native peoples with the best of intentions, smallpox was still completely devastating.

    (And by the way, there are many cases of smallpox being passed from French traders to native peoples. Check out the movie Black Robe directed by Denys Arcand.)

    Always fun and engaging to talk with you, Maju.

    Ebizur, thanks for the wonderful data.

    Don't know about you guys, but it's time for me to get some shut-eye!

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  45. Very informative data, as always, Ebizur.

    I gather that, if Taiwan Aborigines are the mold of "the pure Austronesian blood", then it's almost all about O1a, at least by male side. Filipinos then have like 11% of that blood, West Indonesians 21% and Malays not more than 7%.

    Instead O2a (and sure, all that mysterious K*) looks pre-Austronesian. Malays are then like 51% "Orang Asli" (where O2a is dominant), Vietnamese like 40%, West Indonesians like 21% and Filipinos barely a 6%. However is this O2a pre-Austroasiatic or rather Austroasiatic. I don't know who are those reference Orang Asli that seem so crucially informative: Senoi, Negritos or both?

    I guess that the almost 50% K* of Philippines represents also a pre-Austronesian substrate, though maybe different from that of the other groups. They look very much "Malay" to me in phenotype anyhow (another reason to distrust phenotype studies surely).

    I'm anyhow trying to figure out what O3 may mean. Could it be an "Austroasiatic" signature preceding the Austronesian colonization of Sundaland?

    "I suppose that the bearers of the Hoabinhian technocomplex may have belonged to some subclade of K-M9 that is now rare in continental Southeast Asia".

    I don't gather that because Hoabinhian reaches only (at late dates) to the Malay Peninsula (maybe with an offshoot into North Borneo but that's all). So if anything I'd say it could be associated to O2a, with K* being pre-Hoabinhian surely (cf. Philippines).

    "Also note the finding of F-P14(xH-M69, J-12f2, K-M9) in eastern Borneo (2/60 = 3.3%) and Flores (6/284 = 2.1%); it would be nice to have these typed for markers of haplogroup G and haplogroup I".

    I guess you can discard them. Must be F-other, a remnant of the early Eurasian colonization.

    ReplyDelete
  46. I (partly) back from what I just said about the Borneo F*. With one R1a1a around, it might hypothetically be I or G. However the lack of R1b basically excludes a meaningful impact from West Europeans (Dutch, Portuguese, whatever) and suggests that the R1a1a, also spotted in Java and Bali has probably Indian origins. It'd be interesting to test also for the minor known F lineages, most of which are Indian but (following Terry here) F2 seems to be East Asian. They are in any case Asian lineages more likely to find than G or I.

    ReplyDelete
  47. Please compare the data reported in the aforementioned article by Karafet et al. (2005) with the data derived from the same samples and reported in the supplementary material of Hammer et al. (2006):

    Vietnam (Hammer et al. 2006)
    3/70 = 4.3% C3-M217(xC3c-M86)
    2/70 = 2.9% D1-M15
    2/70 = 2.9% J-12f2
    2/70 = 2.9% N1-LLY22g(xN1a-M128, N1b-P43, N1c1-M178)
    7/70 = 10.0% O3-M122(xM134, LINE)
    11/70 = 15.7% O3a3c-M134
    10/70 = 14.3% O3-LINE
    4/70 = 5.7% O1a-M119(xO1a2-M110)
    1/70 = 1.4% O2*-P31(xO2a-M95, O2b-SRY465/P49)
    1/70 = 1.4% O2b-SRY465/P49(xO2b1-47z)
    2/70 = 2.9% O2b1-47z
    5/70 = 7.1% O2a-M95(xO2a1-M111)
    14/70 = 20.0% O2a1-M111
    5/70 = 7.1% Q1-P36
    1/70 = 1.4% R-M207

    Malay (Hammer et al. 2006)
    1/32 = 3.1% C-RPS4Y711(xC1-M8, C2-M38, C3-M217)
    1/32 = 3.1% D1-M15
    2/32 = 6.3% G-M201
    2/32 = 6.3% K-M9(xL-M20, M1-M5, NO-M214, P-P27, S-M230)
    1/32 = 3.1% M1-M5
    1/32 = 3.1% NO-M214(xN1-LLY22g, O-M175)
    4/32 = 12.5% O3-M122(xM134, LINE)
    3/32 = 9.4% O3a3c-M134
    3/32 = 9.4% O3-LINE
    2/32 = 6.3% O1a-M119(xO1a2-M110)
    10/32 = 31.3% O2a-M95(xO2a1-M111)
    1/32 = 3.1% O2a1-M111
    1/32 = 3.1% R-M207

    Karafet et al. (2005)
    Malaysians
    1/32 = 3.1% C-RPS4Y711
    1/32 = 3.1% DE-YAP
    2/32 = 6.3% G-M201
    2/32 = 6.3% K-M9(xL-M20, M1-M5, N1-LLY22g, O1a-M119, O2-P31, O3-M122, P-P27, S-M230)
    1/32 = 3.1% M1-M5(xM1a-P34)
    5/32 = 15.6% O3-M122(xM134, LINE)
    3/32 = 9.4% O3a3c-M134
    3/32 = 9.4% O3-LINE
    2/32 = 6.3% O1a-M119
    11/32 = 34.4% O2a-M95
    1/32 = 3.1% R1-M173

    Karafet et al. (2001)
    Malaysian (Austronesian)
    1/32 = 3.1% H12 (=D1-M15)
    1/32 = 3.1% H16 (=C-RPS4Y711(xC1-M8/DYS263, C2a1-P33/DYS194, C3-M217))
    1/32 = 3.1% H20 (=F-P14(xI-P19/DYS190, G2a-P15/DYS221, J-p12f2, K-M9))
    1/32 = 3.1% H22 (=G2a-P15/DYS221)
    2/32 = 6.3% H25 (=K*-M9)
    4/32 = 12.5% H29 (=O3-M122(xLINE1, M134))
    3/32 = 9.4% H30 (=O3a3c-M134)
    3/32 = 9.4% H31 (=O3-M122+LINE1)
    3/32 = 9.4% H32 (=O1a-M119)
    11/32 = 34.4% H34 (=O2a-M95)
    1/32 = 3.1% H37 (=M1-M5)
    1/32 = 3.1% H45 (=R1a1-SRY10831.2)
    [Note that the Malay individual who has been categorized as NO-M214(xN1-LLY22g, O-M175) in the supplementary material of Hammer et al. 2006 has been categorized as O3-M122(xM134, LINE) in the article by Karafet et al. 2005 and as O1a-M119 in the article by Karafet et al. 2001.]

    Philippines (Hammer et al. 2006)
    1/48 = 2.1% C3-M217(xC3c-M86)
    22/48 = 45.8% K-M9(xL-M20, M1-M5, NO-M214, P-P27, S-M230)
    1/48 = 2.1% S-M230 [Note another discrepancy here; Karafet et al. 2005 have reported 0/48 S-M230 in this same Filipino sample.]
    11/48 = 22.9% O3-M122(xM134, LINE) [vs. 12/48 = 25.0% according to Karafet et al. 2005]
    2/48 = 4.2% O3a3c-M134
    3/48 = 6.3% O3-LINE
    1/48 = 2.1% O1a-M119(xO1a2-M110)
    4/48 = 8.3% O1a2-M110
    1/48 = 2.1% O2a-M95(xO2a1-M111)
    1/48 = 2.1% O2a1-M111
    1/48 = 2.1% R-M207 [vs. 0/48 P-P27 according to Karafet et al. 2005]

    Taiwan aborigines
    1/48 = 2.1% C3-M217(xC3c-M86)
    3/48 = 6.3% O3-M122(xM134, LINE)
    34/48 = 70.8% O1a-M119(xO1a2-M110)
    9/48 = 18.8% O1a2-M110
    1/48 = 2.1% O2a1-M111

    Indonesia, West
    1/25 = 4.0% C-RPS4Y711(xC1-M8, C2-M38, C3-M217)
    1/25 = 4.0% F-P14(xG-M201, H-M69, I-P19, J-12f2, K-M9)
    1/25 = 4.0% K-M9(xL-M20, M1-M5, NO-M214, P-P27, S-M230)
    3/25 = 12.0% O3-M122(xM134, LINE)
    2/25 = 8.0% O3a3c-M134
    4/25 = 16.0% O3-LINE
    4/25 = 16.0% O1a-M119(xO1a2-M110)
    1/25 = 4.0% O1a2-M110
    2/25 = 8.0% O2b-SRY465/P49(xO2b1-47z)
    2/25 = 8.0% O2b1-47z
    3/25 = 12.0% O2a-M95(xO2a1-M111)
    1/25 = 4.0% R-M207 [Changes from Karafet et al. 2005: O1a-M119 total has increased by one, R-M207 total has decreased by one, four O2b individuals have been added/revealed]

    ReplyDelete
  48. Maju said,

    "I guess you can discard them. Must be F-other, a remnant of the early Eurasian colonization."

    The Karafet team's sample of Malaysians seems to include 1/32 G2a-P15 and 1/32 G-M201(xG2a-P15). According to Karafet et al. 2001, their Vietnamese sample includes 1/70 J2-M172 and 1/70 J-12f2(xJ2-M172). They have found F-P14(xG-M201, H-M69, I-P19, J-12f2, K-M9) only in their samples of southern Indians (40/405 = 9.9% according to Karafet et al. 2005 and Hammer et al. 2006), Sri Lankans (9/91 = 9.9% according to Karafet et al. 2005 and Hammer et al. 2006), Yi people from Sichuan (2/43 = 4.7% according to Hammer et al. 2006 and, with lower resolution, Karafet et al. 2001), western Indonesians (1/25 = 4.0% according to Hammer et al. 2006; 1/21 = 4.8% according to Karafet et al. 2005), and Syrians (1/87 = 1.1% according to Karafet et al. 2005). It is possible that the F-P14(xH-M69, J-12f2, K-M9) individuals from Flores and eastern Borneo might belong to F*(xG, H, I, J, K) since an individual from western Indonesia has been assigned to this paragroup previously, but the data from Malaysia suggest that G2a-P15 and G-M201(xG2a-P15) are also likely to be found in this region. (Remember that Malaysia and Brunei share the northern third of the island of Borneo/Kalimantan, and Lansing et al. have sampled two villages in East Kalimantan Province of Indonesia that are not particularly far from the border with Malaysia.)

    ReplyDelete
  49. "That claim is inconsistent with the evidence pointing to south to north migration, not just of Y-DNA O but of most of the genetic pool of East Asia in general.

    Obviously this flow should be pre-Neolithic and there may have been some Neolithic back-flow from South China since Neolithic times. Maybe O3? "

    I agree with Maju, the neolithic inhabitants from the south of Yangtze river were anthropologically similar to the present Malay Mongoloid groups while the native EA asian during the same period were australiod-looking groups that suggests a back-flow from south China, there're the mixed types from the sites mentioned above, that probably because it's hard to find the 100% pure native inhabitant's remains before the first back-flow migration.

    ReplyDelete
  50. Dear marnie, I'm from east Inner Mongolia where the neolithic Hongshan inhabitants were anthropologically similar to the inhabitants of Manchuria(Xinkailiu culture), Russia far east's Boisman culture and Japan's Jomon culture(not including the australoid-looking paloelithic natives), so I collected the related anthropology knowledge before I know any DNA markers. but it's really regretful that we get nothing about the anthrological traits of any Korean inhabitants during the neolithic period, so I can't judge it's a migration from Korea or Sakhalin to Japan during the neolithic period, may DNA could answer some day.

    ReplyDelete
  51. "I gather that, if Taiwan Aborigines are the mold of "the pure Austronesian blood", then it's almost all about O1a, at least by male side. Filipinos then have like 11% of that blood, West Indonesians 21% and Malays not more than 7%. "

    what happened in Taiwan seems similar to ES asia during neolithic and bronze period, the native neolithic groups before ancestors of the present Taiwanese's native people, were anthropologically similar to the present Polynesian-Micronesian groups.

    the related paper:
    Taiwan Aboriginals and Peoples of the Pacific-Asia Region: Multivariate Craniometric Comparisons

    and it's very interesting that the Dawenkou neolithic inhabitants of lower yellow river of North China, were also anthropologically similar to the present Polynesian groups, according to Zhenbiao Zhang. and there's a relatively high frequence of mtdna Halpotype B from aDNA of Linzi, upper yellow river, that may give us a genetic link between ancient Linzi and the present Polynesians.

    ReplyDelete
  52. Bing Su, Li Jin, Peter Underhill, Jeremy Martinson, Nilmani Saha, Stephen T. McGarvey, Mark D. Shriver, Jiayou Chu, Peter Oefner, Ranajit Chakraborty, and Ranjan Deka, "Polynesian origins: Insights from the Y chromosome," PNAS, vol. 97, no. 15, 8225–8228 (July 18, 2000):

    Extreme Southeast Asia

    Javanese (Java, Indonesia)
    1/11 = 9.1% H1 (=Y*(xDE-DYS287, F-M89))
    1/11 = 9.1% H4 (=F-M89(xK-M9))
    3/11 = 27.3% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    1/11 = 9.1% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    2/11 = 18.2% H9 (=O1a-M119(xO1a2-M50/M110/M103))
    1/11 = 9.1% H10 (=O1a2-M50/M110/M103)
    2/11 = 18.2% H11 (=O2a-M95(xO2a1-M88/M111))

    Orang Asli
    4/17 = 23.5% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    1/17 = 5.9% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    1/17 = 5.9% H7 (=O3a3b-M7)
    11/17 = 64.7% H11(=O2a-M95(xO2a1-M88/M111))

    Malay
    1/27 = 3.7% H4 (=F-M89(xK-M9))
    5/27 = 18.5% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    9/27 = 33.3% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    6/27 = 22.2% H8 (=O3a3c-M134)
    1/27 = 3.7% H9 (=O1a-M119(xO1a2-M50/M110/M103))
    4/27 = 14.8% H10 (=O1a2-M50/M110/M103)
    1/27 = 3.7% H11 (=O2a-M95(xO2a1-M88/M111))

    Cambodian
    1/26 = 3.8% H1 (=Y*(xDYS287, M89))
    1/26 = 3.8% H3 (=D1-M15)
    3/26 = 11.5% H4 (=F-M89(xK-M9))
    3/26 = 11.5% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    1/26 = 3.8% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    4/26 = 15.4% H8 (=O3a3c-M134)
    1/26 = 3.8% H9 (=O1a-M119(xO1a2-M50/M110/M103))
    1/26 = 3.8% H10 (=O1a2-M50/M110/M103)
    6/26 = 23.1% H11 (=O2a-M95(xO2a1-M88/M111))
    3/26 = 11.5% H12 (=O2a1-M88/M111)
    1/26 = 3.8% H14 (=P-M45(xQ1a1-M120, Q1a3a-M3, R1a1a-M17))
    1/26 = 3.8% H16 (=R1a1a-M17)

    Batak (Sumatra, Indonesia)
    1/18 = 5.6% H1 (=Y*(xDE-DYS287, F-M89))
    1/18 = 5.6% H4 (=F-M89(xK-M9))
    2/18 = 11.1% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    2/18 = 11.1% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    3/18 = 16.7% H7 (=O3a3b-M7)
    4/18 = 22.2% H9 (=O1a-M119(xO1a2-M50/M110/M103))
    5/18 = 27.8% H11 (=O2a-M95(xO2a1-M88/M111))

    Kota Kinabalu (Sabah, northeastern Borneo, Malaysia)
    2/19 = 10.5% H1 (=Y*(xDE-DYS287, F-M89))
    1/19 = 5.3% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    2/19 = 10.5% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    6/19 = 31.6% H9 (=O1a-M119(xO1a2-M50/M110/M103))
    2/19 = 10.5% H10 (=O1a2-M50/M110/M103)
    5/19 = 26.3% H11 (=O2a-M95(xO2a1-M88/M111))
    1/19 = 5.3% H14 (=P-M45(xQ1a1-M120, Q1a3a-M3, R1a1a-M17))


    Melanesia

    Banks & Torres (northernmost Vanuatu)
    2/6 H1 (=Y*(xDE-DYS287, F-M89))
    2/6 H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    1/6 H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    1/6 H17 (=M1-M5)

    Maewo (northeastern Vanuatu)
    6/10 H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    2/10 H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    2/10 H17 (=M1-M5)

    Santo (i.e. Espiritu Santo, the largest island of Vanuatu, located in the northwestern part of the archipelago)
    4/4 H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))

    Vanuatu total
    2/20 = 10% H1 (=Y*(xDE-DYS287, F-M89))
    12/20 = 60% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    3/20 = 15% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    3/20 = 15% H17 (=M1-M5)

    Nasioi (non-Austronesian, southern Bougainville)
    3/3 H17 (=M1-M5)

    New Guinea
    14/90 = 15.6% H1 (=Y*(xDE-DYS287, F-M89))
    2/90 = 2.2% H4 (=F-M89(xK-M9))
    39/90 = 43.3% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    35/90 = 38.9% H17 (=M1-M5)


