RSS

Very skeptic on claim of Neolithic flow from India to Australia

17 Jan
I feel quite skeptic about the claims held by this paper but in any case it is worth mentioning.
Irina Pugach et al., Genome-wide data substantiate Holocene gene flow from India to Australia. PNAS 2013. Pay per view (6-month embargo, then freely accessible) → LINK [10.1073/pnas.1211927110 ]

Abstract

The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early “southern route” migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India. 

The evidence for this claim is all derived exclusively by statistical inference on autosomal DNA. Suspiciously enough, even if the authors claim admixture levels of as much as 11% and as recent as a mere 4000 years ago, no patrilineage (Y-DNA) nor matrilineage (mtDNA) [correction: see update below] has been ever detected that could be associated with this purported migration. 
Additionally c. 4000 years ago Southern India, the alleged origin of the genetic flow, was already immersed in a flourishing agricultural economy and it looks very strange that the migrants, people who were exchanging crops with Africa for example, would not carry a single element of this new economy to the island continent. Of course this inconsistency could easily be fixed by merely arguing that the molecular clock estimates used tick too quickly, which is a general problem anyhow and therefore no real surprise.
If the hypothesized migration happened earlier, in the Epipaleolithic or Late Upper Paleolithic, then it would also be easier to explain that, with smaller populations, genetic drift could have caused the extinction of whatever Indian uniparental markers that the migrants carried with them initially. It still causes my eyebrows to rise instinctively. 
Even then, if this was the case, we should be able to identify some sort of techno-cultural elements that the migrants may have carried with them, like microlithic stone technologies or whatever. As far as I know nothing of the like exists. 
The only techno-cultural burden that the migrants might have brought with them to Australia would therefore have been the dingo, but this dog has lots of relatives in Island SE Asia, where the authors could not detect any significant Indian admixture.
So the hypothesis looks weak to me. Let’s see the evidence they present:

Above we can see the ADMIXTURE K=4 result, probably not the optimal one (which would probably produce an Australian-specific cluster (mostly but not fully masked as Papuan) and surely two different Indian ones, partly masked as European and Onge affinity) but the one the authors decided to show us as evidence for their hypothesis.
Not only this is surely not the optimal clustering level but also Australian Aborigines are comparatively undersampled, while Indian weight is overwhelming. This is a clear example of how NOT to design a scientifically useful sampling strategy for ADMIXTURE-like comparisons like this (because oversampled populations tend to overshadow the rest just by the weight of numbers). 
As it is, this graph proves nothing but rather suggests that some Indian affinity is part of Australian Aborigine ancestral or founder specificity, when compared with Papuans. This may have many explanations first of which is a mere artifact by reason of a poor sampling and depth design of the experiment. ADMIXTURE is a powerful neutral tool, just a like a test tube or the Geneva particle accelerator, but what we do with it may well not be neutral, either by reason of mischievous manipulation or mere error.
In this case I find the test very poorly designed and executed. If I have some time later in the weekend, I may try to perform an alternative test according to my humble possibilities – I promise nothing however.
A complementary test that the authors perform used Tree Mix. As I have discussed elsewhere, TreeMix often produces very strange results and I do not consider it a reliable tool at all, but for whatever is worth here it is what they got:

While the purported migrations generated by the Tree Mix algorithm appear to suggest a secondary genetic flow from India to Australia (orange arrow at C) the data on which such result is based (D) only gives the most tenuous level (green) of extra genetic affinity between Southern Indians (DRA) and Australian Aborigines (AUA). Meanwhile the highly questionable algorithm identifies Dravidians and North Chinese (CHB) as being genetically very close (blue), when they are not in fact.
So what do I get from this paper? TreeMix’ usual senseless noise and apparent mismanagement of ADMIXTURE, a powerful tool when used properly.
Less than inconclusive, I’d say. But your take of course.

Update: G Horvat (see comments) points me to Kumar 2009 (so far unchallenged at PhyloTree)  for a shared mitochondrial lineage between Australia and India, known as M42. This haplogroup has the following structure (each → indicates a coding region mutation according to PhyloTree, Kumar originally listed a few more):
    • → M42’74 
      • → M42 
        • →→→→ M42a (Australian Aborigines)
        • → M42b (India)
      • →→ M74 (South China, Vietnam, India)
This allows for a potential mtDNA backing of this purported connection, however it is a very small lineage and Kumar claimed that M42 coalesced long ago, in the context of the first colonization of Asia and Australasia by Homo sapiens:

The divergence of the Indian and Australian M42 coding-region sequences suggests an early colonization of Australia, ~60 to 50 kyBP, quite in agreement with archaeological evidences. 

Yet the relatively long stem leading to M42a does allow for a later time-frame of arrival to Australia. Neolithic anyhow looks still most unlikely to me.

Update (Jan 18): Dingo DNA:

An important element to consider here are the origins of the dingo as the Australian wild dog is known. This dog variant suffered a strong founder effect upon arrival to Australia described mainly by two variants of the haplotype A29. This lineage only links to East Asia however, having arrived almost without doubt, via Indonesia from mainland East Asia (either Indochina or China or both).

It is clearly not related to Austronesian expansion and could have arrived either within the early Neolithic of ISEA (arguably Austroasiatic in language) or even earlier. At least one of the papers I checked rather supports a pre-Neolithic introduction and certainly before the archaeologically supported age of c. 3000 years ago.

The Y-DNA of dingos also shows a strong founder effect (only two haplotypes, with overlapping but distinct distributions) and again the most obvious connections seem to be in SE Asia.

See (freely accessible):

Update (Jan 18): It is probably interesting also to mention that Australian Aborigines show no difference with Papuans in their overall amount of Denisovan ancestry. This also appears as contradictory with the idea of significant external admixture, which should have diluted at least minimally that Denisovan component (Indians have none).

Update (Apr 7): A new “working paper” has been published on this matter, sharing my critical stand towards the sloppiness of Puhach’s team but still considering plausible a Holocene gene flow from India. I have commented in a new entry.

    Advertisements
     
    122 Comments

    Posted by on January 17, 2013 in Australia, autosomal DNA, India, South Asia

     

    122 responses to “Very skeptic on claim of Neolithic flow from India to Australia

    1. G Horvat

      January 17, 2013 at 7:32 pm

      With regards to mtDNA links, there was this paper but the conclusion is not too certain, IMO, due to the frequent recurrence of mtDNA mutations: http://www.biomedcentral.com/1471-2148/9/173I've been trying to locate references to A29 dog mtDNA sequences in India. I thought the sequences closest to those of the Dingo were all in SE Asia.

       
    2. Maju

      January 17, 2013 at 9:15 pm

      Good find, thanks. As far as I can check the claim has not been challenged so far and the survey was done on full mitochondrial sequences first submitted to the Anthropological Survey of India, 27 on 14-OCT-2008. All branches are described by one or more coding mutations, looking pretty solid to me. Refs. http://www.phylotree.org/tree/subtree_M.htm, http://www.ncbi.nlm.nih.gov/nuccore/FJ380216 (and others taken from the PhyloTree source). However notice please the extremely contradictory age estimates, with Kumar claiming that:The divergence of the Indian and Australian M42 coding-region sequences suggests an early colonization of Australia, ~60 to 50 kyBP, quite in agreement with archaeological evidences. Another element to consider is that the related lineage M74 is found in SE Asia (South China, Vietnam) as well as India (Nihal), according to the info we have been gathering in the wiki. This lineage does suggest a flow from South Asia to SE Asia and Australia (maybe together both branches or maybe not). However, judging from Kumar's estimates (or even shortening them somewhat) that would have happened within the wider wave colonization of East Asia and Australasia from South Asia. Even if we'd consider it (tentatively) a secondary "late" wave it does not look "recent", hanging M42'74 just one coding region (CR) mutation away from M and M42 one mutation downstream from M42'74. On the other hand, the Australian branch hangs downstream of 5 CR mutations (judging from Kumar'09) what allows for a longer coalescence, maybe still in South Asia (or half-way, in a "lost" SE Asian locality). Even in the latter case, I still find it extremely difficult to believe in a Neolithic time-frame for this arrival to Australia. As for the dingo I can't say. I thought that their DNA had been sequenced and compared but a search I performed earlier produced no results other than morphological comparisons with Island SE Asian and also Indian dogs. Both seem related but the closest ones are probably those from Indonesia.

       
    3. G Horvat

      January 18, 2013 at 12:50 am

      Maju – Do a search for the following terms in Google Scholar: Dingo A29 mtdna. There has also been at least one Dingo Y chromosome study.

       
    4. Raimo Kangasniemi

      January 18, 2013 at 2:52 am

      When it comes to agriculture, immigrants not bringing it with them, this might have been a very small group of people ending up in Australia unintentionally without seeds etc and incapable of keeping up their way of life – if the immigration even happened.That said, last year archaeological evidence was found for Lapita culture in the Torres Strait Islands, dated at about 3000 years ago. It wouldn't have been a long step for them to get to Australia after that, so similar claims like the Indian connection might come up from that direction.

       
    5. Maju

      January 18, 2013 at 5:46 am

      Nobody questions that the agricultural peoples of SE Asia and Melanesia could reach Australia and in fact did… punctually and without other obvious long-term consequences than the introduction of the dingo. The question here is about a necessarily larger and more consolidated migration, which was able to influence Australian Aborigines as much as 11% of their ancestry (curiously without apparently diluting the "Denisovan" ancestry, which remains as high as among Papuans).

       
    6. Maju

      January 18, 2013 at 5:54 am

      Got the mtDNA ones. I'll add a mention as update, thanks again: very useful contributions.

       
    7. Joy

      January 18, 2013 at 8:10 am

      Agree with all of the above, plus, a significant incursion of neolithic people from India would result in linguistic evidence, which has not been detected in Australia.In contrast, the Chipewyans of Canada, who speak a Na-Dene language, have only 10 percent of their genes from the later wave of migrants bearing Na-Dene culture yet were linguistically wholly transformed.

       
    8. CJ

      January 18, 2013 at 4:03 pm

      To really look at this, more data from in-between places (Indonesia, Timor, other little islands) and other Aboriginals from different parts of Australia plus more Papuans and other Melanesians are needed. There are always early adopters and late adopters or even Luddite type people for any new toolkit. That goes for the latest cell phone, fashion, and music in a modern context. Same applies for bigger techno-cultural packages.What if some of the Aboriginals were "Luddites" who had been more in touch with Island S.E. Asia until a new toolkit was introduced that they rejected. They then left or got pushed south until they eventually appear as immigrants, maybe bringing their own "Luddite" toolkit and some Indian admixture to Australia. Food for thought: http://en.wikipedia.org/wiki/Wandjina

       
    9. Ethio Helix

      January 18, 2013 at 7:03 pm

      I am in general skeptical about these model based programs ability to detect real admixture between old world populations, especially those that may already be closely related whether due to geography or ancient demographics. It is very hard for these programs to discern if reported results are due to common ancestry or really admixture, and this is because of the recombining nature of Autosomal DNA, the chromosomes simply can not be traced back to a single common ancestor.

       
    10. Maju

      January 18, 2013 at 7:14 pm

      What should be done is to make (at least) a tripartite India, Papua, AA comparison, with roughly equal-sized samples, with ADMIXTURE set with cross-validation. This tells you how many clusters are most realistic (and which K values are very unrealistic). Most probably the realist result will show no appearance of admixture but a distinct homogeneous AA cluster, maybe with minor Papuan admixture but no Eurasian one. The DIY process is described pretty well by Razib at this post: http://blogs.discovermagazine.com/gnxp/2011/03/analyzing-ancestry-with-admixture-step-by-step/ – which includes all the necessary tools to start toying around with ADMIXTURE and a good global dataset, that you can reform to your likes. Sadly that dataset does not include Australian Aborigines and I fear I am not techy enough to be able to locate and insert a sample in the dataset. So I will not do it for the time being. The "luddite" hypothesis sounds totally far fetched to me. Even if AAs would have been radical "luddites", nothing should have prevented the Indian immigrants from establishing their own successful farmer colonies – after all, according to the hypothesis proposed by Pugach they were at some point in enough numbers to be 10% of the population and AAs were organized in small hunter-gatherer bands that could pose no effective resistance against such a large number of farmers. Also, even in the worst case, some animals like goats or maybe some renaturalized crops could have prospered even after abandonment by their human masters (as presumably did the dingoes). Similar scenarios can be reconstructed for example in the Neolithic of many parts of Europe but there the 10-20% Neolithic immigrants (with haplogroups like Y-DNA E-V13, G2a, etc.) were indeed able to establish themselves as soon as they arrived, no matter how "luddite" were the aborigines (aDNA shows them still distinct some time after arrival). Not sure what you mean with your wondjina link but I discussed recently an observed paleo-climatic phenomenon that seems directly linked to that mythology: http://forwhattheywereweare.blogspot.com.es/2012/12/megadrought-may-have-affected-nw.html

       
    11. Maju

      January 18, 2013 at 7:22 pm

      Mostly agreed. If you look from many angles (different sampling strategies and such) and the results repeat in general terms (the proportions will surely vary somewhat) you can infer that those repeating patterns are saying something, looking at Fst distances (a complementary measure) and other values like cross-validation, you can get a decent idea. But it's not rocket science at all.

       
    12. terryt

      January 19, 2013 at 1:09 am

      "I feel quite skeptic about the claims held by this paper" I know you'll find it surprising but I'm inclined to agree with you. Regarding the dingo: "This lineage only links to East Asia however, having arrived almost without doubt, via Indonesia from mainland East Asia" That is a huge problem for the authors and perhaps shows that the dingo is a separate issue. "Even then, if this was the case, we should be able to identify some sort of techno-cultural elements that the migrants may have carried with them, like microlithic stone technologies or whatever. As far as I know nothing of the like exists". We do have ther Pirri points. Unfortunately all the references I could find are to extracts from books, but try this one: http://www.archaeologywordsmith.com/lookup.php?category=&where=headword&terms=Pirri+pointThe small tool tradition does match the date suggested reasonably closely. "The divergence of the Indian and Australian M42 coding-region sequences suggests an early colonization of Australia, ~60 to 50 kyBP, quite in agreement with archaeological evidences". That eliminates M42'74 from having anything to do with the movement suggested in the paper. "This lineage does suggest a flow from South Asia to SE Asia and Australia (maybe together both branches or maybe not)". Or possibly to both India and Australia from South China. "We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact" For some reason the authors automatically assume such gene flow would be from west to east. "even if the authors claim admixture levels of as much as 11% and as recent as a mere 4000 years ago, no patrilineage (Y-DNA) nor matrilineage (mtDNA) [correction: see update below] has been ever detected that could be associated with this purported migration". We do have a patrilineage that suggests movement from near Australia back to India: Y-DNA K1. Most K-M9 is east of Wallace's Line. Just K1 is from west of the line, in South Asia. Could it be that it is an indication of westward movement across Wallace's Line a mere 4,230 years ago? But that leaves the problem of 11% in common. K1 is a very rare lineage.

       
    13. CJ

      January 19, 2013 at 4:52 am

      http://www.australianstamp.com/Coin-web/feature/history/abdream.htm has some Wondjina stories. Take out the magical-mythological association with bringing rain, and the Wondjina sound like a foreign group of people. The Wonjina rock art shows up in the Kimberly around 3800 B.P., around the time of this study's Indian gene flow.

       
    14. Maju

      January 19, 2013 at 8:55 am

      The Pirri Point tech is curious (looks totally like an MSA variant btw) but without knowing IF and how it might relate with South Asia (where mode 4 microlithism was mainstream since c. 38 Ka ago) we can't judge. On first impression (google for images) it looks a "primitive" Middle Paleolithic Levallois-based tech to me, much like MSA. If this diagnostic is correct then we should reject even more any idea of human or cultural waves of any relevance arriving to Australia in recent times. Sadly I do not know enough about the prehistoric techno-cultures of Australia to judge but my first impression is rather as negative evidence than positive one for the Pugach hypothesis."That eliminates M42'74 from having anything to do with the movement suggested in the paper". Not necessarily. Remember that age estimates are just educated guesses without any weight as evidence."For some reason the authors automatically assume such gene flow would be from west to east".That's what the shown Tree Mix and ADIMXTURE results (as I say questionable both) suggest. We see no "Papuan" genetics in India (while describing, by affinity, 90% of the Australian sample). Whatever one may think there's no way one can deduce an Australia → India flow from that data."We do have a patrilineage that suggests movement from near Australia back to India: Y-DNA K1".And all P as well (P is South Asian at origin beyond reasonable doubt).But neither is found in Aboriginal Australia as such and your "near Australia" is probably mainland SE Asia (maybe Sundaland but hardly farther to the SE). The current knowledge of MNOPS [aka K(xLT)] is surely too shallow to justify your claim because is for sure that MNOPS holds several (now hidden) dual branches underneath and is likely that one of them includes all the Oceanian lineages (not sufficiently researched as of now). Even if we'd accept the current 7-parts division (which as I say is surely just an approximation to the real thing), three branches are still continental (Eurasian) and not more than four Oceanian (and none of them Australian). But most likely all four Oceanian branches are just one (to be described as of now).