    Micronesia

    Truk
    1/17 = 5.9% H1 (=Y*(xDE-DYS287, F-M89))
    11/17 = 64.7% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    1/17 = 5.9% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    1/17 = 5.9% H8 (=O3a3c-M134)
    1/17 = 5.9% H14 (=P-M45(xQ1a1-M120, Q1a3a-M3, R1a1a-M17))
    2/17 = 11.8% H17 (=M1-M5)

    Majuro
    1/9 = 11.1% H4 (=F-M89(xK-M9))
    6/9 = 66.7% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    2/9 = 22.2% H10 (=O1a2-M50/M103/M110)

    ReplyDelete
  53. Kiribati
    7/11 = 63.6% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    1/11 = 9.1% H8 (=O3a3c-M134)
    3/11 = 27.3% H12 (=O2a1-M88/M111)

    Guam
    1/6 = 16.7% H1 (=Y*(xDE-DYS287, F-M89))
    1/6 = 16.7% H2 (=DE-DYS287(xD1-M15))
    2/6 = 33.3% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    2/6 = 33.3% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))

    Palau
    1/13 = 7.7% H1 (=Y*(xDE-DYS287, F-M89))
    1/13 = 7.7% H4 (=F-M89(xK-M9))
    8/13 = 61.5% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    3/13 = 23.1% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))

    Phonpei
    3/10 = 30.0% H1 (=Y*(xDE-DYS287, F-M89))
    7/10 = 70.0% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))

    Nauru
    2/7 = 28.6% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    5/7 = 71.4% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))

    Micronesia total
    6/73 = 8.2% H1 (=Y*(xDE-DYS287, F-M89))
    1/73 = 1.4% H2 (=DE-DYS287(xD1-M15)) [only one case from Guam, so probably due to recent Japanese or European admixture]
    2/73 = 2.7% H4 (=F-M89(xK-M9))
    36/73 = 49.3% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    18/73 = 24.7% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    2/73 = 2.7% H8 (=O3a3c-M134)
    2/73 = 2.7% H10 (=O1a2-M50/M103/M110) [only Majuro]
    3/73 = 4.1% H12 (=O2a1-M88/M111) [only Kiribati]
    1/73 = 1.4% H14 (=P-M45(xQ1a1-M120, Q1a3a-M3, R1a1a-M17))
    2/73 = 2.7% H17 (=M1-M5) [only in Truk]

    Micronesia (Karafet et al. 2005, Hammer et al. 2006)
    1/17 = 5.9% C-RPS4Y(xC1-M8, C2-M38, C3-M217)
    1/17 = 5.9% C2-M38(xC2a1-P33)
    1/17 = 5.9% D2a-M116(xD2a1-M125) [Excluded from the data table of Karafet et al. 2005 because of presumed Japanese admixture?]
    6/17 = 35.3% K-M9(xL-M20, M1-M5, NO-M214, P-P27, S-M230)
    1/17 = 5.9% M1-M5(xM1a-P34)
    3/17 = 17.6% O3-M122(xLINE1, M134)
    2/17 = 11.8% O1a-M119(xO1a2-M110)
    1/17 = 5.9% O2b-SRY465/P49(xO2b1-47z)
    1/17 = 5.9% P-P27(xQ1-P36, R-M207) [I have heard that this P* result is erroneous.]

    It seems that K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5) is about equally common in Micronesia as it is in Melanesia. According to this team's data, K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5) is also quite common in southern parts of Southeast Asia (Cambodia, Malaysia, Indonesia), though I suppose some of these should turn out to be N1, O2b, O2*, or (as in Bali) L. In any case, the overwhelming predominance of C2a1-P33 that is characteristic of populations of the "Polynesian triangle," which perhaps has stemmed from Samoa, evidently does not extend westward to the Micronesian realm, though haplogroup C Y-DNA is found with at least moderate frequency in Micronesia. However, haplogroup C Y-DNA is almost completely absent from the Solomon Islands Archipelago of Melanesia, with only one individual out of about 120 from the Solomon Islands Archipelago (including Bougainville) that I have encountered in the literature belonging to haplogroup C. I'd like to see some data from other parts of Island Melanesia, such as New Caledonia and the Loyalty Islands, but I suppose that testing of these Melanesians would probably be hindered by their meddlesome French government.

    ReplyDelete
  54. Dear yungsiyebu,

    Thanks so much for your insightful commments. It's wonderful that you are blogging here, with your special insight on Mongolia, an area the seems to be a key point between East and West and also Asia and indigenous North America.

    "it's really regretful that we get nothing about the anthrological traits of any Korean inhabitants during the neolithic period, so I can't judge it's a migration from Korea or Sakhalin to Japan during the neolithic period, may DNA could answer some day."

    Yes, it would be great if we could know more about Koreans during they neolithic (and how and when the link with Japan was formed.)

    I have a single observation about Koreans that maybe you could fill me in on. Also, does this custom extend into other parts of Asia. It is this:

    Koreans grow wheat (or barley) during the winter. They make a special tea from it. They are the only Asia culture I know of that grows wheat. With the Japanese, Vietnamese and Chinese, it seems to be all rice. I am not sure about Mongolia. I'm wondering when and where wheat/barley growing was introduced into Korea.

    It's a pleasure talking with you, yungsiyebu.

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  55. "They are the only Asia culture I know of that grows wheat. With the Japanese, Vietnamese and Chinese, it seems to be all rice".

    Northern Chinese traditionally grow wheat and millet. Since the very beginning of Neolithic they grew millet (guess wheat arrived later). This is an ecological divide because the South has been traditionally cultivating rice as you say. It's probably all due to climate.

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  56. Hoping not to get lost into the labyrinth of data that Ebizur seems to manage so easily...

    "It seems that K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5) is about equally common in Micronesia as it is in Melanesia".

    We can't be sure if it's one or several stocks of K*, however it makes sense if Micronesia was colonized after assimilating Philippines and Polynesia after contacting (and partly assimilating too) Melanesia and Wallacea (C2a).

    Your K* data is interesting but we can't be sure of how to read it because we lack phylogenetic resolution. In general it seems that the highest levels of K*, excluding the islands only colonized within Polynesian expansion, are related to Philippines, New Guinea and (to a lesser extent) to what may be (??) part of the the deeper layers of Sundaland's population (Java, Orang Asli).

    "... but I suppose that testing of these Melanesians would probably be hindered by their meddlesome French government".

    What's the policy of France re. DNA testing? I always complain of the lack of French samples (in the context of Europe) but I know of no such restrictive DNA laws as is the case with India (another critical and yet country often skipped). After all France is a EU member and is bound by EU laws.

    "Changes from Karafet et al. 2005: O1a-M119 total has increased by one, R-M207 total has decreased by one, four O2b individuals have been added/revealed".

    Interesting. Do you think it correlates with a "Neolithic" Austroasiatic flow? It's also apparent in Vietnam as O(xO2a).

    "The Karafet team's sample of Malaysians seems to include 1/32 G2a-P15 and 1/32 G-M201(xG2a-P15)".

    Ok. I take notice of that.


    ...

    @Yungsiyebu:

    "what happened in Taiwan seems similar to ES asia during neolithic and bronze period, the native neolithic groups before ancestors of the present Taiwanese's native people, were anthropologically similar to the present Polynesian-Micronesian groups".

    So you think the Taiwanese aborigines, that so similar look to Malays (and sometimes also remind to me, along with Malays, of some Native American peoples) used to be "less Mongoloid" at the origins of the Austronesian expansion. Maybe but I can't make too much sense of it, specially as the influence of Filipino and Melanesian lineages seem so clear in Micronesia and Polynesia respectively.

    In any case, linguistically at least, the main Austronesian language branch, Malayo-Polinesian, seems most closely related to the language of the southern tip of Taiwan (Paiwan language), rather then to other aboriginal groups. I don't know if this can imply some sort of founder effect from that specific area at the very origins of Austronesian expansion.

    "and it's very interesting that the Dawenkou neolithic inhabitants of lower yellow river of North China, were also anthropologically similar to the present Polynesian groups, according to Zhenbiao Zhang. and there's a relatively high frequence of mtdna Halpotype B from aDNA of Linzi, upper yellow river, that may give us a genetic link between ancient Linzi and the present Polynesians".

    Yes, it's interesting indeed. Thanks.

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  57. Erratum: "It's also apparent in Vietnam as O(xO2a)" should read "...as O2(xO2a)", which is probably O2b. Another parallel between Vietnam and West Indonesia, in particular Java.

    ReplyDelete
  58. I hate this comment format that prevents editing.

    Forget about "Another parallel between Vietnam and West Indonesia, in particular Java". One individual alone can't say too much (and it's not even specifically Java - meh!)

    ReplyDelete
  59. Maju - re the French authorities' attitude to DNA testing

    Conspiracy theorists would say that they are "institutionally hostile" to the whole idea because they fear the results would undermine "la unite/ de la France".

    They fear that people in Alsace-Lorraine (and maybe Burgundy) would "look" German, Corsicans and Savoyards Italian, Provenc,als Catalan, Bretons British.

    It sounds like paranoia but the French state does certainly an institutional memory of a time not so long ago (late C19) when 30%(?) of French citizens did not have French as their first language. Not just Basques and Bretons but large areas of eastern and southern France.

    They made a concerted effort over many decades to make France a monolingual nation state and they succeeded (with apologies to you as a Euskaldun).

    They have an instinctive reaction against anything which might reopen old identities and lead to Italian- or Spanish-style regionalist/separatist tendencies.

    ReplyDelete
  60. Thanks, Matt. I understand that very well but my question is about what does the law say. Because I'm quite sure that researchers would not be hindered by mere "attitudes", there may be a law that restricts DNA testing somehow and I wonder if it really exists and what does it say.

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  61. I've been searching a bit and found this EU reference site. However I see no legal or otherwise peculiar situation of France-

    There are two possibilities: one that French law, like Indian one, forbids export of genetic material (in order to prevent genetic theft), what would be considered a liability by foreign researchers but not any unsurmontable obstacle (just set up a local lab or make a joint venture with a local university) and, two, that researchers just don't think France is an interesting object of genetic research, maybe because they make fetish of other groups like Basques (well researched at both sides of the border) or Northern Europeans (arguably more relevant for US-centric perceptions of Europeanness) or because of its diversity they prefer to work at its periphery in order to get neatly cut population categories.

    I'm inclined to think that it's researchers who actually disdain France, rather than France which puts obstacles to research. But unsure.

    ReplyDelete
  62. The recent study of R1b1b2's diversity included hundreds of samples from different parts of France (Balaresque, 2009).

    And there's another recent study that I really want to get:

    Phylogeography of French male lineages

    555 y-dna samples from France. Tested for 27 SNPs, including 5 R1b1b2 subhaplogroups. Also tested for STRs. 7 different regions of French geography, specifically: Nord-Pas-de-Calais (Lille), Bretagne (Rennes), Alsace (Strasbourg), Île-de-France (Paris), Auvergne (Clermont-Ferrand), Provence-Alpes-Côte d’Azur (Marseille) and Midi-Pyrénées (Toulouse).

    ReplyDelete
  63. Love you man! :D

    Still reading it but the "four phases" proposed are:

    1. Early colonization reaching to Sahul. Lineages: C*, K*, C2, M and S. Dated to c. 45 Ka.

    2. Second flow affecting only Sundaland. Lineages: O1a1, O2a, O3(xO3a3) and O1a. Dated to 30-15 Ka.

    3. Austronesian colonization. Lineages: O1a2 and O3a3(xO3a3b). Dated to 4-3 Ka.

    4. Late arrivals from India, West Asia and China. Lineages: H, L, J and O3a3b.

    I imagine that the first two waves were probably made up of diverse groups, in accordance to the diversity of the lineages involved. I would also keep some precaution on the dates proposed, specially for the older waves.

    There are other minor lineages listed, basically: F* (East Indonesia) and R (West Indonesia), which probably correspond with phase 1 and 4 respectively.

    ReplyDelete
  64. "The recent study of R1b1b2's diversity included hundreds of samples from different parts of France (Balaresque, 2009)".

    But they did not provide all the data, only the one they used, and they (decisively) failed to analyze it within the phylogenetic structure. So getting an idea of what is what is hard work and largely a guess game on haplotypes.

    They had no interest in clarifying anything, just "demonstrating" their pet theory, for which it was preferable to keep everything as blurry as possible.

    Enfin. Sorry for the off topic.

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  65. I'm also still going through it, but one ugly little detail I noticed is that it seems all the 1269 samples from the Lansing study I linked yesterday have been reused in this study, just retested for many more SNPs. :( So really we're only getting about 700 new samples, not 2000.

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  66. Glancing at the recently published paper by Kayser et al. (2010), I see that the Friedlaenders' team has sampled the mtDNA of 25 New Caledonian individuals, so perhaps we will have a decent volume of data regarding populations of French-controlled territories soon enough. The New Caledonians seem to belong mainly to mtDNA haplogroup P (mostly P2, but also some P1, both of which seem to be shared with populations of Papua New Guinea), various Melanesian subclades of mtDNA haplogroup M (Q2, M27, M28, M29), and haplogroup B4a1a1a (the typical Polynesian mtDNA haplogroup).

    ReplyDelete
  67. We genotype an
    extensive battery of Y chromosome markers, including 85 SNPs/indels and 12 Y-STRs


    But they don't include the STR data in the supplementary file...

    ReplyDelete
  68. "However, sharing of 12-locus Y-STR haplotypes associated with P203 chromosomes was found between Taiwanese aboriginals and Indonesians (i.e., from Nias, Mentawai, Java, and Bali), while no such sharing was found between the Taiwanese aboriginal and mainland Southeast Asian P203 chromosomes in our sample. This suggests that some portion of Indonesian O-P203 chromosomes may have migrated from Taiwan".

    This is interesting and somewhat self-contradictory because the four phases basic scenario says that O1a* and O1a1 are not in principle of Austronesian origin. Even if not fully explicit, this scenario may suggest that O1a as a whole might have originated in Sundaland and migrated northwards within some moment of the lengthy phase 2 (dotted arrow in map B). However, some amount of O1a could still be attributed to the Austronesian back-flow.

    The interesting element is that, as Taiwan Aborigines are essentially O1a2 (with some O1a1 but no O1a*), and as O1a as a whole looks original from Sundaland, they would have ultimate (Paleolithic) roots at the very Sundaland that they colonized/assimilated at a much later stage.

    Hence these two peoples could well be morphologically and culturally akin (to some extent at least) even before the Austronesian expansion happened. However any hypothetical linguistic affinity would have been almost totally dissolved in the more than 10 thousand years that separate these two events.

    ReplyDelete
  69. aargiedude wrote,
    "Indonesia y-dna (Lansing, 2009) - SNPs only.xls".

    Do you mean Mona 2009? or Lansing 2007?

    ReplyDelete
  70. Maju said,

    "We can't be sure if it's one or several stocks of K*, however it makes sense if Micronesia was colonized after assimilating Philippines and Polynesia after contacting (and partly assimilating too) Melanesia and Wallacea (C2a).

    Your K* data is interesting but we can't be sure of how to read it because we lack phylogenetic resolution. In general it seems that the highest levels of K*, excluding the islands only colonized within Polynesian expansion, are related to Philippines, New Guinea and (to a lesser extent) to what may be (??) part of the the deeper layers of Sundaland's population (Java, Orang Asli)."