       
    15. Maju

      January 19, 2013 at 8:56 am

      I would not dare to interpret the Wondjina as "people" much less as foreign people. Spirits appear in dreams, visions.

       
    16. terryt

      January 19, 2013 at 11:51 pm

      "without knowing IF and how it might relate with South Asia (where mode 4 microlithism was mainstream since c. 38 Ka ago) we can't judge". From what I've read over the years no connection with any SE Asian technology. But that doesn't mean it wasn't 'influenced' by something SE Asian. "I would not dare to interpret the Wondjina as 'people' much less as foreign people. Spirits appear in dreams, visions". Yes, I saw that link while searching for 'Pirri points' and decided exactly the same.

       
    17. terryt

      January 20, 2013 at 1:22 am

      "But neither is found in Aboriginal Australia as such and your 'near Australia' is probably mainland SE Asia (maybe Sundaland but hardly farther to the SE)". Extremely likely to be so. But 'Sundaland' is a lot closer to Australia than it is to South Asia. "Even if we'd accept the current 7-parts division (which as I say is surely just an approximation to the real thing), three branches are still continental (Eurasian) and not more than four Oceanian (and none of them Australian)". I see there has been a re-arrangement at ISOGG although the old nomenclature survives at Wikipedia. The old K1-M174 has dissappeared, so that eliminates the South Asian K. The other three Ks have been reduced by one digit but none can be considered 'continental', although K-P79 is found in Indonesia as well as Melanesia and K-P261 is Balinese. Haven't you consistently maintained that greatest diversity equals origin? So taking the latest ISOGG at face value we therefore have 5/7 haplogroups from Wallacea/New Guinea/Australia. South Asian K has dissappeared so that leaves just two outside the Wallacean region: NO in East asia and P probably in South Asia. That's a lot of diversity in comparison to anywhere else.

       
    18. terryt

      January 20, 2013 at 2:16 am

      This is fascinating. I've found where K1-M174 has dissapeared to: http://www.isogg.org/tree/ISOGG_HapgrpK.htmlQuote: "M147 is downstream of M256. Listed 6 August 2012". As far as I can discover that makes the old K1 part of MNOPS. So yes, we do have just two MNOPS haplogroups east of Wallace's line and three west of it.

       
    19. Maju

      January 20, 2013 at 8:01 am

      I won't allow you to hijack the thread. You're warned, Terry."Haven't you consistently maintained that greatest diversity equals origin?"Roughly yes. I still do. It's just that the apparent diversity is most unlikely to be real but an artifact of unequal research levels by region.

       
    20. Raimo Kangasniemi

      January 20, 2013 at 8:07 am

      This comment has been removed by the author.

       
    21. Raimo Kangasniemi

      January 20, 2013 at 8:08 am

      After some 2400 years even a very small group could have had a that kind of effect, especially if the population it was contact with was a relatively small. This study also is not about all the Aboriginals of Australia, just from the NW and the exact population history there is relatively unknown. The aboriginal populations were hardly static, so we could make – for argument's sake – a totally theoretical assumption that later immigration from other parts of Australia could have greatly influenced the population that was in contact with the immigrants, possibly diluting their effect on the NW population and also helping to keep the Denisovan heritage on the level that it is.

       
    22. Maju

      January 20, 2013 at 8:23 am

      M256 does not seem to exist. Is it maybe P256? Typo? Please double-check and, if confirmed, send email to Alice Fairhurst. It is a small private lineage but M-P256 has previously been reported in Afghanistan, so it's becoming the less Melanesian of all Melanesian lineages in fact – whatever that means. K* (i.e. excluding a few locally common lineages like R or NO) is found with some frequency in Eurasia but nobody pays it much attention. Maybe you should.

       
    23. Maju

      January 20, 2013 at 8:24 am

       
    24. Maju

      January 20, 2013 at 8:53 am

      Where are the other less slippery data: the Y-DNA, the mtDNA, the archaeological evidence… this is a mere artifact, almost a scientific prank. Your proposal seems so unlikely to me that I cannot take it even half-seriously without some clear evidence."… diluting their effect on the NW population and also helping to keep the Denisovan heritage on the level that it is".That's simply not possible (after all we are talking of all AAs almost evenly sharing that component, no variations we can spot). The only reasoning that could be applied to the lack of dilution of the Denisovan component would be that it was once higher in AAs than Papuans, so dilution did happen but exactly to the Papuan reference level… but that would be a most strange coincidence. Your suggestions sound to me as quasi-religious rationalizations ex-post-facto of data that is simply wrongly generated. If you want to have faith in the tools and the researchers' ability to use them properly and without trickstery, then you have to reach out to such unlikely explanations, of course. But I find much easier simply not to have such faith. I find much more reasonable to discard TreeMix produce as noise (more often than not at least, in my experience), ADMIXTURE's one as a very likely mismanagement by the authors (we are not presented with the proper list of K-depths so we can see if the appearance of an Indian component is real or mere artifact caused by the 60Ka ago origin in that area, where most diversity is preserved, nor we are told of a cross-validation that supports that particular slice as optimal – also the already mentioned oversampling issue that normally causes heavy distortions in ADMIXTURE results) and the molecular-clock-o-logical estimates as the usual nonsense that sadly surrounds this matter. So all the data we are offered is at best dubious, hence the conclusion is also dubious. Said that, it has one use, stated in the paper: to reject the hypothesis that most AAs carry European admixture.There seems to be some extremely thin India-Australia link in some haploid DNA (including Afghanistan and maybe other parts of Eurasia) but a simpler explanation is that it belongs to a late wave within the Middle Paleolithic process of Eurasian expansion or something like that. Not Neolithic.

       
    25. Ebizur

      January 20, 2013 at 1:18 pm

      Karafet et al. 2010Southeast Asia (China=383 (Han=165, Yao=60, Miao=58, She=51, Tujia=49), Vietnam=70, Taiwanese Aboriginals=48, Philippines=48, Malaysia=32)C-RPS4Y (n=43), including 26 C3-M217 and 17 C-RPS4Y(xC2-M38, C3-M217)Variance = 0.676O-M175 (n=462)Variance = 0.550MNOPS*-M526 (n=24), including 22 from the Philippines and 2 from MalaysiaVariance = 0.381C-RPS4Y(xC2-M38, C3-M217) (n=17)Variance = 0.179Western IndonesiaMNOPS*-M526 (n=12), including 5 Batak Toba (Sumatra), 5 Borneo, and 2 JavaVariance = 0.720O-M175 (n=804)Variance = 0.547C-RPS4Y (n=40), including 39 C-RPS4Y(xC2-M38, C3-M217) and 1 C3-M217Variance = 0.165Eastern IndonesiaMNOPS*-M526 (n=62), including 24 Flores, 14 Sumba, 9 Alor, 5 Moluccas, 4 Mandar (Sulawesi), 3 Lembata, and 3 TimorVariance = 0.698C-RPS4Y (n=456)Variance = 0.650O-M175 (n=166)Variance = 0.597M-P256 (n=121)Variance = 0.587Oceania (n=182), including 44 Maewo (Vanuatu), 33 PNG Highland, 24 Tahiti, 16 Micronesia, 15 PNG Coastal, 12 Tonga, 12 Western Samoa, 10 Nasioi, 10 Rapa Nui, 6 American SamoaO-M175 (n=31), including 18 O3a2-P201, 5 O3-M122(xO3a2-P201), 4 O1a*-M119(xP203, M110), 2 O-P203, 1 O-M110, and 1 O2b-SRY465(xO2b1-47z) Variance = 1.031O3-M122 (n=23), including 18 O3a2-P201(xO3a2c1-M134) (5 Tonga, 3 Micronesia, 3 Tahiti, 2 Vanuatu-Maewo, 2 Western Samoa, 1 PNG Coastal, 1 PNG Highland, 1 American Samoa), 3 O3a2c1-M134 (from Tahiti), and 2 O3a-P197(xO3a1c-JST002611, O3a2-P201) (1 Vanuatu-Maewo, 1 Tahiti)Variance = 0.981MNOPS*-M526 (n=20), including 7 Micronesia, 6 Maewo (Vanuatu), 5 PNG Highland, 1 PNG Coastal, and 1 TahitiVariance = 0.898O3a2-P201(xO3a2c1-M134) (n=18)Variance = 0.792M-P256 (n=46)Variance = 0.706C-RPS4Y (n=59), including 40 C2a1-P33 (15 Tahiti, 9 Rapa Nui, 8 Western Samoa, 4 American Samoa, 4 Tonga), 5 C2a-M208(xC2a1-P33) (2 PNG Coastal, 1 Vanuatu-Maewo, 1 Tahiti, 1 Western Samoa), 12 C2*-M38(xC2a-M208) (9 Vanuatu-Maewo, 2 PNG Highland, 1 Micronesia), 2 C-RPS4Y(xC2-M38, C3-M217) (1 PNG Coastal, 1 Micronesia)Variance = 0.460C2-M38 (n=57)Variance = 0.377Maju, MNOPS*-M526(xM-P256, NO-M214, P-M45, S-M230) is clearly of ancient (original?) presence in Austronesia-Oceania (including Sahul, Wallacea, the Philippines, and marginally Sundaland). The distribution of MNOPS*-M526 and two of its close relations, M-P256 and S-M230, is largely limited to populations of this region, and MNOPS*-M526 is the most diverse Y-DNA haplogroup throughout Indonesia. It would also be the most diverse Y-DNA haplogroup in Oceania if it were not for the strangely high diversity of O-M175 (and O3-M122 in particular) Y-DNA in this pool of Oceanian samples. If one excludes the three O3a2c1-M134 Tahitian individuals, the O3a-P197(xO3a1c-JST002611, O3a2-P201) individual from Tahiti, and the O3a-P197(xO3a1c-JST002611, O3a2-P201) individual from Maewo, Vanuatu on the grounds of being suspect of recent Asian admixture, then we are left with a variance of 0.792 for the 18 O3a2-P201(xO3a2c1-M134) Y-chromosomes that are more likely to be of ancient Austronesian ancestry. This, again, is lower than the variance of the MNOPS*-M526 samples from Oceania.

       
    26. Ebizur

      January 20, 2013 at 1:20 pm

      Western IndonesiaMNOPS-M526 (n=876)Variance = 0.594C-RPS4Y (n=40), including 39 C-RPS4Y(xC2-M38, C3-M217) and 1 C3-M217Variance = 0.165Eastern IndonesiaMNOPS-M526 (n=484)Variance = 0.738C-RPS4Y (n=456)Variance = 0.650OceaniaMNOPS-M526 (n=121)Variance = 0.982C-RPS4Y (n=59), including 40 C2a1-P33 (15 Tahiti, 9 Rapa Nui, 8 Western Samoa, 4 American Samoa, 4 Tonga), 5 C2a-M208(xC2a1-P33) (2 PNG Coastal, 1 Vanuatu-Maewo, 1 Tahiti, 1 Western Samoa), 12 C2*-M38(xC2a-M208) (9 Vanuatu-Maewo, 2 PNG Highland, 1 Micronesia), 2 C-RPS4Y(xC2-M38, C3-M217) (1 PNG Coastal, 1 Micronesia)Variance = 0.460Southeast Asia (China=383 (Han=165, Yao=60, Miao=58, She=51, Tujia=49), Vietnam=70, Taiwanese Aboriginals=48, Philippines=48, Malaysia=32)C-RPS4Y (n=43), including 26 C3-M217 and 17 C-RPS4Y(xC2-M38, C3-M217)Variance = 0.676MNOPS-M526 (n=519)Variance = 0.604However, C-RPS4Y(xC2-M38, C3-M217) (n=17)Variance = 0.179As you can see, even limiting our scope of consideration to the major clades MNOPS-M526 and C-RPS4Y, which together account for practically all Y-DNA in all populations of the region in question, MNOPS-M526 is more diverse than C-RPS4Y in all sample sets except the China/Southeast Asia sample set. However, the higher variance of haplogroup C in the China/Southeast Asia sample set is due to the combined presence of two deeply divergent subclades of C-RPS4Y, one being C3-M217 and the other being a not-yet-defined subclade of C-RPS4Y that has rather little internal variance.

       
    27. Maju

      January 20, 2013 at 1:58 pm

      Not sure what you understand from what I said, Ebizur, but all I mean is that:1. I think most unlikely that MNOPS migrated from Wallacea or Australasia to continental Eurasia (instead I imagine a continental SE Asian origin, maybe as far as Sundaland but not beyond Wallace Line). 2. This issue of MNOPS belongs to the early colonization of Eurasia and Australasia c. 60-40 Ka ago and not to any "Neolithic" or otherwise recent flows.What you say about C* or O3 does not seem related to Australian Aborigines and their hypothetical relations with India. I don't understand why you even mention them in this topic unless you want to conflate two distinct discussions, what I beg you do not.

       
    28. Maju

      January 20, 2013 at 2:00 pm

      Is Australasian MNOPS more SRY-diverse than continental Eurasian one? The correlation with C (or rather lack of any correlation at all) is trivial here.

       
    29. Ebizur

      January 20, 2013 at 2:46 pm

      Maju wrote,"What you say about C* or O3 does not seem related to Australian Aborigines and their hypothetical relations with India. I don't understand why you even mention them in this topic unless you want to conflate two distinct discussions, what I beg you do not."I have responded to your suggestions that the apparent diversity of MNOPS in Oceania is "most unlikely to be real but an artifact of unequal research levels by region" and that the K-M147 and M-P256 singletons that have been observed rarely in some samples from South Asia deserve to be given greater weight than they have been in the past in the consideration of the region of origin of MNOPS-M526. You have not presented any evidence to support your suggestions; therefore, they reek of a sort of Eurocentrism (specifically, attempting to "whitewash" your Y-DNA haplogroup R ancestor by placing his tribe as close to Europe as possible).Maju wrote,"Is Australasian MNOPS more SRY-diverse than continental Eurasian one? The correlation with C (or rather lack of any correlation at all) is trivial here."According to the data from Karafet et al. 2010, the answer would be "yes":Oceania (n=182)MNOPS-M526 (n=121)Variance = 0.982Eastern Indonesia (n=957)MNOPS-M526 (n=484)Variance = 0.738Southeast Asia (n=581, including China=383 (Han=165, Yao=60, Miao=58, She=51, Tujia=49), Vietnam=70, Taiwanese Aboriginals=48, Philippines=48, Malaysia=32)MNOPS-M526 (n=519)Variance = 0.604Western Indonesia (n=960)MNOPS-M526 (n=876)Variance = 0.594The variance of MNOPS is high in the pool of samples from Oceania, intermediate in the pool of samples from Wallacea, and low in the pools of samples from China, Vietnam, Malaysia, the Philippines, and western Indonesia.

       
    30. Maju

      January 20, 2013 at 5:24 pm

      "I have responded to your suggestions that the apparent diversity of MNOPS in Oceania is "most unlikely to be real but an artifact of unequal research levels by region""…Apparent basal diversity. I use to work with that for mtDNA but in Y-DNA it may be misleading. "According to the data from Karafet et al. 2010, the answer would be "yes"".OK. sure. What does "Oceania" mean in Karafet's context? Melanesia, Polynesia and maybe some parts of Micronesia. Where does that diversity come from? From the excess diversity of introducing Asian O sublineages most likely. Also I asked about Euriasia in general not just East Asia. I know that you do not have the data but that is what we would like to contrast: all MNOPS(xNO,P) of Australia and Near Melanesia (include Wallacea if you wish but NO and P must be excluded because we know for sure they are recent arrivals East and South of Wallace Line) and all MNOPS of continental Eurasia, which is mostly NO and P. That way we can estimate if, prior to Neolithic, there was more MNOPS diversity East or West of Wallace Line. The question must be answered properly, carefully, seriously. Otherwise we are onto the paradoxic situation of Brazil being (may well be) more genetically diverse than Portugal… but that's not because Portugal was colonized from Brazil but because Brazilian diversity drank of many different sources. Careful there. When we compare the genetic fraction which must have arrived from Portugal to Brazil and only that, the result must be that Brazil is less diverse than Portugal for that fraction of the genome (because it's impossible that all Portuguese lineages fed Brazilian roots, there's always some level of "bottleneck", of founder effect, even if mild, in any such colonization). There's room for noise, confusion and, I guess, manipulation (if one is into that crap) in this but let's try not to sow confusion willingly, OK? I believe that you can perfectly discern the nuances of this population genetics' little problem, can't you?