    Only the Karafet team has reported finding K-M9(xL-M20, M1-M5, NO-M214, P-P27, S-M230) Y-DNA with such high frequency in a sample from the Philippines. For comparison:

    Hurles et al. (2005)
    Philippines
    1/28 = 3.6% K-M9(xK1-M147, L-M61, M1-M4/M5, M2a-SRY9138, N1-LLY22g, O-M175, P-P27/M45, T-M70)
    9/28 = 32.1% O1a-M119(xO1a1a-M101, O1a2-M50)
    1/28 = 3.6% O1a2-M50
    14/28 = 50.0% O3-M122(xO3a3c-M134)
    3/28 = 10.7% O3a3c-M134

    Kayser et al. (2008)
    Philippines
    4/37 = 10.8% C-RPS4Y711(xC2-M38, C3-M217)
    1/37 = 2.7% F-M89(xK-M9)
    1/37 = 2.7% K-M9(xK3-P79, M1-M4, M2-M353, M3-P117, NO-M214, P-M74, S-M230)
    1/37 = 2.7% O-M175(xO1a-M119, O2a-M95, O3-M122)
    11/37 = 29.7% O1a-M119(xO1a2-M110)
    5/37 = 13.5% O1a2-M110
    1/37 = 2.7% O3-M122(xO3a-M324)
    10/37 = 27.0% O3a-M324(xO3a3b-M7, O3a3c-M134)
    1/37 = 2.7% O3a3c-M134
    1/37 = 2.7% O2a-M95
    1/37 = 2.7% R1-M173

    Han-Jun Jin et al. (2009)
    Philippines
    2/69 = 2.9% Y*(xC, DE, K)
    2/69 = 2.9% C
    6/69 = 8.7% K(xNO)
    2/69 = 2.9% O
    11/69 = 15.9% O1
    1/69 = 1.4% O2(xO2a, O2b)
    1/69 = 1.4% O2a
    1/69 = 1.4% O2b(xO2b1)
    34/69 = 49.3% O3(xO3c)
    9/69 = 13.0% O3c

    Han-Jun Jin et al. (2003)
    Philippines
    3/77 = 3.9% Y*(xC-RPS4Y711, DE-YAP, K-M9)
    3/77 = 3.9% C-RPS4Y711
    8/77 = 10.4% K-M9(xO-M175)
    52/77 = 67.5% O-M175(xLINE1, O2a-M95, O2b-SRY465)
    9/77 = 11.7% O-LINE1
    1/77 = 1.3% O2b-SRY465(xO2b1-47z)
    1/77 = 1.3% O2a-M95

    However, Hurles et al. (2005) have found 1/28 = 3.6% K-M9(xK1-M147, L-M61, M1-M4/M5, M2a-SRY9138, N1-LLY22g, O-M175, P-P27/M45, T-M70) and Kayser et al. (2008) have found 1/37 = 2.7% K-M9(xK3-P79, M1-M4, M2-M353, M3-P117, NO-M214, P-M74, S-M230) in their samples from the Philippines; the fairly high phylogenetic resolution of these studies is helpful, because it allows us to see that at least some of the so-called K* Y-DNA in the Philippines really is some very rare sort of haplogroup K. I would not be surprised if the Aeta of the Philippines carried this sort of haplogroup K* Y-DNA, perhaps in addition to some C(xC2, C3), but the Y-DNA of the majority of the Aetas may have already been replaced by some subclades of O-M175.

    I'd really like to see those four 4/17 = 23.5% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5)) Orang Asli from Su Bing's sample retested for all currently known subclades of haplogroup K. By the way, the authors of that study have not described their Orang Asli sample at all, so I cannot say whether they are Austroasiatic>Aslian-speaking Orang Asli, Austronesian>Malayo-Polynesian-speaking Orang Asli, or a mix of both.

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  71. Maju said,

    "Forget about "Another parallel between Vietnam and West Indonesia, in particular Java". One individual alone can't say too much (and it's not even specifically Java - meh!)"

    I don't know what you are rambling about here. Hammer et al. (2006) have reported 1/70 O2*-P31(xO2a-M95, O2b-SRY465/P49), 1/70 O2b-SRY465/P49(xO2b1-47z), and 2/70 O2b1-47z in the Karafet team's sample from Vietnam, and 2/25 O2b-SRY465/P49(xO2b1-47z) and 2/25 O2b1-47z in the Karafet team's sample from western Indonesia. In the article by Karafet et al. (2005) about Balinese Y-DNA, the Vietnamese O2b and O2* samples have been lumped together as 4/70 = 5.7% O2-P31(xO2a-M95), whereas the western Indonesian O2b samples have been hidden/excluded from the data table altogether (or, to give the authors the benefit of the doubt, perhaps these four western Indonesian individuals had not been sampled or genotyped by the time the Bali paper was submitted for publication).

    ReplyDelete
  72. Do you mean Mona 2009? or Lansing 2007?

    "Male dominance rarely skews the frequency distribution of Y chromosome haplotypes in human populations"
    Lansing, 2008

    ReplyDelete
  73. "Only the Karafet team has reported finding K-M9(xL-M20, M1-M5, NO-M214, P-P27, S-M230) Y-DNA with such high frequency in a sample from the Philippines".

    That's interesting to know. Thanks, Ebizur.

    The other sources emphasize O3 instead. Hmmm... could it be at the origin of the O3a3(xO3a3b) that Karafet claims arrived with Austronesians? I didn't make too much sense of that.

    "I would not be surprised if the Aeta of the Philippines carried this sort of haplogroup K* Y-DNA, perhaps in addition to some C(xC2, C3), but the Y-DNA of the majority of the Aetas may have already been replaced by some subclades of O-M175".

    Don't know. AFAIK nobody seems to have sampled the Aetas or any other Filipino Negritos yet. I don't know why because they are an obvious interesting group to target.

    "By the way, the authors of that study have not described their Orang Asli sample at all, so I cannot say whether they are Austroasiatic>Aslian-speaking Orang Asli, Austronesian>Malayo-Polynesian-speaking Orang Asli, or a mix of both".

    My question was rather about if they were Senoi (who are Orang Asli, i.e. pre-Malay, but not Negrito) or true Negritos (Semang or whatever), rather than the language... because languages change, genes do not.

    "I don't know what you are rambling about here".

    Just correcting myself. I was for a moment under the impression that there was some Y-DNA affinity between West Indonesia and Vietnam, once excluded the Austronesian-specific lineages. But I realized I was wrong.

    Never mind.

    ReplyDelete
  74. "It's hard to categorized the original halpogroup O to one of the Mongoloid groups if they originated from one of archaic groups in south China or ES Asia at 30,000-35,000 BP, because there're no typical Mongoloid skulls found there yet".

    It's quite possible that O didn't originate in 'south China or ES Asia'.

    "That claim is inconsistent with the evidence pointing to south to north migration, not just of Y-DNA O but of most of the genetic pool of East Asia in general".

    The evidence is hardly comnvincing, so a 'south to north migration' could be wrong. And certainly some Os appear to have moved in a southerly direction.


    "the overwhelming predominance of C2a1-P33 that is characteristic of populations of the 'Polynesian triangle,' which perhaps has stemmed from Samoa, evidently does not extend westward to the Micronesian realm"

    The Micronesians are assumed to have moved north direct, even some from dirsct west (or even Japan), rather than back-migrated from Polynesia. So although both groups moved out at about the same time they may originate in different regions.

    "So you think the Taiwanese aborigines, that so similar look to Malays (and sometimes also remind to me, along with Malays, of some Native American peoples) used to be 'less Mongoloid' at the origins of the Austronesian expansion".

    Mainly because the Mongoloid expansion was just getting under way.

    "the native neolithic groups before ancestors of the present Taiwanese's native people, were anthropologically similar to the present Polynesian-Micronesian groups".

    That's very interesting. Most anthropologists in this part of the world suggest that the Polynesians are a hybrid of Papuan and East Asian physical types.

    ReplyDelete
  75. OMG! I just noticed that Karafet et al. (2010) have retested their K* Filipinos for M526 and found them to be positive:

    Philippines
    22/48 = 45.8% MNOPS*-M526(xM-P256, NO-M214, P-P27, S-M230)

    Malaysia
    2/32 = 6.3% MNOPS*-M526(xM-P256, NO-M214, P-P27, S-M230)

    The Y-STR variance associated with MNOPS*-M526 is highest in Oceania (0.898), followed by Western Indonesia (0.720), Eastern Indonesia (0.698), and finally Southeast Asia (0.381). The Y-STR variance associated with MNOPS-M526 as a whole (including known subclades) is highest in Oceania (0.982), followed by Eastern Indonesia (0.738), Southeast Asia (0.604), and finally Western Indonesia (0.594).

    Also of note:

    Bali
    6/641 = 0.94% K4-P261
    (Unfortunately, the authors have not made it clear whether K4-P261 belongs to MNOPS-M526.)

    China (Han)
    2/165 = 1.2% N*-M231(xN1-LLY22g)

    ReplyDelete
  76. Here are all the MNOPS*-M526 results from Karafet et al. (2010):

    Mainland/Southeast Asia
    0/48 Taiwanese Aboriginals
    22/48 = 45.8% Philippines
    0/70 Vietnam
    2/32 = 6.3% Malaysia
    0/165 China (Han)
    0/58 China (Miao)
    0/51 China (She)
    0/49 China (Tujia)
    0/60 China (Yao)

    Western Indonesia
    0/641 Bali/Balinese
    2/61 = 3.3% Java/Dieng(n=35)+composite group(n=26)
    5/38 = 13.2% Sumatra/Toba
    5/86 = 5.8% Borneo
    0/60 Nias/Gomo(n=47)+Hilitobara(n=13)
    0/74 Mentawai

    Eastern Indonesia
    24/394 = 6.1% Flores/Bere Manggarai(n=11)+Boawae(n=27)+Cibol(n=55)+Rampasasa(n=95)+Seso Borowa(n=30)+Wogo(n=35)+Woloara(n=29)+Wolotopa(n=46)+Bama(n=49)+Bena(n=17)
    4/54 = 7.4% Sulawesi/Mandar
    14/350 = 4.0% Sumba/Anakalang(n=50)+Kodi(n=44)+Lamboya(n=49)+Loli(n=38)+Mamboro(n=53)+Rindi(n=27)+Wanokaka(n=52)+Wunga(n=37)
    3/92 = 3.3% Lembata/Hadakewa(n=46)+Waipukang(n=46)
    9/28 = 32.1% Alor
    3/9 = 33.3% Timor
    5/30 = 16.7% Moluccas

    Oceania
    6/44 = 13.6% Maewo (Vanuatu)
    0/10 Nasioi (Bougainville)
    1/15 = 6.7% Papua New Guinea coast
    5/33 = 15.2% Papua New Guinea highland
    7/16 = 43.8% Micronesia
    0/6 American Samoa
    0/10 Rapa Nui (also known as "Easter Island")
    1/24 = 4.2% Tahiti
    0/12 Tonga
    0/12 Western Samoa

    This team has found the highest frequencies of MNOPS*-M526 in their samples from the Philippines (22/48 = 45.8%), Micronesia (7/16 = 43.8%), Timor (3/9 = 33.3%), Alor (9/28 = 32.1%), and the Moluccas (5/30 = 16.7%).

    ReplyDelete
  77. "OMG! I just noticed that Karafet et al. (2010) have retested their K* Filipinos for M526 and found them to be positive:
    Philippines
    22/48 = 45.8% MNOPS*-M526(xM-P256, NO-M214, P-P27, S-M230)
    Malaysia
    2/32 = 6.3% MNOPS*-M526(xM-P256, NO-M214, P-P27, S-M230)"

    Well, well, well. Thanks Ebizur. I knew you could do it. Now track down the Y-hap C*s if you have time (and the resources).

    "This team has found the highest frequencies of MNOPS*-M526 in their samples from the Philippines (22/48 = 45.8%), Micronesia (7/16 = 43.8%), Timor (3/9 = 33.3%), Alor (9/28 = 32.1%), and the Moluccas (5/30 = 16.7%)".

    I've already said I regard the Philippines as Wallacea. So the the only region here that's not Wallacean is Micronesia, and the MNOPS there probably come from the Philippines anyway.

    "The Y-STR variance associated with MNOPS*-M526 is highest in Oceania (0.898), followed by Western Indonesia (0.720), Eastern Indonesia (0.698), and finally Southeast Asia (0.381)".

    What was that Maju was claiming about MNOPS not being anywhere near Wallacea?

    ReplyDelete
  78. "I just noticed that Karafet et al. (2010) have retested their K* Filipinos for M526 and found them to be positive".

    That's pretty cool. Nice finding, Ebizur.

    "I've already said I regard the Philippines as Wallacea. So the the only region here that's not Wallacean is Micronesia, and the MNOPS there probably come from the Philippines anyway".

    Terry:

    1. Philippines is not Wallacea.
    2. Ebizur has already mentioned that this Filipino sample's high frequencies of K* (MNOPS*) are oddly high and inconsistent with other samples, dominated by O3.
    3. There is also a high frequency of K* among the Orang Asli of Malaysia (24%), which is also probably MNOPS*.
    4. Relax.

    ReplyDelete
  79. "What was that Maju was claiming about MNOPS not being anywhere near Wallacea?"

    I could not say that. M and S and K* are found in Sahul at high frequencies, so I would never say that. I just wish that you'd stop babbling once and again "Wallacea" as if it was some magical place.

    ReplyDelete
  80. @ marnie

    The crop common in Korean cooking is "buckwheat" rather than a true wheat. Its origins and classification I restate here Wikipedia's entry on Buckwheat:

    "Buckwheat refers to plants in two genera of the dicot family Polygonaceae: the Eurasian genus Fagopyrum. . . The crop plant, common buckwheat, is Fagopyrum esculentum. . . . Despite the common name and the grain-like use of the crop, buckwheat is not a cereal or grass. It is called a pseudocereal to emphasize that it is not related to wheat. . . . The agricultural weed known as Wild Buckwheat (Fallopia convolvulus) is in the same family, but not closely related to the crop species. Within Fagopyrum, the cultivated species are in the cymosum group, with F. cymosum L. (perennial buckwheat), F. giganteum and F. homotropicum. The wild ancestor of common buckwheat is F. esculentum ssp.ancestrale. F. homotropicum is interfertile with F. esculentum and the wild forms have a common distribution, in Yunnan. . . . Common buckwheat was domesticated and first cultivated in inland southeast Asia, possibly around 6000 BC, and from there spread to Central Asia and Tibet, and then to the Middle East and Europe. Domestication most likely took place in the western Yunnan region of China. Buckwheat is documented in Europe in the Balkans by at least the Middle Neolithic (circa 4000 BC) and the oldest known remains in China so far date to circa 2600 BC, and buckwheat pollen has been found in Japan from as early as 4000 BC. It is the world's highest elevation domesticate, being cultivated in Yunnan on the edge of the Tibetan Plateau or on the Plateau itself. Buckwheat was one of the earliest crops introduced by Europeans to North America. Dispersal around the globe was complete by 2006, when a variety developed in Canada was widely planted in China."

    ReplyDelete
  81. I made a map showing the frequency distribution of Australasian lineages, which I arbitrarily decided was C(xC1,3,5), K*, M, S.

    Asia-Australasia y-dna divide - Australasian lineages.gif

    The Philippine samples "6/33" are from ysearch.

    Anyone know of any y-dna studies of Thailand or Vietnam? Not aggregated into regional results (like "southeast Asia").

    China and India most likely have 0%, all their "Australasian" results belonged to asterisk samples, like C*, and probably are members of very different lineages than those in Australasia.

    "The Y-STR variance associated with MNOPS*-M526 is highest in Oceania (0.898), followed by Western Indonesia (0.720), Eastern Indonesia (0.698), and finally Southeast Asia (0.381)".

    That's clearly not the variance estimates we are accustomed to, that produce a TMRCA age. These are instead measures of diversity of haplotypes. I think.

    There is also a high frequency of K* among the Orang Asli of Malaysia (24%)

    Aha, a study I'm not aware of. What is it?

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  82. I was looking at the Hurles (2005) study of Madagascar, and I compared their y-dna O results with all the Karafet results from this new study. The 2 places that best approximated the composition of Madagascar's O samples were Borneo and Sulawesi. They had both groups and in roughly equal proportions, plus not too much of other O haplogroups.

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  83. [3rd post... I would have put all of this into a single comment]

    Does anyone know of any other Madagascar y-dna study? The Hurles' study only tested 35 Madagascar samples, and half of them were African. Not too great for comparisons.

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  84. "Aha, a study I'm not aware of. What is it?"

    Posted above by Ebizur:

    "Bing Su, Li Jin, Peter Underhill et al., "Polynesian origins: Insights from the Y chromosome," PNAS, vol. 97, no. 15, 8225-8228 (July 18, 2000):

    Orang Asli
    4/17 = 23.5% H5 (=K-M9(xM1-M5, O1a-M119, O2a-M95, O3-M122, P-M45))
    1/17 = 5.9% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    1/17 = 5.9% H7 (=O3a3b-M7)
    11/17 = 64.7% H11(=O2a-M95(xO2a1-M88/M111))"

    It's not even clear which of the various Orang Asli ethnicities they sampled but anyhow...

    "I was looking at the Hurles (2005) study of Madagascar, and I compared their y-dna O results with all the Karafet results from this new study. The 2 places that best approximated the composition of Madagascar's O samples were Borneo and Sulawesi. They had both groups and in roughly equal proportions, plus not too much of other O haplogroups".

    Makes sense because they are believed original from somewhere in Borneo.

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  85. Argiedude: I have linked to your map at the relevant post at Leherensuge. If you have any problem, just say so.

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  86. argiedude said,

    "That's clearly not the variance estimates we are accustomed to, that produce a TMRCA age. These are instead measures of diversity of haplotypes. I think."

    I have taken those numbers from the present study's (Karafet et al. 2010) supplementary table S3 ("STR Variance Associated with Y-Chromosome Haplogroup/Paragroup Lineages").

    argiedude said,

    "Aha, a study I'm not aware of. What is it?"

    Here Maju has quoted me, and I have quoted Bing Su, Li Jin, Peter Underhill, Jeremy Martinson, Nilmani Saha, Stephen T. McGarvey, Mark D. Shriver, Jiayou Chu, Peter Oefner, Ranajit Chakraborty, and Ranjan Deka, "Polynesian origins: Insights from the Y chromosome," PNAS, vol. 97, no. 15, 8225–8228 (July 18, 2000):

    Orang Asli
    4/17 = 23.5% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    1/17 = 5.9% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    1/17 = 5.9% H7 (=O3a3b-M7)
    11/17 = 64.7% H11(=O2a-M95(xO2a1-M88/M111))

    The authors have not provided any description, linguistic or otherwise, of their Orang Asli sample.