       
    31. terryt

      January 20, 2013 at 8:56 pm

      "M256 does not seem to exist. Is it maybe P256? Typo?" I suspect it's a typo. Perhaps M147 is downstream of P256, in which case K1 is a subclade of M. Either way K1 seems to be a product of back movement from Wallacea. "The variance of MNOPS is high in the pool of samples from Oceania, intermediate in the pool of samples from Wallacea, and low in the pools of samples from China, Vietnam, Malaysia, the Philippines, and western Indonesia". Thanks. That supports the conclusion I came to when examining the 2005 McDonald maps. Maju has vehemently opposed my occasional suggestions that such could be the case. "You have not presented any evidence to support your suggestions; therefore, they reek of a sort of Eurocentrism (specifically, attempting to 'whitewash' your Y-DNA haplogroup R ancestor by placing his tribe as close to Europe as possible)". Maju is not the only one with a desire to place European ancestry as close to Europe as possible (and I seem to remember Maju saying he was J). I see the problem as arising from an inability to see human expansion as other than unidirectional, probably related to primitive beliefs in some Garden of Eden. "Roughly yes. I still do. It's just that the apparent diversity is most unlikely to be real but an artifact of unequal research levels by region". Still at it. "What does 'Oceania' mean in Karafet's context? Melanesia, Polynesia and maybe some parts of Micronesia. Where does that diversity come from? From the excess diversity of introducing Asian O sublineages most likely". And there he goes again. Karafet presumably includes all those regions in 'Oceania', but O is not particularly common except in Polynesia and Micronesia. And it seems from Ebizur's first set of data that Karafet has excluded O from MNOPS. "I think most unlikely that MNOPS migrated from Wallacea or Australasia to continental Eurasia" Why? Is it that Melanesians are too primitive to have done so? "include Wallacea if you wish but NO and P must be excluded because we know for sure they are recent arrivals East and South of Wallace Line" We don't actually know that. It is true of O and R, but NO and P may have originated near Wallace's Line. And you wrote earlier: "but M-P256 has previously been reported in Afghanistan, so it's becoming the less Melanesian of all Melanesian lineages in fact" So we know that Y-DNA from Wallacea moved a huge distance. "That way we can estimate if, prior to Neolithic, there was more MNOPS diversity East or West of Wallace Line". A side issue. My bet would be that MNOPS coalesced either side of Wallace's Line, in Wallacea itself. Any population capable of developing the boating technology required to cross wallace's Line would have a sufficiently superior boating technology to be able to expand back through regions already occupied, exploiting the environment in new ways.

       
    32. Maju

      January 20, 2013 at 9:52 pm

      You guys can't take just one side of the K problem. K(xL,M,N,O,P,T) was found in many populations of India, for example, at low but non-negligible frequencies: 0-9% (most often: 2-6%). This is probably not K1 (a private lineage) and can or not be within MNOPS or whatever (but looks like not LT) → http://www.krepublishers.com/06-Special%20Volume-Journal/T-Anth-00-Special%20Volumes/T-Anth-SI-03-Anth-Today-Web/Anth-SI-03-31-Trivedi-R/Anth-SI-03-31-Trivedi-R-Tt.pdf.Less clearly there are many cases, in Europe for example, in which K* is not properly tested for some minor clade markers, like T (formerly K2) but the doubt remains. For example it was reported at Rootsweb (http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2011-08/1312559170) a case in which Alsacians and Auvernians appear with some K(xL,N1c,P,T). They look single individuals (one each) but they still weight more than 1%.Even if we'd be able to have all the relevant data properly collected and filed (a nightmare on its own right), we would not be able to evaluate in any realistic way the basal diversity or general diversity of K, whose rare variants are clearly scattered all around Eurasia and Oceania.

       
    33. Maju

      January 20, 2013 at 10:26 pm

      "You have not presented any evidence to support your suggestions; therefore, they reek of a sort of Eurocentrism (specifically, attempting to 'whitewash' your Y-DNA haplogroup R ancestor by placing his tribe as close to Europe as possible)". I missed this quote. Who wrote that? Whoever did, (s)he's very wrong. Regardless of the origins of MNOPS, it is extremely clear for anyone looking at the data that P is from South Asia (where the three basal subclades, P*, R and Q exist with deep roots – Q may be from Iran but not too far) as is probably the case of R and maybe R1 and R1a, Q instead seems to be from West/Central Asia. This is beyond question.MNOPS seems to originate farther to the East but a backflow from Oceania at the levels required for the impact of Y-DNA P and NO, which are the largest ones by far in Eurasia, would imply a much clearer genetic signal, like more much more distributed Denisovan genetics and Oceanian mtDNA lineages, etc. In general I think that Oceania is a cul-de-sac and whatever goes in does not go out. Why? Because anything arriving to Oceania must have originated (at least before Modern Age) at Eurasia, where technology would be therefore similar or better and where populations numbers were also high. Only very strange circumstances could allow for a back-migration from Oceania in the terms you speculate with. That could be for example the Toba catastrophe… but we do not see the signature anyhwere. Mind you that I considered long ago that K (MNOPS was not yet known) might have originated in Melanesia for the very same simplistic reasons you're arguing here but I was quickly talked out of such idea by people of Chinese ethnicity. The logic is the very same I'm arguing here: that Melanesian K/MNOPS is not well studied and will probably some day be shown to be a single joint clade. This is a good hypothesis, not confirmed yet but not proven wrong either.Also I think that Y-DNA K/MNOPS and mtDNA R are related somehow, and in Melanesia there's only so much mtDNA R (P actually). Part of my reasoning is that if only one clade of mtDNA R arrived to Melanesia, it's plausible that it was also only one clade of Y-DNA MNOPS which did on the patrilineal side. So in general I do expect that all Melanesian MNOPS will converge to a single lineage MS."I seem to remember Maju saying he was J"Wrong. I do not know. I never bothered testing: I'm interested in the genetics of peoples not individuals. "… but NO and P may have originated near Wallace's Line".Not for all I know. P looks like original from the North of South Asia, maybe towards Bengal but not further East, where all presence of P is anecdotal and derived. NO looks original from Southern China or somewhere very close. So the whole thing looks like originating from SE Asia and I have even argued that MNOPS (after factoring the Melanesian aspect) might have originated at Sundaland (what you, Terry, opposed, can't recall why, some bias against Sundaland you have – also apparent in the O1 debate). "Any population capable of developing the boating technology required to cross wallace's Line would have a sufficiently superior boating technology to be able to expand"…Problem is that we see no evidence whatsoever of any such expansion: neither in the material record, nor in the mtDNA one, nor the autosomal one (this data suggests only India→Australia, never Sahulland→Eurasia has been claimed on autosomal DNA: nothing, nada, rien de rien), nor in the issue of Denisovan genetics. The claim you make regarding K/MNOPS is a burning nail and should not hold the test of time. Also it's probable that your mystified Wallaceans actually arrived there on boat most of the way from Africa. Finally it is unclear whether this or that tech should give superiority. Personally I lean for the dog, which was domesticated in SE Asia… what a coincidence (not).

       
    34. Ebizur

      January 20, 2013 at 11:27 pm

      Maju,The K(xL,N1c,P,T) individuals from France probably belong to some sort of haplogroup N. N(xN1c) has been reported from Italy, Slovenia, Czechia, etc., so I see no reason why some of it could not have settled in France.The finding of K(xL,M,N,O,P,T) Y-DNA in India seems more interesting to me, but I would like to see this finding reproduced by an independent set of researchers.

       
    35. terryt

      January 21, 2013 at 3:51 am

      "Who wrote that? Whoever did, (s)he's very wrong". Ebizur wrote it, and I believe he is correct. Otherwise why would you be so hostile to the idea that MNOPS coalesced somewhere other than in South Asia? "In general I think that Oceania is a cul-de-sac and whatever goes in does not go out. Why? Because anything arriving to Oceania must have originated (at least before Modern Age) at Eurasia, where technology would be therefore similar or better" False assumption. Do you really believe that Melanesians were incapable of innovation? "Problem is that we see no evidence whatsoever of any such expansion" Yes we do. The expansion of P and NO. Not to mention mt-DNA R. Using your logic it would be impossible for R to have expanded either, even from South Asia as you so passionately believe. "I considered long ago that K (MNOPS was not yet known) might have originated in Melanesia for the very same simplistic reasons you're arguing here but I was quickly talked out of such idea by people of Chinese ethnicity". Makes sense. They like to believe they are the superior people in the region. And they certainly don't want to accept that they may descend from the totally inferior Melanesians. "The logic is the very same I'm arguing here: that Melanesian K/MNOPS is not well studied and will probably some day be shown to be a single joint clade". It has certainly been studied a lot more since I first became interested in the subject. The fact that K1 has been subsumed by some other clade does show more will be discovered but I doubt you are totally correct in your Hypothesis. I'm inclined to the idea that MNOPS may be shown to have branched progressively, just as IJK has been shown to have. "So in general I do expect that all Melanesian MNOPS will converge to a single lineage MS". Who's jumping to conclusions with no eveidence now? "Also it's probable that your mystified Wallaceans actually arrived there on boat most of the way from Africa". Based on what evidence? "Part of my reasoning is that if only one clade of mtDNA R arrived to Melanesia, it's plausible that it was also only one clade of Y-DNA MNOPS which did on the patrilineal side" You're ignoring the fact that 3 clades of M arrived in New Guinea/Melanesia as well, and actually 4 clades within P from Australia. Admittedly P is just one clade of R but other clades of mt-DNA N crossed Wallace's Line to Australia, along with several non-Melanesian M clades. So it is quite possible that several Y-DNA clades reached New Guinea/Melanesia.

       
    36. terryt

      January 21, 2013 at 3:53 am

      "K(xL,M,N,O,P,T) was found in many populations of India, for example, at low but non-negligible frequencies: 0-9% (most often: 2-6%). This is probably not K1 (a private lineage) and can or not be within MNOPS or whatever (but looks like not LT)" In the link you provided it's not K(xL,M,N,O,P,T). I notice the paper was published before T was defined and the K-M70 is actually T1a. But what the K* represents is still a mystery because they say: "none of our studied samples showed the presence of haplogroup K3-M147" So K* is not what until very recently we've been calling K1. Not present? Perhaps the presence of K* is a result of minor movement west from Wallacea. It does seem to be most common in the northeast. And an aside from the present subject in the link: "The present analysis showed none of the deletions (DYS390.1 or DYS 390.3) associated with Australian or Polynesian C* chromosomes, contesting theclaims of link between India and Australian aboriginals" So there goes another theory. And another aside: "Haplogroup D, a monophyletic branch of M168 lineage, defined by an Alu insertion and M174C mutation, on the other hand, was restricted in Bhutia and Tharu tribal groups. Its presence among them is most likely due to gene flow from Tibet, where this haplogroup has earlier been reported". So that's goodbye to any movement through South Asia for the haplogroup. "Even if we'd be able to have all the relevant data properly collected and filed (a nightmare on its own right), we would not be able to evaluate in any realistic way the basal diversity or general diversity of K, whose rare variants are clearly scattered all around Eurasia and Oceania". You are absolutely determined to avoid conceding that MNOPS may have coalesced in Wallacea. What is your problem?

       
    37. Maju

      January 21, 2013 at 7:05 am

      Look, Ebizur: I can't bother searching for days or weeks for all instances of strange K* found around the World. I'm just stating that it does exist (and these examples are not the only ones, just the ones I could most easily find – you are the collector of haplogroups, you should know). It might be N*? Of course: that or K-other, that's how it goes. K1 might also be M, or K3 be S or all them be part of a yet undescribed MS lineage, as I speculate… we just don't know. We therefore have to shrug and accept the limitations of this single-angle approach and look at complementary evidence like archaeology or mtDNA or even autosomal DNA for whatever is worth. And none of those seem to support a migration out of Australasia. So that's extra reason to doubt yours and Terry's simplistic reading of the apparent diversity of K-MNOPS in the region. Time will tell in any case.

       
    38. Maju

      January 21, 2013 at 7:07 am

      "Otherwise why would you be so hostile to the idea that MNOPS coalesced somewhere other than in South Asia?" SE Asia but this side of Wallace Line. You have not read what I wrote, I'm not going to read what you write. Next time answer read first, answer later, please.

       
    39. Maju

      January 21, 2013 at 7:19 am

      "Do you really believe that Melanesians were incapable of innovation?"No. Who stands for Melanesian principal in the Oceanic expansion issue? That's not you but me. I just say that, everything else equal, consolidated populations hold their ground everywhere. The exceptions (few but some) must be quite obvious anyhow (for example North Africa, where African specific mtDNA is only 25%). "And they certainly don't want to accept that they may descend from the totally inferior Melanesians". Junk! We all descend from totally cool ancient Homo sapiens: Melanesians and us are close cousins. You are defaming people just because it suits your polemicist strategy. It's a mere matter of physics: consolidated populations normally don't let others go through, much less in great numbers. …I don't want to argue with you about every single detail. Either you focus or no debate.

       
    40. Maju

      January 21, 2013 at 7:27 am

      "So K* is not what until very recently we've been calling K1".Nice that you could contrast that. It may still be K(xMNOPS,LT) and be more related to the origin of K as such than to that of MNOPS [aka K(xLT)] but the matter is that "the asterisk zone" is muddy everywhere, not just in Melanesia. If K(xLT,MNOPS), then it would support my idea of K originating in South Asia and migrating eastward only to go back as P or proto-P. This is also supported by the relative geography of F (SA), IJK(SA/WA) and MNOPS (SEA) and by similar patterns of tropical flow and backflow SA→SEA→SA→WEA quite obvious in the mtDNA. In any case we are going to the Great Eurasian expansion and not to a recent flow of Neolithic times.

       
    41. Maju

      January 21, 2013 at 7:40 am

      "So that's goodbye to any movement through South Asia for the haplogroup". Nobody knows how proto-D arrived to SE Asia. SA is just the most parsimonious (shorter, less obstacles) route. But whatever happened the evidence is lost to us by now. "You are absolutely determined to avoid conceding that MNOPS may have coalesced in Wallacea. What is your problem?"First of all, K/MNOPS is minor in Wallacea. It's an area dominated by C2, a lineage that definitely never made it back to Eurasia in any meaningful numbers. So it'd be a Papuan and not Wallacean origin if anything (or in the Near Melanesian islands NE of Papua or even Filipino Negrito but NOT WALLACEAN). Second, we see nothing of what they have in the mtDNA or autosomal sides of the equation that you so dearly avoid discussing. Third, it is unlikely by the very geography that sets them apart: Wallace Line. That is a major biogeographical barrier added to the basic tendency of populations to stay put and either absorb or reject newcomers, acting as filters, buffers, and not as channels for migrations. But in any case: you should have a holistic theory, including archaeology, autosomal DNA, mtDNA and not just the slippery Y-DNA. If you cannot think about a problem from all angles, I do not need to even consider your "solutions" seriously because they lack the basics: holism.