    Since you have asked about Vietnamese and Thai Y-DNA, here are some other data from the same study by Su Bing et al. (2000)

    North Thai
    4/20 = 20.0% H2 (=DE-DYS287(xD1-M15))
    1/20 = 5.0% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    6/20 = 30.0% H8 (=O3a3c-M134)
    4/20 = 20.0% H11 (=O2a-M95(xO2a1-M88/M111))
    4/20 = 20.0% H12 (=O2a1-M88/M111)
    1/20 = 5.0% H14 (=P-M45(xQ1a1-M120, Q1a3a-M3, R1a1a-M17))

    Northeast Thai
    1/20 = 5.0% H4 (=F-M89(xK-M9))
    1/20 = 5.0% H5 (=K-M9(xO3-M122, O1a-M119, O2a-M95, P-M45, M1-M5))
    1/20 = 5.0% H6 (=O3-M122(xO3a3b-M7, O3a3c-M134))
    1/20 = 5.0% H7 (=O3a3b-M7)
    1/20 = 5.0% H9 (=O1a-M119(xO1a2-M50/M110/M103))
    1/20 = 5.0% H10 (=O1a2-M50/M110/M103)
    9/20 = 45.0% H11 (=O2a-M95(xO2a1-M88/M111))
    4/20 = 20.0% H12 (=O2a1-M88/M111)
    1/20 = 5.0% H14 (=P-M45(xQ1a1-M120, Q1a3a-M3, R1a1a-M17))

    And more Thai data:

    Tajima et al. (2004)
    Thai
    1/34 = 2.9% C-RPS4Y711(xC1-M8, C3-M217)
    1/34 = 2.9% D1-M15
    15/34 = 44.1% (N?)O-AS1(xO1a-M119, O3-M122)
    12/34 = 35.3% O3-M122
    3/34 = 8.8% O1a-M119
    1/34 = 2.9% P-P27(xR1a1-SRY10831b)
    1/34 = 2.9% BT-SRY10831a(xC-RPS4Y711, DE-YAP, K-M9)

    Han-Jun Jin et al. (2003)
    Thais
    4/55 = 7.3% Y(xC-RPS4Y711, DE-YAP, K-M9)
    1/55 = 1.8% DE-YAP
    3/55 = 5.5% K-M9(xO-M175)
    15/55 = 27.3% O-M175(xLINE1, O2b-SRY465, O2a-M95)
    3/55 = 5.5% O-LINE1
    1/55 = 1.8% O2b*-SRY465(xO2b1-47z)
    2/55 = 3.6% O2b1-47z
    26/55 = 47.3% O2a-M95

    Han-Jun Jin et al. (2009)
    Thais [basically the same sample as Han-Jun Jin et al. (2003), but with a loss of five samples and with the typing of a few additional SNPs]
    4/50 = 8.0% Y*(xC, DE, K)
    1/50 = 2.0% DE
    1/50 = 2.0% K(xNO)
    1/50 = 2.0% NO(xO)
    3/50 = 6.0% O1
    6/50 = 12.0% O2(xO2a, O2b)
    24/50 = 48.0% O2a
    2/50 = 4.0% O2b1
    5/50 = 10.0% O3(xO3c)
    3/50 = 6.0% O3c

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  87. The present study by Karafet et al. contains some of the most informative data on Vietnamese Y-DNA in the entire literature as far as I know.

    Karafet et al. (2010)
    Vietnam
    3/70 = 4.3% C3-M217
    2/70 = 2.9% D1-M15
    1/70 = 1.4% J*-M304(xJ1-M267, J2-M172)
    1/70 = 1.4% J2-M172(xJ2b-M12)
    2/70 = 2.9% N1-LLY22g(xN1a-M128, N1c1-M178) [according to Hammer et al. (2006), these individuals are also negative for N1b-P43]
    2/70 = 2.9% O3a*-P197
    1/70 = 1.4% O3a3*-P201
    4/70 = 5.7% O3a3b-M7
    10/70 = 14.3% O3a4-JST002611
    11/70 = 15.7% O3a3c-M134
    4/70 = 5.7% O1a1-P203
    1/70 = 1.4% O2*-P31(xO2a-M95, O2b-SRY465)
    1/70 = 1.4% O2b-SRY465(xO2b1-47z)
    2/70 = 2.9% O2b1-47z
    5/70 = 7.1% O2a-M95(xO2a1-M111)
    14/70 = 20.0% O2a1-M111
    5/70 = 7.1% Q1-P36(xQ1a3-M346)
    1/70 = 1.4% R1a1a-M17

    Here are some additional data on Vietnamese Y-DNA:

    Kayser et al. (2008)
    Vietnam
    1/6 C3-M217
    1/6 O3a3b-M7
    4/6 O2a-M95

    Han-Jun Jin et al. (2003)
    Vietnamese
    11/50 = 22.0% C-RPS4Y711
    2/50 = 4.0% K-M9(xO-M175)
    23/50 = 46.0% O-M175(xLINE1, O2b-SRY465, O2a-M95)
    2/50 = 4.0% O-LINE1
    5/50 = 10.0% O2b-SRY465(xO2b1-47z)
    2/50 = 4.0% O2b1-47z
    5/50 = 10.0% O2a-M95

    Han-Jun Jin et al. (2009)
    Vietnamese
    9/41 = 22.0% C
    1/41 = 2.4% NO(xO)
    1/41 = 2.4% O(xO1, O2, O3)
    2/41 = 4.9% O2(xO2a, O2b)
    5/41 = 12.2% O2a
    5/41 = 12.2% O2b(xO2b1)
    2/41 = 4.9% O2b1
    14/41 = 34.1% O3(xO3c)
    2/41 = 4.9% O3c

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  88. This is all very interesting. It looks like the islands between Java/Borneo and New Guinea have the exact same genetic composition as the Polynesians.

    Looking at the map I posted a few comments above, we can see that the Pacific islands have an Australasian y-dna that varies between 50% and 90%. This is most similar to the y-dna of the people between Java/Borneo and New Guinea. Instead, in New Guinea it varies between 90% and 100%, and west Indonesia is even further away, at near zero.

    Mtdna. New Guinea has 85% P/Q. We can consider these as the Australasian mtdna lineages, though Australia itself has only about 10% P/Q. Anyhow, the frequency of P/Q steadily drops westwards, averaging about 10% in the island between Java and New Guinea, 1% in west Indonesia, and 0% in southeast Asia and Taiwan. The frequency of P/Q in several Polynesian islands is 5%. Once again, this is closest to the islands between Java/Borneo and New Guinea.

    Figure something like there was an explosion of oceanic exploration coming out of the Borneo/Sulawesi/Moluccas region, and as they spread into every direction, they mostly encountered inhabited land, such as Sumatra, Java, Philippines, New Guinea, and even Australia, Africa and South America, so in these places the small sea faring party just became lost into the population. But in the occasional uninhabited island they came across, they became the sole inhabitants, such as in Madagascar and the Polynesian/Micronesian islands. Afterwards, in the case of islands that were very close to inhabited mainland, there were subsequent population movements that gave rise to the mixed people of Madagascar and maybe the Melanesians.

    Maybe I've just stated an obvious thing, but well, I'm just finally getting into the genetics of Oceania, something I've always royally ignored. I have a vague recollection that geneticists are proposing theories of Austronesian males/females mixing with Melanesian females/males, or something like that, in order to explain their mix of y-dna and mtdna. Borneo/Sulawesi/Moluccas come with the necessary ingredients from the start: their mtdna is Asian, their y-dna is Melanesian. And, as we've been discussing in this thread, the sharp separation of the y-dna along the Wallace Line indicates a paleolithic continuity, so their peculiar genetic make up probably isn't itself the result of recent events.

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  89. I spot some differences between Wallacea/Eastern Indonesia and Polynesia/Micronesia:

    Wallacea is high in C* and C2*, while Polynesia is not (C2a instead, absent in Wallacea, even if derived).

    Wallacea has some good frequency of MNOPS*-M256, while Polynesia does not (though Micronesia does).

    Wallacea is high in M1a and S, as is Melanesia, Polynesia not.

    Wallacea has some O1a, Polynesia almost none.

    Maybe the overall frequencies for some groupings match somehow but the detail seems quite different.

    Tahiti for instance is essentially C2a and O3a3. Maybe the apportion of C2a matches with the overall apportion of C+MNOPS at Wallacea and maybe the apportion of O3a3 matches with the overall O found in Wallacea but the details are quite different, specially if O3a3 arrived from Taiwan or mainland East Asia, as Karafet suggests, and as C2a is more directly shared with Melanesia.

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  90. Erratum: "of C+MNOPS" should say "of C + MNOPS(xNO,P)", as the contrast lineage is nearly all O.

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  91. "I could not say that. M and S and K* are found in Sahul at high frequencies, so I would never say that".

    You have. Consistently.

    "I just wish that you'd stop babbling once and again 'Wallacea' as if it was some magical place".

    Just admit you were wrong. The Philippines have as much right to be included in Wallacea as do any other islands in the region never connected to either Sunda or Sahul.

    "Ebizur has already mentioned that this Filipino sample's high frequencies of K* (MNOPS*) are oddly high and inconsistent with other samples, dominated by O3".

    And why might the sample be 'oddly high and inconsistent with other samples'? Might it be because MNOPS coalesced there?

    "There is also a high frequency of K* among the Orang Asli of Malaysia (24%), which is also probably MNOPS*".

    Perhaps. But Ebizur wrote, 'This team has found the highest frequencies of MNOPS*-M526 in their samples from the Philippines (22/48 = 45.8%), Micronesia (7/16 = 43.8%), Timor (3/9 = 33.3%), Alor (9/28 = 32.1%), and the Moluccas (5/30 = 16.7%)'. So where is Malaysia in relation to that list?

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  92. "It looks like the islands between Java/Borneo and New Guinea have the exact same genetic composition as the Polynesians".

    That's the region I refer to for convenience as 'Wallacea', a term Maju strongly objects to. The Polynesians are Austronesian-speaking, and actually developed way out beyond Fiji. Their ancestry goes back to the Lapita pottery people in New Britain though. Further back still the Austronesians are believed to have formed in Wallacea from a mixture of the locals and people from Taiwan, although many of the islands were probably uninhabited when the Austronesians first arrived.

    "the Pacific islands have an Australasian y-dna that varies between 50% and 90%".

    Genetically Australasia consists of three reasonably discrete genetic groups: Australia, New Guinea and Oceania, although Y-hap C is present in all three. But as different versions: C4 in Australia, C6 in New Guinea and C2 in Oceania (and Wallacea). K, M and S are New Guinea haplogroups although some have traveled further into the Pacific with the Austronesian migration.

    "New Guinea has 85% P/Q. We can consider these as the Australasian mtdna lineages, though Australia itself has only about 10% P/Q".

    The Polynesians have very little mtDNA other than B, an Asian Haplogroup. And Australian Aborigines have very little Q, although they do have quite a lot of R-derived P. I strongly suspect that the presence of P and Q to the west of New Guinea is a product of back migration.

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  93. "You have. Consistently".

    If you are going to accuse me of something I'm quite sure it's false, the least I can ask, Terry, is to be shown the evidence (links and quotations). Otherwise recoil and shut up.

    "The Philippines have as much right to be included in Wallacea as do any other islands in the region never connected to either Sunda or Sahul".

    Again conveniently twisting the facts in favor of your pet theory. Let's see:

    1. I've seen nowhere that Philippines is considered part of Wallacea, because it's at the continental side of Wallace Line.

    2. The Y-DNA pool of Filipinos is clearly different from that of Wallaceans, either following Karafet (high MNOPS* but no M, S or C) or following the various other sources provided by Ebizur (dominated by O3 but similarly different to the Wallacean Y-DNA pool).

    If you wish, Philippines could be a different province... with a different name... and different characteristics. But by no means you can dump it into Wallacea without creating an outmost mess.

    "And why might the sample be 'oddly high and inconsistent with other samples'? Might it be because MNOPS coalesced there?"

    Probably because Philppines is a diverse country and the various samples come from various different popualtions. I imagine that most are Tagalogs from near Manila, while Karafet's sample smells to some other distinct group or groups, with important pre-Austronesian ancestry (obviously).

    "Perhaps. But Ebizur wrote, 'This team has found the highest frequencies of MNOPS*-M526 in their samples from the Philippines (22/48 = 45.8%), Micronesia (7/16 = 43.8%), Timor (3/9 = 33.3%), Alor (9/28 = 32.1%), and the Moluccas (5/30 = 16.7%)'. So where is Malaysia in relation to that list?"

    Fair enough. It does seem that the second wave of Karafet essentially displaced MNOPS(xO) to near nothingness west of Wallace Line.

    Also you should check the diversity data (in principle more meaningful than the frequency) that would rather support if anything a Melanesian ancestral homeland for MNOPS (and the paraphyletic MNOPS* maybe too, as well as M and S, of course).

    On the other hand Wallacea is a the best candidate for the origins of C* (if a single clade) and C2, but not for C as whole, which looks more likely to be from SE Asia.

    So MNOPS, if anything, would not be a Wallacean issue but a Melanesian (or maybe Australian, not tested yet) one. What makes me recall certain Iranian who claimed that Papuans and "Middle-Easterners" were very much alike. Who knows, maybe he was onto something.

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  94. "... a term Maju strongly objects to".

    I don't object to call Wallacea what is Wallacea. What I hate is that you all the time use that term and don't even care about Wallace or Liddeker lines. You are making me hate Wallacea so much you repeat that name mostly within nonsense contexts but I have no problem with a region of that name being for real and virtually identical to East Indonesia (plus East Timor minus West New Guinea).

    What I have a problem is with you fusing Melanesia, Sundaland and Philippines (and even Australia) at will within that concept when it fits your whim. And I have a problem with your absurd hypothesis of boats being only invented upon arrival to Wallacea and not somewhere in Africa maybe 100,000 (or a million) years earlier.

    "C6 in New Guinea"

    I asked you before: source? Nobody seems to know where C6 is. Plus the C at New Guinea seems to be mostly C2.

    From Karafet's data:

    PNG-coastal: C*=1, C2a=2 (n=15)
    PNG-highland: C2=2 (n=33)

    C*, which might include C6 (only might) is found in West and East Indonesia, as well as in mainland SE Asia. But only two individuals in Oceania (the other one in Micronesia, that is closer to Asia than to Sahul).

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  95. Andrew Oh-Willeke,

    Thanks for your generous information on the history of the crop buckwheat. I noticed this at a little family run Korean cafe. It seems to be customary and very traditional for families to store their tea (buckwheat) in a big jar, so you can look at it.

    I'm used to Japanese Rice tea, so when the cafe was serving a grain tea that was not rice, it seemed to be unusual. The family explained that they grow the tea grain in the winter, on the same fields where rice grows in the summer.

    Working from your suggestion that the tea is buckwheat, I checked, and aparently, buckwheat isn't nitrogen fixing. However, it doesn't require much nitrogen to grow and it mobilizes phosphorus. If the plants were cultivated back into the fields, they would provide phosphorus for the summer crop of rice.

    Very much appreciated on all the dates, the hardiness, genus names and distribution.

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  96. This comment has been removed by the author.

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  97. Ebizur,

    I'd really like to be able to visualize some of the data you've been putting up.

    I had a look online and found "Matlab Population Genetics & Evolution Toolbox."

    I haven't had a chance to download it yet. It looks like it has pie charting capability, but is not combined with a map.

    Do you use one of these standard plotting routines to visualize your data? Something like the map that appears in the mtDNA Uzbekestan" paper.

    It would be nice to have a standardized matlab routine that can suck in your data and produce a map with pie charts for the various populations you are talking about. Adding latitude and longtitude coordinates for each population would be all that is required to complete the data sets.

    Such a routine would also allow comparison of different papers more easily. (Space permitting, you could have paired pie charts for each population.)

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  98. correction:

    Something like the map that appears in the "mtDNA variation in Uzbekistan" paper.

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  99. One other thing that might be nice to see on a pie chart is the population size. That could be annotated at the edge of each pie.

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  100. "If you are going to accuse me of something I'm quite sure it's false, the least I can ask, Terry, is to be shown the evidence"

    Yes, you readily accept that 'M and S and K* are found in Sahul at high frequencies', but you bend over backwards to distance the remainder of the MNOPS haplogroup (the NOP part) from that region. Even to the extent of eliminating K from the haplogroup so your belief would be less likely to conflict with the evidence. I can't be bothered searching through your blog but I'm sure you'll find many occasions.

    "I've seen nowhere that Philippines is considered part of Wallacea, because it's at the continental side of Wallace Line".

    Maju, you're an idiot. When have the Philippines ever been connected to any mainland? You're the one 'conveniently twisting the facts in favor of your pet theory'.