       
    42. terryt

      January 22, 2013 at 3:53 am

      "In any case we are going to the Great Eurasian expansion and not to a recent flow of Neolithic times". I agree, but I will make a few more comments. "If you cannot think about a problem from all angles, I do not need to even consider your 'solutions' seriously because they lack the basics: holism". Maju. You have consistently failed to think about a problem from all angles yourself. You have formulated an hypothesis and then looked at the evidence with the aim of proving that hypothesis. For example: "Look, Ebizur: I can't bother searching for days or weeks for all instances of strange K* found around the World. I'm just stating that it does exist" As a result of your failure to think about the problem from all angles you concentrate on the very few individuals through Eurasia typed as unresolved K*-M9 while ignoring the far greater number of unresolved K*-M9 individuals in Australia and Melanesia. Consequently you are able to conclude that the haplotype moved from the region of very little presence to the region of much greater presence. You are obliged then to invoke 'founder effect' as an explanation, because that is the only way you can make the evidence fit your hypothesis. You also conveniently ignore the opposite possibility because it doesn't fit your hypothesis. "I just say that, everything else equal, consolidated populations hold their ground everywhere". I tend to agree, but no human population has spread out like ink through blotting paper. They occupy regions they are most used to at first, leaving regions less familiar to them to be exploited by later arrivals. After all in most single regions of the world haplogroups from several different regions are mixed today. "Nobody knows how proto-D arrived to SE Asia. SA is just the most parsimonious (shorter, less obstacles) route. But whatever happened the evidence is lost to us by now". It is surely unlikely that D would have been completely wiped out through greater India by any later human expansion. Today many haplogroups survive in regions later over-run by another population. On the other hand Neanderthal Y-DNA is no longer with us. "First of all, K/MNOPS is minor in Wallacea". It's very prominent either side of it though. Apart from NO and P more plentiful east of it than west. "It's [Wallacea] an area dominated by C2, a lineage that definitely never made it back to Eurasia in any meaningful numbers". I agree. In fact that alone suggests that Y-DNA K reached Wallacea from the Philippines, not via Nusa Tenggara. "Second, we see nothing of what they have in the mtDNA or autosomal sides of the equation that you so dearly avoid discussing". I have brought mt-DNA up up many times. You've got a very short memory Maju. I'll discuss it any time.

       
    43. Maju

      January 22, 2013 at 8:03 am

      You are intently confusing "looking at the problem from all angles", i.e. to think holistically, on one side and not to be willing to do more work, i.e. to be lazy, tired or whatever you wish. Think vs. work. If you do the tiresome job… I'll be glad to think about the data you provide. Thanks in advance. … "no human population has spread out like ink through blotting paper".Not quite but almost so. I already offered some maths in a previous discussion in which it was made evident that 100 founders create a population of millions (if conditions allow) in few centuries. It's exponential and, without resistance, in optimal conditions, each woman can have a good number of reproducing offspring, doubling, tripling or more each generation. And here we are usually talking of spans of many millennia, so more than enough time. "It is surely unlikely"…Your usual logic: if it includes "surely", "unlikely", "certainly" and nothing else, it's Terry stating his unfounded opinion."… that D would have been completely wiped out through greater India by any later human expansion".It seems obvious then (assuming your "logic" is correct, what happened to Toba for example?) that it migrated through huge mobs. "Apart from NO and P"…Which make some 99% of the extant MNOPS, at least in numbers, and are two of the most widespread Y-DNA haplogroups on Earth. You are removing 99% of the evidence on an most unlikely trust that the current ISOGG tree is absolutely real (it has been amended once and again and will be in the future).I cannot share that faith.

       
    44. Ebizur

      January 22, 2013 at 2:47 pm

      Maju wrote,"First of all, K/MNOPS is minor in Wallacea. It's an area dominated by C2, a lineage that definitely never made it back to Eurasia in any meaningful numbers. So it'd be a Papuan and not Wallacean origin if anything (or in the Near Melanesian islands NE of Papua or even Filipino Negrito but NOT WALLACEAN)."Actually, MNOPS-M526 comprises the majority of Y-DNA in the Karafet team's samples of populations from Wallacea:Eastern Indonesia (Karafet et al. 2010)145/957 = 15.2% C-RPS4Y(xC2-M38, C3-M217) [115/394 = 29.2% Flores, 21/92 = 22.8% Lembata, 6/54 = 11.1% Mandar (West Sulawesi), 1/9 = 11.1% Timor, 1/28 = 3.6% Alor, 1/350 = 0.3% Sumba, 0/30 Moluccas]313/957 = 32.7% C2*-M38(xC2a-M208) [201/350 = 57.4% Sumba, 4/9 = 44.4% Timor, 12/28 = 42.9% Alor, 10/30 = 33.3% Moluccas, 19/92 = 20.7% Lembata, 61/394 = 15.5% Flores, 6/54 = 11.1% Mandar (West Sulawesi)]13/957 = 1.4% F-P14(xG-M201, H-M69, I-P19, J-M304, L-M20, MNOPS-M526, K3-P261) [3/54 = 5.6% Mandar from Sulawesi, 4/92 = 4.3% Lembata, 6/394 = 1.5% Flores]1/957 = 0.1% J2-M172(xJ2b-M12) [1/54 = 1.9% Mandar from Sulawesi]62/957 = 6.5% MNOPS*-M526 [3/9 = 33.3% Timor, 9/28 = 32.1% Alor, 5/30 = 16.7% Moluccas, 4/54 = 7.4% Mandar from Sulawesi, 24/394 = 6.1% Flores, 14/350 = 4.0% Sumba, 3/92 = 3.3% Lembata]10/957 = 1.0% M-P256(xM1a-P34, M1b-P87, M2-M353, M3-P118) [10/394 = 2.5% Flores]111/957 = 11.6% M1a-P34 [72/394 = 18.3% Flores, 5/30 = 16.7% Moluccas, 4/28 = 14.3% Alor, 11/92 = 12.0% Lembata, 17/350 = 4.9% Sumba, 2/54 = 3.7% Mandar (West Sulawesi), 0/9 Timor]7/957 = 0.7% O3*-M122(xO3a-P197) [7/350 = 2.0% Sumba]34/957 = 3.6% O3a2-P201(xO3a2b-M7, O3a2c1-M134) [9/54 = 16.7% Mandar (West Sulawesi), 1/9 = 11.1% Timor, 3/30 = 10.0% Moluccas, 18/394 = 4.6% Flores, 3/350 = 0.9% Sumba, 0/28 Alor, 0/92 Lembata]30/957 = 3.1% O1a*-M119(xO1a1-P203, O1a2-M110) [2/394 = 0.5% Flores, 7/54 = 13.0% Mandar (West Sulawesi), 19/350 = 5.4% Sumba, 2/92 = 2.2% Lembata, 0/9 Timor, 0/28 Alor, 0/30 Moluccas]41/957 = 4.3% O1a1-P203 [36/394 = 9.1% Flores, 1/30 = 3.3% Moluccas, 1/92 = 1.1% Lembata, 3/350 = 0.9% Sumba, 0/9 Timor, 0/28 Alor, 0/54 Mandar (West Sulawesi)]27/957 = 2.8% O1a2-M110 [4/54 = 7.4% Mandar (West Sulawesi), 22/350 = 6.3% Sumba, 1/30 = 3.3% Moluccas, 0/9 Timor, 0/28 Alor, 0/92 Lembata, 0/394 Flores]26/957 = 2.7% O2a1-M95(xO2a1a-M111) [7/54 = 13.0% Mandar (West Sulawesi), 18/394 = 4.6% Flores, 1/350 = 0.3% Sumba, 0/9 Timor, 0/28 Alor, 0/30 Moluccas, 0/92 Lembata]1/957 = 0.1% R2a-M124 [1/54 = 1.9% Mandar (West Sulawesi)]1/957 = 0.1% R1a1a-M17 [1/54 = 1.9% Mandar (West Sulawesi)]8/957 = 0.8% S*-M230(xS1-M254) [2/92 = 2.2% Lembata, 3/350 = 0.9% Sumba, 3/394 = 0.8% Flores, 0/9 Timor, 0/28 Alor, 0/30 Moluccas, 0/54 Mandar (West Sulawesi)]127/957 = 13.3% S1-M254(xS1d-M226) [29/92 = 31.5% Lembata, 59/350 = 16.9% Sumba, 5/30 = 16.7% Moluccas, 29/394 = 7.4% Flores, 2/28 = 7.1% Alor, 3/54 = 5.6% Mandar (West Sulawesi), 0/9 Timor]485/957 = 50.7% MNOPS-M526 total [165/957 = 17.2% O-M175 total, 135/957 = 14.1% S-M230 total, 121/957 = 12.6% M-P256 total, 62/957 = 6.5% MNOPS*-M526, 2/957 = 0.2% R-M207 total]458/957 = 47.9% C-RPS4Y total14/957 = 1.5% F-P14(xG-M201, H-M69, I-P19, L-M20, MNOPS-M526, K3-P261) total