    "The Y-DNA pool of Filipinos is clearly different from that of Wallaceans"

    Why must different regions of Wallacea be defined by the human Y-haps present?

    "Probably because Philppines is a diverse country and the various samples come from various different popualtions".

    And so is the remainder of Wallacea.

    "would rather support if anything a Melanesian ancestral homeland for MNOPS"

    Obviously you're now prepared to accept an eastern origin even more extreme than I've ever proposed. You perhaps remember strongly objecting to the sentence, 'There seems to have then been an expansion of Y-chromosome K and his descendants north to the East Asian point (N and O) and west through the Indian subpoint and onto the Iranian plateau (L and P)' in my essay:

    http://remotecentral.blogspot.com/2008/01/human-evolution-on-trial-mitochondrial.html

    At that stage the haplogroup MNOPS was unheard of and L and T were included in what was all called 'K'. But you seem now more open to accepting that proposition.

    "What I have a problem is with you fusing Melanesia, Sundaland and Philippines (and even Australia)"

    That's rubbish Maju. I've never included Australia or Melanesia as part of Wallacea.

    "I have no problem with a region of that name being for real and virtually identical to East Indonesia"

    I've tried to point out to you that it's not anything like 'virtually identical to East Indonesia' but trying to communicate with you is like talking to a brick wall.

    "Nobody seems to know where C6 is. Plus the C at New Guinea seems to be mostly C2".

    The brick wall wins again. Ebizur has already mentioned that C6 is New Guinea. And I think it was at your blog. But you obviously took no notice. Sure, most of the New Guinea C is C2 and arrived with the Austronesians.

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  101. "I'd really like to be able to visualize some of the data you've been putting up".

    What would be really helpful is if some clever person could co-ordinate the two sets of maps Dienekes recently put up (Australia and East Asia). I mean, does the Australia/New Guinea map really need to show us the exact distribution of the several different mtDNA Bs? We know that B marks the Austronesian expansion into the Pacific. In the East Asian map, on the other hand, the Bs labeled are quite revealing. So co-ordinating the two maps would reveal even more.

    The mtDNA M42a in SE Australia is worth looking at in relation to the Ms in the East Asian map but correlation is difficult. And the order the authors place the mtDNA haplogroups in the key seems very strange. Surely mtDNA haplogroups M, N and R is the logical order. But I can't see any reasoning in the different orders in the two maps The same arrangement and colours in both sets of maps would let trends stand out.

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  102. "... but you bend over backwards to distance the remainder of the MNOPS haplogroup (the NOP part) from that region".

    That's very different from what you accused me of. I should demand an apology but you won't issue it anyhow, right?

    Whatever the case, it's clear that neither N nor P coalesced anywhere east or south of Wallace Line. Even you will have to accept that.

    "Maju, you're an idiot. When have the Philippines ever been connected to any mainland?"

    And you are abusive, insulting and distorting things to your convenience. Philppines is this side of Wallace Line (or "that side" from your NZ viewpoint). I don't care if it was or was not connected to the mainland. You can summon the ghost of Alfred Russel Wallace (or more pragmatically ask a living biologist or geologist) and ask them why Philippines is this side and not that side.

    But the fact is that it is that way and hence it's NOT part of Wallacea.

    "Why must different regions of Wallacea be defined by the human Y-haps present?"

    Wallacea and Philippines, not "different regions of Wallacea". Call things by their name because the only thing you do is having a diffuse shrinking and expanding region at your convenience and confusing everybody with that.

    For me in particular it's tiresome to spend time and energy correcting this fact (and many other of such blurry ideas of you) once and again, when it's as obvious that even just a quick search clarifies it.

    Whatever the case, they are not defined by them... but they are confirmed by them and it's you (and nobody but you) who wants to attach a human Y-DNA value to the "magic word" Wallacea.

    "That's rubbish Maju. I've never included Australia or Melanesia as part of Wallacea".

    You use them to argue your myth about Wallacea, as if they were part of it. If you must say Melanesia, say so.

    But you want to say Wallacea because it's where you have built your "magic house of cards". So it doesn't matter if the data points, if anything, to Melanesia, you'll spell it Wallacea anyhow. And if it points to Sundaland, you'll say Wallacea, and if it's Philippines you'll say Wallacea and if it'd be Yemen... you'd say Wallacea too.

    It's really wallaceannoying, like only terrywallacea can wallaceabe!!!

    "Ebizur has already mentioned that C6 is New Guinea".

    Link? Reference? All I recall is link to Wikipedia, where it's (it was?) claimed but not supported by any source.

    "Sure, most of the New Guinea C is C2 and arrived with the Austronesians".

    For Karafet C2 is not Austronesian but part of the earliest colonization of the area. Only C2a2 can to some extent be associated to Austronesians (specifically Polynesians and not others) but seems original from Melanesia.

    Read the paper again, please:

    "C-M208 being limited to Melanesia and the Pacific islands (i.e., remote Oceania)".

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  103. Maju said,

    "Link? Reference? All I recall is link to Wikipedia, where it's (it was?) claimed but not supported by any source."

    The reference is in both the Wikipedia entry on haplogroup C (Y-DNA) and in a comment that I have made on your blog. Scheinfeldt et al. (2006) have found a Y-chromosome marked by the P55 mutation (i.e. a representative of the clade called C6-P55 by ISOGG 2010 and Karafet et al. (2008)) in a sample from the highlands of New Guinea. We already know that C6-P55 has been found in at least one person from the New Guinea highlands; what we do not yet know is the full extent of this clade's distribution, since the P55 mutation has rarely been tested.

    By the way, I think the present study's Y-STR variance data suggest that the erstwhile NOP hypothesis may be correct after all; note that the Y-STR variance of MNOPS as a whole in Karafet's sample sets from Southeast Asia and Western Indonesia, in which representatives of both NO-M214 and P-M45 have been found, is less than the variance of MNOPS as a whole in Eastern Indonesia and Oceania. Shouldn't this entail that NO and P form a distinct subset/subclade of MNOPS separate from the more diverse Wallacean/Oceanian clades?

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  104. "The reference is in both the Wikipedia entry on haplogroup C (Y-DNA) and in a comment that I have made on your blog. Scheinfeldt et al. (2006) have found a Y-chromosome marked by the P55 mutation (i.e. a representative of the clade called C6-P55 by ISOGG 2010 and Karafet et al. (2008)) in a sample from the highlands of New Guinea. We already know that C6-P55 has been found in at least one person from the New Guinea highlands; what we do not yet know is the full extent of this clade's distribution, since the P55 mutation has rarely been tested".

    Alright. Let's see if I can recall that note.

    Whatever the case we are talking of what otherwise would be included in paragroup C*, which is rare in New Guinea... but somewhat common in Indonesia. Per this paper:

    West Indonesia: 1.3% of total, 97.5% of C.
    East Indonesia: 6.2% of total, 31.4% of C.
    Oceania: 0.1% of total (2 individuals, only one Papuan), 3.4% of C.
    Mainland SEA: 1.0% of total, 39.5% of C.

    Also the diversity of C* is clearly much higher in East Indonesia (Wallacea).

    "By the way, I think the present study's Y-STR variance data suggest that the erstwhile NOP hypothesis may be correct after all; note that the Y-STR variance of MNOPS as a whole in Karafet's sample sets from Southeast Asia and Western Indonesia, in which representatives of both NO-M214 and P-M45 have been found, is less than the variance of MNOPS as a whole in Eastern Indonesia and Oceania. Shouldn't this entail that NO and P form a distinct subset/subclade of MNOPS separate from the more diverse Wallacean/Oceanian clades?"

    I truth I don't know. I am confuse about whether the marker of NOP is or not the same as one of the SNPs describing MNOPS. I think it's the same one but I have no other support than the Wikipedia article, which lacks of clear references. It says:

    "Defining mutations: rs2033003 (M526)".

    The diversity for MNOPS* is greatest in Oceania and then Indonesia (with very little difference between both regions). So if this paragroup would be a single lineage, then New Guinea looks like the ancestral homeland. But if it's several, then they should be treated separately.

    Whatever the case at the current stage of knowledge we MNOPS has four subclades:
    - M and S with clear origins in Melanesia
    - NO with likely origin in Indochina/South China (mainland SEA)
    - P with probable origin in India (though I remain unsure about this)
    - MNOPS* (paragroup!) which also looks original from either Melanesia or Indonesia

    If you join the dots, you should get a most likely original area, which is, it seems to me, Sulawesi (or maybe Borneo).

    However there is another possibility: that M, S and at least part of MNOPS* all form a distinct haplogroup within MNOPS. Haplogroup that it might take years, maybe decades, to discover (considering that these lineages are not normally the main interest of labs).

    The diversity differences don't seem enough to clearly settle the issue, much less as they are considered from a non-phylogenetic perspective (we don't even know the Y-STR median-joining tree of that clade, which could give us some idea at least of what's goig on).

    So, we'll see.

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  105. Erratum: "MNOPS has four subclades" should read "MNOPS has five subclades".

    ReplyDelete
  106. Another self-correction (sorry but details may matter a lot in this discussion):

    "If you join the dots, you should get a most likely original area, which is, it seems to me, Sulawesi (or maybe Borneo)".

    Actually, this depends a lot on where you place the centroids of the five subclades. The result is clearly on Indonesia or Malaysia but as a lot of the debate goes about this or that side of Wallace Line, the exactitude and methodology of this estimation will make things change significantly.

    For example, my first raw estimate was between North Sulawesi and NE Borneo, but rather to Sulawesi (hence Borneo went in parenthesis). But if I move the origin of NO from Yunnan to near Shanghai, then I end with an MNOPS centroid at Sabah (and I haven't even moved the ultra-ambiguous "origin" of P, which I have no real idea where it was in truth).

    And if instead of using a straight axis, I use a curved axis following the Kraa isthmus (as geography demands), then I get the resulting between Borneo and Java.

    So... whatever you prefer.

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  107. Addendum: I've dedicated some time to estimate the composite centroids of all the continental and insular MNOPS phylogeny and the result is (without any geographical constraints, i.e. across South China Sea) Sabah state, or (considering geography) the area between Sarawak and West Kalimantan, around Kuching and Paloh.

    However paragroup MNOPS* appears to have a centroid at north Sulawesi... but we can't be sure how many haplogroups hide under that catchall name (I'd say it's likely that several, because the local geography should have kept populations separated).

    Some uncertainty should persist anyhow but I would now argue with some confidence that MNOPS as whole looks like coalescing at Sundaland.

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  108. I'm really not understanding this discussion about M526. In the ISOGG page we can see that there isn't any connection between M, NOP, and S, because the status of rs2033003 in M and S remains undetermined. So theoretically, M, S, and K-M526 could belong to a single clade, exclusive of NOP.

    ISOGG y-dna tree

    ..........................

    Maju, I agree with your comments after my post about Polynesians being genetically identical to Wallacea. I said Polynesians and Wallaceans had the same percentage of Australasian y-dna and mtdna, which is true, but the subgroups are very different, so I no longer belive this. What I think now is that the population history of these "tiny island" people can be compared to that of Ashkenazi Jews, in that they seem to have gone through population bottlenecks that have resulted in the appearance of their own lineages not found anywhere else, and at high frequencies. This would make perfect sense for a people living on dots on the map. Right now, I'm thinking that the genetic composition of Polynesians, Micronesians, and perhaps also Melanesians (not New Guinea!) is more of a distraction than helpful in trying to decypher how haplogroups diffused through this region.

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  109. ISOGG is clearly being cautious but I imagine that they will accept the MNOPS clade very soon, specially after this research, which has got all regional K* into MNOPS.

    "Right now, I'm thinking that the genetic composition of Polynesians, Micronesians, and perhaps also Melanesians (not New Guinea!) is more of a distraction than helpful in trying to decypher how haplogroups diffused through this region".

    Well, they are another reference but sure: a distinction should be made at least between New Guinea and nearby islands (which were colonized early in the Paleolithic) and the Pacific Ocean islands, which were only colonized in "recent" times.

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  110. I'm still lost. Did this study find that M, O, and S lineages were derived for M526?

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  111. The Chiaroni paper proposed that M, NO, P and S, as well as some K* were all part of single haplopgroup MNOPS.

    However that paper too is pay-per-view, so I don't know the details. For some unclear reason, ISOGG has not fully accepted it yet, but I think it's part of the process of deliberation they usually have (there's surely a draft circulating among experts right now) and we will probably see it officialized in the next version.

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  112. M526 is underhill's renaming of rs2033003.

    As such there is no NOP clade at this moment. It is replaced by MNOPS.

    As someone suggested there may be NOP clade still, but that requires a discovery of additional markers that refine MNOPS clade.

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  113. "I should demand an apology but you won't issue it anyhow, right?"

    Not until you demonstrate some common sense.

    "Whatever the case, it's clear that neither N nor P coalesced anywhere east or south of Wallace Line. Even you will have to accept that".

    I've never claimed they did. KMNOPS probably did, but it seems extremely likely that NO and P developed from members of the KMNOPS haplogroup who had moved back west a little way, but possibly only as far as the western Wallacean shore.

    "I don't care if it was or was not connected to the mainland".

    You may not care, but it's very relevant.

    "I've seen nowhere that Philippines is considered part of Wallacea, because it's at the continental side of Wallace Line".

    How about reading your own link to Wallacea at Wikipedia: 'The Philippines (excluding Palawan which was part of Sundaland) are usually but not always considered a separate region from Wallacea'. Note: not always. But they are certainly not part of either Sunda or Sahul. As you say, 'even just a quick search clarifies it'.

    "Call things by their name because the only thing you do is having a diffuse shrinking and expanding region at your convenience and confusing everybody with that".

    The name you give something doesn't change what it is. And I'm fairly sure that you're the only one confused about the Philippines relationship to Wallacea. I've tried explaining but you're obviously not interested.

    "If you wish, Philippines could be a different province... with a different name... and different characteristics. But by no means you can dump it into Wallacea without creating an outmost mess".

    Perhaps, to keep you contented, we could call the Philippines 'the gateway to Wallacea'. It seems highly likely from the information collected here that humans entered Wallacea from them, rather than via any route further south.

    "The Y-DNA pool of Filipinos is clearly different from that of Wallaceans, either following Karafet (high MNOPS* but no M, S or C)"

    And why might that be so? Have a think about it, for a change. Aren't M and S derived from MNOPS* further east? (in fact we should probably refer to it as KMNOPS*). So don't the different distributions through the whole region make perfect sense?

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  114. "For Karafet C2 is not Austronesian but part of the earliest colonization of the area. Only C2a2 can to some extent be associated to Austronesians (specifically Polynesians and not others) but seems original from Melanesia".

    Again you demonstrate that you have not understood anything anyone has gone to the trouble of writing. C2 is certainly ancient in the region (Southern Wallacea specifically), but the really interesting thing (as Ebizur explained at your blog) is that C2 expands first to parts of Melanesia (possibly 10kya) and then takes off east with the Austronesians as C2a2 about 4kya. The scenario is easy to see if you actually bother look. And I don't have to read the paper again because that scenario has been accepted for years. The paper just clarifies some details.

    "For me in particular it's tiresome to spend time and energy correcting this fact"

    But you wrote, 'Alright. Let's see if I can recall that note'. How many times have I had to repeat that information (and much other). I've mentioned half a dozen times that C6 is found in the New Guinea highlands, but every time I mention that fact again you don't believe me, and we repeat the whole process. And after I've mentioned at least half a dozen times the reference that 'and diamond: M525 that unifies KMNOPS' I see you finally accept it (your comment: 'specially after this research, which has got all regional K* into MNOPS'). It takes a long time to get anything through to you.

    "MNOPS* (paragroup!) which also looks original from either Melanesia or Indonesia".

    And definitely not somewhere in between? I think the evidence is pretty overwhelming.

    "However paragroup MNOPS* appears to have a centroid at north Sulawesi... but we can't be sure how many haplogroups hide under that catchall name"

    Several Ks, surely.

    "a distinction should be made at least between New Guinea and nearby islands (which were colonized early in the Paleolithic) and the Pacific Ocean islands, which were only colonized in 'recent' times".

    But it's becoming quite possible to unravel the pattern.

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  115. "Perhaps, to keep you contented, we could call the Philippines 'the gateway to Wallacea'. It seems highly likely from the information collected here that humans entered Wallacea from them, rather than via any route further south".

    I don't see the why of that claim.

    "Aren't M and S derived from MNOPS* further east? (in fact we should probably refer to it as KMNOPS*). So don't the different distributions through the whole region make perfect sense?"

    Sure: Wallace Line: M, S and C2 are east/south of it.

    "... but the really interesting thing (as Ebizur explained at your blog) is that C2 expands first to parts of Melanesia (possibly 10kya) and then takes off east with the Austronesians as C2a2 about 4kya".

    Thanks goodness we have a second opinion about the age of C2 in this paper. 10Ka makes no sense whatsoever.

    In either scenario, it's too old to be Austronesian-original. Only the C2a2 scatter can be associated with them (but not C2a2 as a whole, which is quite obviously of Melanesian origin).

    "And I don't have to read the paper again because that scenario has been accepted for years".

    You should read the paper to realize that Karafet is proposing C2 being much older than just 10 millennia.

    "And definitely not somewhere in between?"

    Between Melanesia and Indonesia? You kidding: there's nothing in between: they overlap totally. Unless you're thinking in East Timor...

    ...

    Surprised you have nothing to say about MNOPS seemingly centered at Kuchin... Silence=concession?

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  116. I think Jake(I suppose Ebizur)'s observation is almost interesting but this is the prime example of an age estimate from variance NOT working.

    Too many O-175's and too few other M526+'s.

    I am shocked to find out that Jake has been editing Wikipedia. I think he should defer it to more qualified individuals.

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  117. I've noticed something fascinating. The study has apparently found 3 samples of J*, one of the rarest haplogroups in the world! J* is defined by 12f2.1(xM267,M172). In the study they've tested for M304 instead of 12f2.1; they're phylogenetically equivalent, so it shouldn't matter.

    To get an idea of how rare J* is, consider that the most important study done on y-dna J, by Semino in 2004, tested 3000 people from J infested areas and found 700 of them, and NOT ONE belonged to J*, they all fell into J1 or J2. Now that's rare. She tested for 12f2.1 to determine J.

    Semino's study included 37 J samples from India/Pakistan/Nepal. Of course, this is the region from where we presume J in southeast Asia/Indonesia came from.

    The study found 18 J samples from southeast Asia/Indonesia (plus 2 in China & Polynesia), so 3 J* out of 18 J total.

    It's funny, there's another area where J* was also found in abundance, and it's the island of Soqotra off the coast of Somalia. It actually made up the majority of the y-dna in that island. Semino's study included 20 J samples from Sudan/Ethiopia, and of course, none of them were J*. I don't know if J* exists in Somalia, but I do know that J makes up about 3% of their y-dna. The funny part is that these 2 places are in sub-Saharan Africa and East Asia.

    Comments???!!!??? This is a notorious development, I would say! I hope it's not an error. Oh yeah, 1 J* is in Vietnam, and 2 J* are in Bali. Scroll up and download the pdf and or xls file I've uploaded a few days ago, if you haven't yet.

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  118. I've put the Karafet/Hammer paper and data on Zoho viewer.

    http://viewer.zoho.com/docs/odaScbj
    http://viewer.zoho.com/docs/kdaNd9
    http://viewer.zoho.com/docs/ndaMDc

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  119. By the way, I'm trying to get this study, if someone can help:

    Y-STR haplotype diversity in distinct linguistic groups from East Timor

    also titled:

    Y-chromosome STR haplotypes in East Timor: forensic evaluation and population data

    Souto, 2006. It's the same study, for some reason they have 2 different links to it.

    They tested 12-STRs, a nice improvement. I'm trying to get haplotype info on these Australasian clades because yhrd has thousands of samples from southeast Asia/Indonesia and if I could predict these samples then I would be able to perform TMRCA/variance estimates on them, which would be very interesting given what we've been discussing in this thread about how the sharp Wallacean divide of the haplogroups strongly suggests they've been there since the Ice Age.

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  120. Much thanks, Finn! You uploaded the main pdf, which we didn't have yet. I reposted your links because they're not clickable:

    Main pdf

    Supplementary pdf

    Supplementary xls

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  121. Much thanks, Finn! You uploaded the main pdf, which we didn't have yet.

    Actually, we already had the main pdf, which was uploaded by... me. Jesus...

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  122. "I am shocked to find out that Jake has been editing Wikipedia. I think he should defer it to more qualified individuals".

    Ebizur is obviously a very qualified individual. All (or most) of his comments show he has a very keen interest and meticulous documentation of the details of Y-DNA.

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  123. From what I posted on DNA Forums:

    In this paper, K-M526*(MNOPS*) is found in 45.8% of Filipino samples(n=48).

    I wonder if these K-M526* are related to pre-Austronesian lineages, such as "Aeta" lineages.

    Spencer Wells has tested Y-DNA of Aeta people, but that's still unpublished data.

    "The earlier trip with Dr. Rand Allingham yielded data from more than 100 Aeta, and the genetic results we have obtained are fascinating. We're currently writing them up, and don't want to discuss them in too much detail until they have been published, but the Aeta certainly seem to be a mix of both Austronesian and earlier genetic lineages, and their Y-chromosomes appear to be almost completely pre-Austronesian."

    http://blogs.nationalgeographic.com/blogs/genographic/2008/12/meeting-the-ati-peoples-in-the.html

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  124. It seems that Karafet didn't test M175 on these Filipino K-M526* samples.

    But still these samples possibly represent pre-Austronesian lineages.

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  125. I am sure we all would like to know the exact results about the Aeta because there is no published data on Filipino Negritos in general.

    I also think that the MNOPS* found in this Filipino sample of Karafet et al. is with all likelihood pre-Austronesian (Negrito) and may well be the same. However, I would not be surprised if the Aeta showed other early lineages such as C* (or even maybe D*, F*...)

    ...

    @Argiedude: what you say of J(xJ1,J2) is most interesting. It's possible that we are before J3, a SE Asian lineage?

    I have been considering that the Y-DNA lineage most directly related with the expansion of mtDNA R should be IJK as a whole (rather than K or, as Terry seems to believe, MNOPS). This SE Asian J* (J3?) would rather confirm my idea, even if the most important lineage involved in the East is still MNOPS.

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  126. As for Jake's credentials... I remember the hilarious incident where he could not distinguish haplo(sub)group prediction from STR profile and genuine haplogroup assignment from actual SNP typing.

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  127. If you read Karafet's paper, especially "subjects and method" it should be clear that M175 has been tested.

    Since she was considering Paleolithic movements of O-M175 lineages it would be foolish not to have typed M175, thereby missing O-M175*.

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  128. Similarly, there are unique, basal haplogroup
    N mtDNA lineages in the Mamanwa, a Negrito group from
    Mindanao in the Philippines, that are absent from neighboring
    groups (E. Gunnarsdottir and M. Stoneking, unpublished
    data). Some Negrito groups also exhibit high frequencies of
    Y-STR haplotypes on the background of NRY haplogroups
    C-M130 and K-M9 that are not found elsewhere in southeast
    Asia but are associated with Y-STR haplotypes found in
    aboriginal Australians (F. Delfin, M. Stoneking, and M.C.A.
    DeUngria, unpublished data).

    From: http://download.cell.com/current-biology/pdf/PIIS0960982209020673.pdf?intermediate=true

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  129. Interesting, Natsuya. Good to know (though I'd wish the data would be published, damnit! - there should be a law forcing them to publish in 24 months or something).

    ...

    In relation to the J* observation of Argiedude, it must be mentioned that Ebizur also spotted H(xH1,H2) in Bali (2.6%), which seem to be extremely rare even in India. See discussion at Leherensuge for reference.

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  130. The Aeta present a big problem with the notion that the Austronesian haplogroups are of paleolithic presence. Or for that matter, all Negritos people. Their notoriously different appearance with Malays, Indonesians, and Philippinos is a very strong argument in favor of a wave of agriculturalists swamping into southeast Asia/Indonesia from southern China. And from what natsuya said, the y-dna results of the Aeta of the Philippines are going to be overwhelmingly Australasian, and this will hammer the point home even further because, unlike what the Karafet study has found about Philippines, their y-dna is actually very Austronesian. Karafet found 50% Australasian haplogroups in their sample of 50 Philippinos. That's an anomalous result; it happens occasionally. I've accumulated almost 300 Philippine y-dna samples from several studies, and their Australasian y-dna is only 19% (including Karafet's samples, excluding them it's just 13%). So the Philippines' y-dna is very Austronesian, only somewhat higher than in other parts of west Indonesia. Yet the Aeta, it seems, are going to be shown to be almost completely Australasian.

    It seems that Karafet didn't test M175 on these Filipino K-M526* samples.

    Are you saying that because M175 doesn't appear in the haplogroup table? If so, that table shows only 50+ SNPs which were observed, but they tested 80 or more SNPs, and I'd presume M175 would definitely have been included.

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  131. Yes, most Filipino lineages are of Austronesian origin, according to what I saw from elsewhere before. So I was pretty surprised to see so much K-M526* among Karafet's Filipino samples collected from Cebu. Majority of Filipino Y-DNA and mtDNA show close affinity with Taiwanese aboriginals, which is generally accepted.

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  132. The majority of Philippine mtDNA types are shared with Taiwanese aboriginal groups and belong to haplogroups of post-glacial and pre-Neolithic origin which have previously been identified in East Asian and Island Southeast Asian populations.

    Analysis of Hypervariable Segment I sequence variation within individual mtDNA haplogroups indicates a general decrease in the diversity of the most frequent types (B4a1a, E1a1a, M7c3c) from the Taiwanese aborigines to the Philippines and Sulawesi, although calculated standard error measures overlap for these populations. This finding, together with the geographical distribution of ancestral and derived haplotypes of the B4a1a sub-clade including the Polynesian Motif, is consistent with southward dispersal of these lineages "Out of Taiwan" via the Philippines to Near Oceania and Polynesia.

    In addition to the mtDNA components shared with Taiwanese aborigines, complete sequence analyses revealed a minority of lineages in the Philippines which share their origins - possibly dating back to the Paleolithic - with haplogroups from Indonesia and New Guinea. Other rare lineages in the Philippines have no closely related types yet identified elsewhere.

    http://mbe.oxfordjournals.org/cgi/content/abstract/msp215v1

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  133. Where did it say that Karafet's Philippine samples are from Cebu?

    ReplyDelete
  134. Here's another interesting study that I would appreciate if someone could obtain for us:

    The Human Genetic History of East Asia: Weaving a Complex Tapestry

    The Human Genetic History of East Asia: Weaving a Complex Tapestry

    Stoneking, 2010

    Y-dna from Siberia through China to SE Asia, east Indonesia and Philippines.

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  135. "Their notoriously different appearance with Malays, Indonesians, and Philippinos is a very strong argument in favor of a wave of agriculturalists swamping into southeast Asia/Indonesia from southern China".

    But that can be interpreted also as they belonging to the first wave of Karafet and the "Mongoloid" types belonging to the second wave c. 30-15 Ka ago.

    However the limited fossil data does suggest a more "Australoid" (or just "archaic") morphology in SE Asia in general (but also in all East Asia) before Neolithic, so we have what may be two (largely) different issues: genetics and phenotype.

    On the other hand, Australian fossils don't seem clearly "Australoid" either before a recent timeframe (see P. Brown's Australian page), the most archetypally AA skull is that of Roonka, which is about 7000 years old.

    So I suspect it's about time we begin considering morphology not strictly attached to genetics or ancestry. At least I do try to keep some distance from morphology when analyzing all this data because otherwise I'd go not just "hyper-recentist" but even believer in recent arrival from Mars, as there are no clear precusors for the Mongoloid type (there are not even brachi/mesocephalic Paleolithic skulls almost anywhere!, except maybe Minatogawa, but Brown says he's not Mongoloid either).

    So I'd either argue for nutrition, recent social selection for those phenotypes or wild epigenetics, rather than recent replacement from nowhere.

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  136. "Majority of Filipino Y-DNA and mtDNA show close affinity with Taiwanese aboriginals, which is generally accepted".

    That's not what it's seen here (not just Karafet but also the other references posted in this discussion by Ebizur - scroll up), as TAs are like 80-90% O1a and Filipinos (Tagalog?) are mostly O3, with just c.10% O1a.

    However I have no reason to doubt that mtDNA follows this pattern (and I have clear it does in Polynesia but again with lots of hitchhiker Y-DNA C2a2 from Melanesia). This is somewhat odd specially considering that Austronesians are generally patrilocal/patriarchal. Maybe they were matrilocal at the time of the expansion? (Weird idea maybe but many anthropologists have suggested that matrilocality is older than patrilocality).

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  137. Mongoloids are in a sense in the genes not in the morphology. Except the superficial similarities with Peking men etc. Mongoloid morphology is a fairly recent development. Prior to 20000 years ago you don't see any "Mongoloids".

    But the ancestors of Mongoloid people obviously existed prior to that.

    It has been observed in zukoten(?) etc that prior to the advent of Mongoloid morphology people in that region looked either Caucasoid or Australoid.

    The popular interpretation has been that these represent two different influxes from SE Asia and middle east but karafet's work and the discovery of M526 may suggest that they were a single stock with varying morphologies.

    Ainu for instance are Mongoloid genetically but Caucasoid morphologically.

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  138. Austronesians are generally matrilineal. Southeast Asia is a mix. Chinese are known to have been matrilineal in prehistoric times but historically have been patriarchial perhaps due to the influence from the north.

    Tungusic tribes have been known to be strictly patrilineal though not necessarilly partriarchial.

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  139. "Prior to 20000 years ago you don't see any "Mongoloids"".

    But neither do you after 20 Ka, right? One has to wait to Neolithic (i.e. after 7500 BCE in Eastern Asia) to find them at all.

    "But the ancestors of Mongoloid people obviously existed prior to that".

    I don't doubt it but they did not look "Mongoloid".

    "It has been observed in zukoten(?) etc that prior to the advent of Mongoloid morphology people in that region looked either Caucasoid or Australoid".

    Everywhere.

    I'd dare say that a vague "Caucaso-Australoid" continuum is the ancestral phenotype of Eurasians in general. But in no case the more typical local phenotypes don't appear in the fossil record before 15,000 BP (West Europe) or, more commonly, the Neolithic timeframe.

    "Ainu for instance are Mongoloid genetically but Caucasoid morphologically".

    Oh, my! Watch out that Ren will come and scold you for claiming Ainu as "Caucasoids". :D

    I don't think they can be described as Caucasoids in general, even if some individuals may look akin, but they do seem to have preserved until recently (in their local variant) that loose Caucaso-Australoid morphotype I mentioned before.

    But I'd reverse your sentence anyhow for the sake of being thought-provoking, we could well say that "Japanese are Ainu genetically but Mongoloid morphologically". It's damn tricky.

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  140. Ainu are very eastern. It has been shown that even Koreans are genetically closer to Europeans than the Ainu.
    By "genetically mongoloid" I meant "East Eurasian", distant from "West Eurasian" etc.

    Even though the full Mongoloid morphology does not appear until neolithic(called Neo-Mongoloids in anthropology), certain patterns begin to emerge from 20000 yrs ago or so.

    American Indians are thought to represent such "Early(or Paleo) Mongoloids" which had among its variations Caucasoid-Australoid pheonotype as well, as desmonstrated by numerous non-Mongoloid looking remains found throughout Americas.

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  141. "Even though the full Mongoloid morphology does not appear until neolithic(called Neo-Mongoloids in anthropology), certain patterns begin to emerge from 20000 yrs ago or so".

    Can you mention the relevant fossils (and why those and maybe not others). I don't see that clear at all (or why those would be more "Mongoloid" than, for instance, Cro-Magnon types - who also have some such patterns but are not found in the East).

    "American Indians are thought to represent such "Early(or Paleo) Mongoloids" which had among its variations Caucasoid-Australoid pheonotype as well, as desmonstrated by numerous non-Mongoloid looking remains found throughout Americas".

    I can agree with this but when we talk of Native Americans we talk of c. 15,000 BP at most, not earlier. And the oldest individuals, such as Luzia (dated to 11,500 BP) are often claimed as of "Australoid" affinity anyhow.

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  142. Aargiedude, this is the paper you're looking for, actually I've posted it above.

    The Human Genetic History of East Asia: Review
    Weaving a Complex Tapestry

    http://download.cell.com/current-biology/pdf/PIIS0960982209020673.pdf?intermediate=true

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  145. The Filipino samples in this paper are the same sets of Filipino samples in the another paper referring to Balinese Y-DNA. The map in the paper shows the sample location lies near Cebu. Not sure about the exact location, but I remember reading it somewhere.

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  146. Aargiedude, this is the paper you're looking for, actually I've posted it above.

    Thanks! :)

    The Human Genetic History of East Asia: Weaving a Complex Tapestry

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  149. mtDNA of Aeta people are 89.2% of "9 bp deletion", which is haplogroup B?

    Mitochondrial DNA Polymorphism among Five Asian Populations

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1715355/pdf/ajhg00118-0024.pdf

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  150. to aargiedude:

    In the paper I provided, there's some problem inside.

    The majority of Mongolian Y-DNA should be C-M217, not C-M130; Korean haplogroup C should mostly be C-M217, not C-M130.

    And the majority of Chinese Y-DNA should be O-M122, rather than F-M89.

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  151. Looks like some very strange oddities in the substructure of the Indian lineages in Indonesia. J*, H*, etc. And then there's something else. The distribution of the Indian lineages (H, J, L, R1a, R2) seems to have a sharp drop-off right along the Wallace Line! I've been gathering all the studies I can of Indonesia and nearby areas, and tomorrow, hopefully, I'll be able to show this clearly in a map. But you can already see for yourself in Karafet's study (linked several times in this thread).

    Bali has 62/641 "Indian" samples, or 10%, while the rest of west Indonesia has 13/185, or 7%. The 'Wallacean' islands have 3/957, or 0,3%, a difference of almost 30-fold with respect to west Indonesia!

    Did historic Indian movements into Indonesia stop right along Wallace's Line for some odd reason? Or is it possible these haplogroups have existed for a lot longer than we think they did based on our age estimate models like TMRCA?

    mtDNA of Aeta people are 89.2% of "9 bp deletion", which is haplogroup B?

    I didn't see a reference to any 9 bp deletion. But if it's there, yes, that's mtdna B. The results, from 1988 (!), are in RFLP format, they have to be "translated". I didn't understand them, frankly. I think they showed 90% of Aeta had AvaII type 1. I found a reference saying type 8 was equivalent to mtdna W. I think Ann Turner posted a good "translation" guide at rootsweb. I was looking at it last month while trying to understand some mtdna studies of American Indians from the 1990's.

    Thanks for the observation about "The Human Genetic History of East Asia: Weaving a Complex Tapestry", I'll keep that in mind when I read it.

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  152. "Did historic Indian movements into Indonesia stop right along Wallace's Line for some odd reason?"

    The only reason might be that of centrality and cosmopolitanism. But if would be that, we'd find them more in Java and Sumatra, not in Bali. There was no real sea barrier for the Vijayanagar traders and the Muslim ones who followed their trail, obviously. As they traded in spices largely, we should find some of their trail towards Halhamera, I presume... but we don't.

    The concentrations of such rare lineages in Bali is odd in any case.

    "mtDNA of Aeta people are 89.2% of "9 bp deletion", which is haplogroup B?"

    It can be B for what I could find at this site (in Spanish): "El análisis de la deleción de 9-bp (característica del linaje B)"...

    There are two papers with that notice in their title but both are pay-per-view: one is about Chinese and Austronesians and the other about South Indians.

    It doesn't look like a safe marker in any case when taken alone. I suspect it might be listed at PhyloTree as 8281-8289d. But this is also a marker of the following happlogroups: L0a2, M1a1d, D4b1b2, I5a1, A2d1, T2f and K1a11.

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  153. S.S. Alemohammad et al. Distribution of Mitochondrial DNA Intergenic COII/tRNALYS 9 bp Deletion in Iranian Populations. Iranian J Publ Health, 2003. (PDF open access).

    It gives apportions of the said 9 bp deletion through the world and mentions (in spite of being somewhat old) that the marker is not only found in haplogroup B.

    It has a presence in Africa with several samples being over 20%. It's also found at lower levels in West Eurasia.

    Essentially: alone it is an unreliable marker and that may be the reason why there's not anymore a single haplogroup B listed at PhyloTree but R11'B7 and B4'5.

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  154. Natsuya: the link you produced doesn't say much (it's a very old paper from 1988). It just says that Veddas are most distant from all and then Aetas follow, what makes total sense considering that the other three populations are Ainu, Japanese and Korean.

    It does not seem to mention the 9bp deletion at all.

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  155. This study is a big one. This one is truly worth obtaining.

    Genetic admixture history of Eastern Indonesia as revealed by Y-chromosome and mitochondrial DNA analysis

    Genetic admixture history of Eastern Indonesia as revealed by Y-chromosome and mitochondrial DNA analysis

    Genetic admixture history of Eastern Indonesia as revealed by Y-chromosome and mitochondrial DNA analysis
    Mona, 2009

    we investigated seven eastern Indonesian islands, including AN and NAN speakers [???] by means of nonrecombining Y-chromosomal (NRY) and mitochondrial DNA (mtDNA)

    we noted a small fraction of the NRY and mtDNA data shared between eastern Indonesians and Australian Aborigines

    Our data demonstrate a clear example of the lack of the often-assumed correlation between the genes and languages of human populations.

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  156. "Thanks goodness we have a second opinion about the age of C2 in this paper. 10Ka makes no sense whatsoever".

    You're still an idiot Maju. 10k is the time C2 expanded to Melanesia, not the time it arrived in SE Asia. So your comment, 'You should read the paper to realize that Karafet is proposing C2 being much older than just 10 millennia' is stupid.

    "In either scenario, it's too old to be Austronesian-original".

    Do you actually read anything anybody writes? I said, 'and then takes off east with the Austronesians as C2a2 about 4kya'. I didn't claim it was an 'Austronesian-original'. It joined them.

    "It's funny, there's another area where J* was also found in abundance, and it's the island of Soqotra off the coast of Somalia. It actually made up the majority of the y-dna in that island".

    Now that's interesting. J* in Soqotra and '1 J* is in Vietnam, and 2 J* are in Bali'. To get to Soqotra you need fairly good boats.

    "I wonder if these K-M526* are related to pre-Austronesian lineages".

    I would guess so.

    "rather than K or, as Terry seems to believe, MNOPS"

    Wrong. I believe with KMNOPS.

    "Their notoriously different appearance with Malays, Indonesians, and Philippinos is a very strong argument in favor of a wave of agriculturalists swamping into southeast Asia/Indonesia from southern China".

    And probably from even further north: northern China, specifically the Yangtze valley.

    "Yet the Aeta, it seems, are going to be shown to be almost completely Australasian".

    I'm not surprised. The speed of the Austronesian migration suggests they were moving mostly through uninhabited islands. So humans had died out through much of Wallacea as sea level rose, isolating the populations.

    "I was pretty surprised to see so much K-M526* among Karafet's Filipino samples collected from Cebu".

    The simplest explanation is that pre-Austronesian humans may not have died out on that island. Survival or extinction would have been pretty much a lottery.

    "It has been observed in zukoten(?) etc that prior to the advent of Mongoloid morphology people in that region looked either Caucasoid or Australoid".

    So I'd guess that the 'Mongoloid morphology' developed somewhere else.

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  157. AN = Austronesian
    NAN = non-Austronesian

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  158. Genetic Admixture History of Eastern Indonesia as Revealed by Y-Chromosomeand Mitochondrial DNA Analysis

    I've put it on Zoho.

    http://viewer.zoho.com/docs/r62wj

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  159. "You're still an idiot Maju. 10k is the time C2 expanded to Melanesia, not the time it arrived in SE Asia. So your comment, 'You should read the paper to realize that Karafet is proposing C2 being much older than just 10 millennia' is stupid".

    And you are blackmouth and surely more of an idiot than I am.

    I have no particular reason to believe that MCH-hunch is better than others. And anyhow you said C2, not C2a.

    "Do you actually read anything anybody writes?"

    I'm going to start not reading you because your tone is highly annoying and your conversations are not that informative anyhow: loads of heated discussion and too little fructifying exchange.

    "And probably from even further north: northern China, specifically the Yangtze valley".

    So topical. So you think that the Zhoukoudian people, who are also obviously non-Mongoloids were the ancestors of those people.

    And you prefer to ignore the fact that the first known Neolithic of East Asia is from further South (Hunan) and that it's also the Neolithic that domesticated rice, which is the one that was most successful in the region.

    "So humans had died out through much of Wallacea as sea level rose, isolating the populations".

    That's really an unbelievable claim. And that's what I mean when I say that, after a whole year (or more) of discussing with you, you still have no problem in claiming such absurd ideas just because they are convenient to your pre-conceptions.

    This paper seems to evidence that Austronesian colonization only had a limited impact in almost all places, so there was already people before they arrived.

    "So I'd guess that the 'Mongoloid morphology' developed somewhere else".

    Or everywhere else.

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  160. I've been reviewing the mtDNA data at the Mona paper (eastern lesser Sunda islands) that so gently has been provided by Natsuya and converting it to percentages by language group (simplifying a bit just out of laziness).

    My impression is that the main Austronesian-related lineage in that area is not B (which is only weakly related and not even that in the case of B4) but F1a. Then come the "Polynesian Motif" (whatever that means), pre-Z (M8?, CZ?), R14 and N12.

    These above show a clear Austronesian language preference.

    Weakly Austronesian are M7a, B5, P, B*, Y2 and M42. P is surely from Melanesia and M42 is an Australian lineage, if I'm correct.

    You may add here B4b1 (but not B4 as a whole).

    The rest of haplogroups are even, weakly pre-Austronesian or clearly pre-Austronesian. I'd say all these should be pre-Austronesian, logically. They are:

    Even: Q and B4 (but notice the note above about B4b1).

    Weakly NAN: E1 (E1a is even).

    Markedly NAN: other, D, R9c, M7b and U2. The odd man here is U2, an Indian/Central Asian lineage.

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  161. Maju, have you read this paper before?

    A Mitochondrial Stratigraphy for Island Southeast Asia

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1876738/

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  162. And also:

    Traces of Archaic Mitochondrial Lineages
    Persist in Austronesian-Speaking Formosan Populations

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1166350/pdf/pbio.0030247.pdf

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  163. I'm pretty sure I read the Hill paper before but surely not with enough attention, so it's good that you produced that link in the context of this discussion.

    The one on Taiwan Aboriginals is new to me, I believe.

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  164. From the paper:

    All told, these potential Out of Taiwan lineages (M7c1c, D5, Y2, F1a3, and F1a4) account for only ~20% of the current data set. This is superficially similar to the results found for the Y chromosome by Capelli et al., who also found that ~20% of their ISEA sample could be accounted for by possible Taiwanese haplogroups.

    This conclusion seems to correspond to Karafet's conclusion that suggests only <20% of Indonesian Y-DNA were derived from "Out of Taiwan" neolithic farmers.

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  165. I'm pretty much surprised that R9c is said to be Austronesian by Trejaut, when among East Lesser Sunda peoples it is much more frequent among non-Austronesian speakers (7.0%) than among Austronesian ones (2.9%).

    I imagine that this is because a possible Indonesia->Taiwan pre-AN migration has not been taken in consideration. Usually the first answer to a puzzle like this is to resort to the best known (and hence most recent) migrational flows but this simplistic approach has shown often to be wrong.

    However I don't think I can judge the matter of East Asian mtDNA in such detail yet, so I'm open to other opinions. I'm just learning as we talk...

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  166. I'm not familiar with R9c, but I do remember that Trejaut claimed haplogroup E represents a post-glacial/pre-neolithic expansion from Island Southeast Asia to Taiwan about ~8,000 years ago.

    Climate Change and Postglacial Human Dispersals in Southeast Asia

    http://mbe.oxfordjournals.org/cgi/content/full/25/6/1209

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  167. "All told, these potential Out of Taiwan lineages (M7c1c, D5, Y2, F1a3, and F1a4) account for only ~20% of the current data set. This is superficially similar to the results found for the Y chromosome by Capelli et al., who also found that ~20% of their ISEA sample could be accounted for by possible Taiwanese haplogroups".

    Plus B4b1(a). And sure that I did not even pay attention to D5 but it does seem Austronesian too (unlike other D).

    However, the Karafet proposal includes O3a3(xO3a3b), which is a small haplogroup among Taiwanese but the largest part of the supposed wave. So we may be again at a case of matrilocal Y-DNA hitchhiking, similar to that of C2a2 in Polynesia.

    O1a2 (80-90% in Taiwan) only accounts for 2.4-3.8% in Indonesia, while the bulk of the alleged Austronesian Y-DNA is O3a3(xO3a3b) which is rather rare in Taiwan and is probably "borrowed" from some other source.

    I think some researcher has suggested that before but not sure who nor when.

    "I'm not familiar with R9c, but I do remember that Trejaut claimed haplogroup E represents a post-glacial/pre-neolithic expansion from Island Southeast Asia to Taiwan about ~8,000 years ago".

    E seems SE Asian indeed, maybe from the islands. Nobody is probably too familiar with R9 - is one of those minor lineages that only serves to get you even more confused. :)

    I did argue above that O1a (or at least O1a* and O1a1) looks like coalescing at Sundaland, unlike the other 2nd wave O lineages (per Karafet 2010). If so, it would suggest that the overall coalescence area of O1a was at Sundaland and that the Taiwanese (and Austronesian-specific) O1a2 is a derivative.

    This double direction migrational flow makes things more complicated. Anyhow, per Karafet, the migration out of Sundaland should be in the 30-15 Ka period, rather than just 8000 years ago.

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  168. The D5 found in Island Southeast Asia is D5d, a subgroup of D5b, which is different from another widespread branch D5a. D5a is seen in China, Japan and other East Asia populations, but also lower in Siberia and Finland. Ex: My mtDNA is potentially D5a2a, which is East Asian, rather than Austronesian.

    I think most O3* previously found in Taiwan aboriginals are atually O3a3-P201*. The marker P201 is very new, we shall see more results in the near future. And also, most Taiwan aboriginal O1a* could be O1a1-P203.

    The ultimate origin of O1a-M119 is in southern China/mainland SEA. From the homeland, O1a spread via two routes, one to Taiwan and one to Southeast Asia, which means they belong to different branches. The majority of Indonesian forms are of mainland SEA origin, but in neolithic, some Taiwanese forms, such as O1a1-P203 and O1a2-M110, also reached Indonesia. Indonesia is where mainland SEA branch of O1a and Taiwanese branch of O1a met in neolithic. Therefore, we could consider Indonesian forms as a mixture of lineages from both mainland SEA and Taiwan.

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  169. O1a2 isn't the majority of Taiwan aboriginals.

    From data I saw before, Taiwan aborignal Y-DNA go like this:

    O1a-M119* = 65.4%
    O1a2-M110 = 16.7%
    O3-M122* = 8.6%
    O2a* = 1.9%
    O2a1 = 2.5%

    But the data was published some years ago. O1a1-P203 and O3a3-P201 are new found haplogroup. I assume that most of Taiwan aboriginal O1a*/O3* are actually O1a1/O3a3.

    We shall know that Taiwan aboriginals are not homogenous. There are a least over 10 different populations of them, and all of them speak different languages.

    The Amis tribe has 20% O3-M122*, which I suppose they're O3a3-P201.
    The Bunun tribe has 58.8% O1a2 and 17.6% O2a1.
    And Atayal tribe has 95.5% O1a-M119*, which I think they're mostly O1a1-P203.

    http://web2.nmns.edu.tw/PubLib/NewsLetter/98/259/a-4.pdf

    See the page 5 of the article, it's Chinese, but you can see haplogroup frequenies in 9 tribes of Taiwan aboriginals.

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  170. Another English paper referring to the origins of Island Southeast Asian Y-DNA, especially O1a-M119:

    Paternal genetic affinity between western Austronesians and Daic
    populations

    Note: we have to know, when this paper was published, they had not found O1a1-P203 and O3a3-P201 yet, so the conclusions they made is not right. It's like we ignore the new downstream SNPs of R1b1b2, and compare all the STRs of different subclades, which is not very appropriate.

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408594/pdf/1471-2148-8-146.pdf

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  171. "O1a2 isn't the majority of Taiwan aboriginals".

    As I told you at Leherensuge you seem to be totally correct about that. My bad.

    "The ultimate origin of O1a-M119 is in southern China/mainland SEA".

    Not sure about South China/Taiwan but at the Karafet paper, the highest STR diversity for O1a is at Indonesia (O1a at West Indonesia and O1a* at East Indonesia). Mainland SEA has comparatively low diversity levels for this lineage.

    This is also the case for O1a1, with West Indonesia leading the table for the four considered regions.

    "It's like we ignore the new downstream SNPs of R1b1b2, and compare all the STRs of different subclades, which is not very appropriate".

    Totally agree but that does not stop some supposed experts from doing such atrocities (and others to follow their trail).

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  172. Natsuya, thanks so much for all that info! Could you post the supplementary data of this study?

    "Genetic Admixture History of Eastern Indonesia as Revealed by Y-Chromosomeand Mitochondrial DNA Analysis"

    It's supposed to have haplotype info for y-dna and mtdna.

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  173. Natsuya, I'm making an xls file with the results of all these studies, I'm hoping to finish soon, then I'll upload it here. If you or someone who knows Chinese could translate the y-dna table of Taiwan aboriginal results, I could add that to the file. I could add it now, but I'd prefer if I knew better what it's saying. Just the y-dna table, not the study.

    http://web2.nmns.edu.tw/PubLib/NewsLetter/98/259/a-4.pdf

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  174. Back to Karafet and Indonesia... the Indian anomalies just keep on coming!!

    There are 2 R1b1* samples from Bali. Specifically, they're P25(xM269). Amongst known haplogroups, this reduces the possibilities to just 2 lineages.

    It could be R1b1*/R1b1a, which is exceptionally rare in West Europeans, and is very rare amongst Middle Easterners, Egyptians, North Africans.

    Or it could be R1b1b1 (M73), which is the Central Asia variety of the R1b clade.

    A European origin is simply out of the question. Having been found with just 2 R1b1b2 (M269) samples (also in Bali), it's statistically extremely unlikely that these 2 R1b1(xR1b1b2) samples could have come from Europeans. The frequency of R1b1(xR1b1b2) in Netherlands, the colonial master of Indonesia, must be 0,1%, or less even.

    That leaves an Indian origin as a possibility. Sengupta tested 900 Indian/Pakistani samples for M173 (R1), M73 (R1b1b1), M17 (R1a1a), and M269 (R1b1b2). He found 8 R1b1b1, but they were all from Hazara refugees living on the Pakistani border who fled from central Afghanistan. I think we can discard the Hazaras as representative of typical Indo-Pakistanis, so Sengupta didn't find a single sample of M73 in almost 900 samples. What about R1b1*? He found a single sample of R1(xR1a1a,R1b1b1,R1b1b2), but its haplotype looks like R1a, especially with 392=11 and 439=10, values that are extremely rare or unknown in any R1b1* sample. That's it. Basically not a single case, out of almost 900 samples that were taken from many different places in the sub-continent. Yet we have 2 samples of this haplogroup in Bali, out of a pool of supposed Indian origin samples that amounts to 80 or 90 samples (between H, J, L, R1a, and R2).

    To recap: the J samples include several J*, an extremely rare haplogroup within the J clade, the H samples are overwhelmingly H*, while back in India they make up a small fraction of the H clade, and the R1b samples include 2 cases of R1b1(xR1b1b2), which is near impossible to reconcile with a historic European or Indian origin.

    And!... The Indian haplogroups are just as sharply divided by the Wallace Line as are the C, K, O, and S lineages.

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  175. R1b1* should have a West/Central Asian origin. However finding them in Bali of all places is most odd, as they are non-Muslim and Hinduism never penetrated in West Asia.

    ReplyDelete
  176. "I'm going to start not reading you"

    So could you please explain what it is you plan to do differently?

    "So you think that the Zhoukoudian people, who are also obviously non-Mongoloids were the ancestors of those people".

    Why would I think that? It's already been explained that they weren't Mongoloid.

    "the first known Neolithic of East Asia is from further South (Hunan) and that it's also the Neolithic that domesticated rice, which is the one that was most successful in the region".

    The first Neolithic in Hunan did not have rice, and it's probably connected to the Hoabinhian in some way. Rice was a later domesticate and, as you say, allowed a huge expansion which replaced the Hoabinhian.

    "This paper seems to evidence that Austronesian colonization only had a limited impact in almost all places"

    No. The longer the discussion goes on the more obvious it's becoming that the Austronesian influence was substantial through island SE Asia, and even into the mainland to some extent. Their expansion gave rise to substantial movement backwards and forwards through the region. As you say, 'This double direction migrational flow makes things more complicated'.

    "Anyhow, per Karafet, the migration out of Sundaland should be in the 30-15 Ka period, rather than just 8000 years ago".

    Probably both. One around the time of Hoabinhian formation and one leading up to the Austronesian expansion.

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  177. "So could you please explain what it is you plan to do differently?"

    It's simple: I read Terry, I read Wallacea, I skip the whole message. I have done with others before, so don't fuck me.

    I'm patient and tolerant but up to a point.

    "Why would I think that? It's already been explained that they weren't Mongoloid".

    But they are the Paleolithic inhabitants of the area where you said such phenotype originated. Can you please make any sense?

    "The first Neolithic in Hunan did not have rice"...

    Can you document yourself? Read at least Wikipedia, please!:

    "Analysis of Chinese rice residues which were Carbon-14 dated to 8200-7800 BCE show that rice had been domesticated by this time.[3]"

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  178. to aargiedude:

    The supplementary data of

    http://viewer.zoho.com/docs/mSeDg
    http://viewer.zoho.com/docs/sSdTb
    http://viewer.zoho.com/docs/fScJh
    http://viewer.zoho.com/docs/lScgh
    http://viewer.zoho.com/docs/eSbbl
    http://viewer.zoho.com/docs/uSbfi
    http://viewer.zoho.com/docs/mSbQc
    http://viewer.zoho.com/docs/qSacx
    http://viewer.zoho.com/docs/sSa4c

    ReplyDelete
  179. to aargiedude and maju:

    I just found that the Taiwan aboriginal Y-DNA data (in the Taiwan study written in Chinese) was cited right from this paper:

    Here's the link:

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408594/pdf/1471-2148-8-146.pdf

    Please see the Table 2 of the paper.

    There are Y-SNP haplogroup frequencies of 11 nations of Taiwan aboriginals.

    The 11 tribes are Amis, Pazeh, Makatao, Thao, Paiwan, Atayal, Rukai, Pyuma, Tsou, Bunun, Saisiyat.

    Note: They use old names on Y-SNP haplogroups.
    O3a4 is now O3a3b-M7.
    O3a5 is now O3a3c-M134.
    O3a5a is now O3a3c1-M117.
    And they had not found O1a1-P203 and O3a3-P201 back then. So those O1a*/O3* could be O1a1/O3a3 in Taiwan aboriginals.

    As for the distribution of the tribes in Taiwan, you can see the map of this paper:

    http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1166350&blobtype=pdf

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  180. I appreciate your effort, Natsuya but I began this morning to look at some of the mtDNA data alone (the Hui Li paper in fact) and, after a while, I decided that I could easily go crazy trying to decipher the labyrinth of haplogroups and subhaplogroups that criss-cross the East Asian human landscape.

    The only thing that I have more or less clear at the moment is that there have not been real boundaries in mainland East Asia, from Wallace Line to where I can gather in Siberia: no clusters anywhere, just clines and clines overlapping each other.

    At this point I need to relax on this issue, at least till I figure out a strategy for understanding this complexity, which is probably to totally forget about Austronesians and other details and begin looking at the distribution (and diversity if known) of the top level clades, and then gradually go to lower levels in the phylogeny.

    But by the moment I'm taking a mental vacation from the whole matter.

    Enjoy.

    ReplyDelete
  181. "But they are the Paleolithic inhabitants of the area where you said such phenotype originated".

    Rubbish. I said the phenotype must have originated somewhere else. I made no attempt to say where. In fact I don't know.

    "Analysis of Chinese rice residues which were Carbon-14 dated to 8200-7800 BCE show that rice had been domesticated by this time.[3]"

    And the Hoabinhian was ending about that time, probably being replaced by rice-cultivators moving south.

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  182. I make absolutely no sense of your claim of "rice cultivators moving south" when the Pengtoushan Neolithic is the first one that has rice, it seems (and also the oldest of Neolithic of China and very possibly of all East Asia, at least as far as archeology has been able to attest). Also further North they were specialized in sorghum (logically, because of climate imperatives).

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  183. aargie dude, about the J*, I think a good deal of the Yemeni Arab heritage in the Malay world is Soqotran.

    Maju, stop baiting me. I don't respond to silly, uninformed comments anymore.

    ReplyDelete
  184. "Maju, stop baiting me".

    Sorry, it was too good to help. :D

    ReplyDelete
  185. Indonesian y-dna & mtdna studies up to Karafet (2010).xls

    This file has y-dna and mtdna data from all the studies I could find in the last week about Indonesia, New Guinea, and whereabouts.

    I've finished doing the map of the distribution of Indian lineages in this region (H, J, L, R2, R1a), and it's very interesting, maybe I'll be able to post it in a few hours. They are just as sharply divided by Wallace's Line as the paleolithic haplogroups. Also, Bali doesn't have a high frequency of these western lineages, as it appeared from Karafet's study. They're just typical for a west Indonesian isle.

    ReplyDelete
  186. *thumbs up*

    That's a major effort, thanks a lot, Argiedude. :)

    At the Hammer'06 table (mtDNA) you mention: "Others The columns don't add up to 100% and I presume the missing percentage are other haplogroups (H, U, X, etc.) that aren't shown".

    On first thought I was going to say that rather than those Western lineages, they are much more likely to be unsampled Eastern ones, like M8(xCZ), M9(xE), N9(xN9a6)...

    However they did test for M, N and R, so it just does not make any sense.

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  187. "I've finished doing the map of the distribution of Indian lineages in this region (H, J, L, R2, R1a), and it's very interesting, maybe I'll be able to post it in a few hours. They are just as sharply divided by Wallace's Line as the paleolithic haplogroups. Also, Bali doesn't have a high frequency of these western lineages, as it appeared from Karafet's study. They're just typical for a west Indonesian isle".

    That sounds very interesting too.

    An oversampled West Indonesian island...

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  188. Maju, I thought the missing lineages were West Eurasian because the highest amount of missing samples is from the westernmost population: NW China. But then again, populations like Thailand are missing 20%. What I think they did is, after determining what haplogroups were present in the populations they tested (the 11 columns on the right), they compared with the results from published studies (8 columns on the left), but only for the precise exact haplogroups that were discovered in their studied samples (mainly Indonesian), discarding any haplogroup found in the published materials that wasn't found amongst the populations tested in the present study. Maybe, I dunno.

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  189. This image has 2 maps, showing the percentage distribution of Indian haplogroups (H, J, L, R2, R1a) and of Southeast Asian haplogroups (O).

    Asia-Australasia y-dna divide - Indian vs SE_Asian.jpg

    Bali's frequency of Indian haplogroups isn't notable for a west Indonesian island, it's actually average for west Indonesia.

    The lack of Indian haplogroups east of Wallace Line is... incredible. Especially once you realize how uniformly distributed the Indian haplogroups are across all islands in west Indonesia. Keep in mind the sample sizes for most eastern islands is in the several hundreds each. To get a better appreciation of the magnitude of the difference between east and west, perhaps I should have noted the eastern percentages as 0.0% instead of 0%.

    There's a notable similarity between the diffusion of Indian haplogroups and the diffusion of haplogroup O, in that 2 islands east of Wallace's Line that have notable levels of Indian haplogroups, Sulawesi and Lombok/Sumbawa, are also the only 2 islands east of Wallace's Line that very high levels of haplogroup O. Both islands also happen to be the 2 nearest contact points between east and west, with Sulawesi next to Borneo, and Lombok/Sumbawa being the first islands eastwards of Bali. In both islands, the frequency of Indian and O haplogroups is halfway between their frequencies in east and west Indonesia.

    I think the map is very clear. We can see that the Indian haplogroups are uniformly distributed throughout all the massive area west of Wallace's Line, and then suddenly drop to virtually 0.0% to the east of it. Everything about this distribution is almost screaming "paleolithic diffusion". And as we have been discussing in this thread, there are some very interesting details about some of these Indian haplogroups that are very hard to explain as a historic diffusion, namely, the presence of J*, H*, and R1b1*.

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  190. Very interesting Argiedude, thanks.

    "The lack of Indian haplogroups east of Wallace Line is... incredible".

    True. It does suggest that they are pre-Austronesian, right?

    "There's a notable similarity between the diffusion of Indian haplogroups and the diffusion of haplogroup O, in that 2 islands east of Wallace's Line that have notable levels of Indian haplogroups, Sulawesi and Lombok/Sumbawa, are also the only 2 islands east of Wallace's Line that very high levels of haplogroup O".

    I also noticed that. It may be related to "short-distance" flows within Indonesia after (or within) the Austronesian expansion.

    The differences between "Indian" lineages and haplogroup O in the Pacific Ocean islands also suggests that these flows were unrelated to the Polynesian expansion, which was participated with lots of O (and C2a2 from Melanesia) but lack the "Indian" lineages. This suggests a split between Malays (senso lato) and Polynesians at Philippines, with Polynesians migrating directly to Micronesia and along the North Wallacea/Melanesia chain into Polynesia proper.

    "Everything about this distribution is almost screaming "paleolithic diffusion".

    Could also be pre-Austronesian Neolithic, specially in regard to some or all South Asian lineages. But in any case these don't seem to belong to the fourth recent phase D of Karafet's proposal.

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  191. "Everything about this distribution is almost screaming 'paleolithic diffusion'".

    Almost the opposite. We know that Indian influence through SE Asia was substantial. Religions have progressively been introduced from there, presumably accompanied by people, especially males. Hinduism, Buddhism and Islam have all entered the region from India.

    "There's a notable similarity between the diffusion of Indian haplogroups and the diffusion of haplogroup O"

    Which also argues for relativle recent arrival. Thre was nothing across Wallace's line to attract them.

    "It does suggest that they are pre-Austronesian, right?"

    Possibly, but not necessarily. Certainly not involved in the eastern part of its expansion. Possibly kept out of Wallacea by the Austronesians.

    "But in any case these don't seem to belong to the fourth recent phase D of Karafet's proposal".

    Could easily do so.

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  192. "Which also argues for relativle recent arrival".

    Only if you claim a massive recent demic replacement, which seems hard to prove and is clearly against what Karafet is arguing here.

    "Thre was nothing across Wallace's line to attract them".

    Spices!!!

    And there was nothing at Wallace Line to stop them if they are so recent.

    "Possibly kept out of Wallacea by the Austronesians".

    Uh? Fencing off desperately, eh?

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  193. to Argiedude:

    Thanks for the Asia-Pacific Y-DNA/mtDNA data excel.

    May I ask where those Chinese data in "Hill 2006" came from? What are the previous studies you mentioned in the excel?

    Thanks again for your effort.

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  194. Natsuya, here's the Hill study.

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1876738/

    Hill tested the samples in the 11 columns on the right, plus 78 Taiwanese, and the 8 columns on the left were included in their study as a reference from previous published studies. I suppose the study has the specific references of where each of them came from.

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  195. "Only if you claim a massive recent demic replacement, which seems hard to prove and is clearly against what Karafet is arguing here".

    I agree with Dienekes' original comment: 'isn't it strange that the authors claim a Paleolithic gene pool, while, at the same time, discovering a sharp divide? Common sense dictates that genetic distinctions across a long time span would be blurred, and there would be no sharp divide.
    Sharp divides are created by recent population movements and are maintained by insurmountable geographical barriers'.

    If Wallace's Line provided an 'insurmountable geographical barrier' it suggests that most of the Y-hap Os did not originally have sea-faring ability. Some of them borrowed it. The fact that Austronesians do not possess a common main Y-hap also hints strongly at this possibility. In other words O entered SE Asia mostly by land. The fact that some 'Negritos' now have Y-hap O is irrelevant. The groups now speak 'recently introduced' languages so probably also have absorbed 'recently introduced' Y-chromosomes.

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  196. "Common sense dictates that genetic distinctions across a long time span would be blurred, and there would be no sharp divide".

    Precisely. That's why the divide is at major biological divide: Wallace Line, which acted as effective barrier against such blurring for all that time. West and North of the barrier the genetic pool has no sharp divisions whatsoever.

    "Sharp divides are created by recent population movements"...

    I can't imagine how you came to that conclusion.

    "... and are maintained by insurmountable geographical barriers".

    There are no such absolute barriers. But there are barriers that are difficult enough to keep gene flow at levels that are effectively indistinct from zero.

    There are also less densely populated areas that act as buffers against genetic flow, such as NE India, Eastern Iran or Central Asia, absorbing most of the flows in either direction and keeping the possibility of noticeable genetic impact at the other side extremely low.

    These two types of barriers are very similar in their effective function and are only overcome when there is nothing (or almost) at the other side (founder effects) or when technology (such as horses or camels or ships) alters the situation in a fundamental sense.

    "If Wallace's Line provided an 'insurmountable geographical barrier' it suggests that most of the Y-hap Os did not originally have sea-faring ability".

    It was not insurmountable, just challenging enough to make sure that the few occasional arrivals in either direction were absorbed and "drifted out", as statistically should happen sooner or later, with all minority components when the population is at Paleolithic levels.

    "The fact that some 'Negritos' now have Y-hap O is irrelevant".

    Not if O and its subclades are as old as 30 or 40 Ka and specially if the Negrito subclades are different and found at higher levels than among surrounding populations. And not as well if Negritos don't have other lineages that represent the older substrate.

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  197. This paper finds a similar ancestry cline using ancestry informative SNPs on the X and autosomes:

    http://massey.genomicus.com/publications/Cox_2010_ProcRSocB_v277_p1589.pdf

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  198. Thanks for that link. Good old Massey University, where I got my degree. But I'm sure Maju will claim the article is too old to be useful. After all it dates as far back as January of this year. However the article merely expands on what anthropologists in the region have accepted for more than twenty years. People in island SE Asia are a mix of two originally distinct phenotypes.

    Also note, Maju, where the authors place Wallace's line: To the west of the Philippines. They include the Philippines in Wallacea, although genetically the Aeta are mostly Asian.

    "That's why the divide is at major biological divide: Wallace Line"

    It's not really at the line. It's a little east of it, especially in the south (and in the Philippines).

    "Not if O and its subclades are as old as 30 or 40 Ka and specially if the Negrito subclades are different and found at higher levels than among surrounding populations".

    The authors seem to accept that the Aeta are different to some extent: their Y-haps are relatively recent 'Asian' immigrants whereas the Aeta mtDNA is (unusually for the region) pre-Asian to a surprising extent. The authors also seem quite prepared to maintain that the 'Asian' phenotype is relatively recent into SE Asia, and came from the north. They are very reluctant to place it in the Paleolithic, although they do concede it's remotely possible some elements may be that old.

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