       
    45. Ebizur

      January 22, 2013 at 2:49 pm

      Granted, the difference in total frequency between MNOPS-M526 and C-RPS4Y in Wallacea is insignificant, and the raw frequency of C-RPS4Y is actually somewhat higher than that of MNOPS-M526 when O-M175 is excluded on the basis of being more closely related to N-M231, which is basically found only on continental Eurasia (though it has been found in a few individuals from at least Borneo and Fiji as I recall from my reading of other studies), but the difference is not really significant in either case, and the fact remains that even Australasian-specific subclades of MNOPS-M526 exhibit Y-STR variance that is approximately equal to or greater than that of C-RPS4Y in Australasia: Western IndonesiaMNOPS-M526 (n=876)Variance = 0.594O-M175 (n=804)Variance = 0.547C-RPS4Y (n=40), including 39 C-RPS4Y(xC2-M38, C3-M217) and 1 C3-M217Variance = 0.165Eastern IndonesiaMNOPS-M526 (n=484)Variance = 0.738C-RPS4Y (n=456)Variance = 0.650O-M175 (n=166)Variance = 0.597M-P34 (n=111)Variance = 0.590M-P256 (n=121)Variance = 0.587Oceania (n=182), including 44 Maewo (Vanuatu), 33 PNG Highland, 24 Tahiti, 16 Micronesia, 15 PNG Coastal, 12 Tonga, 12 Western Samoa, 10 Nasioi, 10 Rapa Nui, 6 American SamoaO-M175 (n=31), including 18 O3a2-P201, 5 O3-M122(xO3a2-P201), 4 O1a*-M119(xP203, M110), 2 O-P203, 1 O-M110, and 1 O2b-SRY465(xO2b1-47z) Variance = 1.031MNOPS-M526 (n=121)Variance = 0.982M-P256 (n=46)Variance = 0.706C-RPS4Y (n=59), including 40 C2a1-P33 (15 Tahiti, 9 Rapa Nui, 8 Western Samoa, 4 American Samoa, 4 Tonga), 5 C2a-M208(xC2a1-P33) (2 PNG Coastal, 1 Vanuatu-Maewo, 1 Tahiti, 1 Western Samoa), 12 C2*-M38(xC2a-M208) (9 Vanuatu-Maewo, 2 PNG Highland, 1 Micronesia), 2 C-RPS4Y(xC2-M38, C3-M217) (1 PNG Coastal, 1 Micronesia)Variance = 0.460S-M230 (n=23)Variance = 0.428If the variance of M-P256 is not significantly less than the variance of C-RPS4Y (which includes C2-M38) in Australasia, then there is no way to support the hypothesis of an earlier expansion of C-RPS4Y into Australasia followed by a later expansion of the MNOPS-M526 group that would become the ancestor of M-P256. Extant C-RPS4Y and M-P256 Y-chromosomes in Australasia reflect expansions that have bequeathed approximately the same amount of Y-STR variance to modern populations in the region, so they should be assumed to have begun their expansion in the region at approximately the same time without any evidence to the contrary (à la O-M175).

       
    46. Maju

      January 22, 2013 at 6:12 pm

      @Ebizur: indeed you are right and I stand corrected on my previous claim re. K in Wallacea. Still there's a lot of other reasons to question the origin of MNOPS [K(xLT)] beyond Wallace line, for example the lack of 'Denisovan' admixture in mainland Eurasia (but very marked in non-admixed Aboriginal Australasians) or the much more clear to gauge diversity of mtDNA R (or whatever other mtDNA-focused viewpoint you wish to adopt), never mind the archaeological issues.As for the variance issue you mention, I find not very useful to compare variance between different haplogroups. Personally I think it's plausible that C arrived first or that C and MNOPS arrived together, having diverse founder effects depending on region. The main reason to imagine the C first model is that MNOPS in Eastern Greater Eurasia (i.e. East Asia plus Near Oceania) appears overall as a wedge between the two main C zones (NE Asia and Australasia-cum-Wallacea) but I reckon that there are other more randomized possibilities to end up with such distribution – so I leave this issue somewhat open.Still, looking again at the mtDNA angle, Y-DNA MNOPS in Eurasia can be somewhat strongly correlated with mtDNA R (R11-F and B especially in East Asia but many other clades in SE Asia and Australasia, and yet many others in South Asia and West Eurasia) and this may support the two successive waves model I am tempted by. They'd be both very early in time, maybe one pre-Toba and the other post-Toba for example – or, if a bit later, one previous to the domestication of dogs in SEA and the other after it (the dogs would give the competitive edge in this case).

       
    47. terryt

      January 22, 2013 at 11:07 pm

      "Not quite but almost so.[no human population has spread out like ink through blotting paper]" Incorrect. Even in Polynesia people occupied the coast first and only moved further inland as it became necessary through population growth. And even today in Africa various groups tend to occupy similar ecological niches while other groups occupy different ones. "100 founders create a population of millions (if conditions allow) in few centuries". Yes, but they generally don't. Habitat constraints kick in. And that 'few centuries' allows all sorts of other developments. "Which make some 99% of the extant MNOPS, at least in numbers, and are two of the most widespread Y-DNA haplogroups on Earth". So now you're claiming what you used to accuse me of doing. Particular haplogroups coalesced everywhere at once. What have the bare 'numbers' in each haplogroup got to do with 'origin'? According to your logic Y-DNA R probably coalesced in North America. "the current ISOGG tree is absolutely real (it has been amended once and again and will be in the future)". The fundmanental tree has not been substantially altered for years now. Mostly just new subclades have been added. The last major alteration was the discovery of MNOPS. I agree that K may have some phylogeny yet to be resolved. "Actually, MNOPS-M526 comprises the majority of Y-DNA in the Karafet team's samples of populations from Wallacea" Thanks yet again for your most informative collection of data. "MNOPS in Eastern Greater Eurasia (i.e. East Asia plus Near Oceania) appears overall as a wedge between the two main C zones (NE Asia and Australasia-cum-Wallacea)" Not entirely true. I hope Ebizur can provide data but I'm sure undifferentiated C*-RPS4Y is reasonably common around the South China Sea. "for example the lack of 'Denisovan' admixture in mainland Eurasia (but very marked in non-admixed Aboriginal Australasians)" I think the whole matter of Denisova admixture is far from clear. I'm sure that further research will reveal much. "Still, looking again at the mtDNA angle, Y-DNA MNOPS in Eurasia can be somewhat strongly correlated with mtDNA R (R11-F and B especially in East Asia" Especially in SE Asia. I've been trying to get you to see that for years. In fact check the distribution of mt-DNA in the region: No basal M or N in Wallacea or Southern Indonesia. Just downstream haplogroups. On the other hand we find R23 straddling Wallace's Line in Bali and Sumba, R22 in the Lesser Sunda Islands and R14 in the Lesser Sunda Islands (as well as in New Guinea and the Nicobars, the latter definitely a later arrival). We also have P in Australia (along with N-derived N13, N14, S and O), R12'21 in Australia and the Malay Negritos). And R11-F and B are fairly close by although basal M and N haplogroups share the region with them. To me is is more than 'just possible' that mt-DNA R and Y-DNA MNOPS coalesced and expanded from very much the same region. The second of the waves you than support would be from east to west, through South Asia.

       
    48. Maju

      January 23, 2013 at 8:13 am

      "Habitat constraints kick in".That may apply for really cold regions or arid ones but hardly for tropical ones: people take what they need and I just don't believe in your arbitrary micro-niche differences between coast and inland or savanna and jungle, differences do exist but not at the level of making some areas effectively impassable, that's an absurd belief."What have the bare 'numbers' in each haplogroup got to do with 'origin'?"Nothing. Just that 99% of numbers may hide much diversity. That was my point. You persuade me with the mtDNA, the Denisovan DNA and the archaeology (or at least two of these three) and I'll believe in your Wallacean hypothesis. Meanwhile not: it's just an artifact caused by irregular research levels."I'm sure undifferentiated C*-RPS4Y is reasonably common around the South China Sea". Undifferentiated? You mean unclassified subclades. There's nothing undifferentiated about "asterisk" clades but our vision (or lack of it thereof). Whatever the case, when I described my impression on C being at the periphery of MNOPS that's obviously based on numbers, so a few rear-guard survivors won't change that. But well, enough. Please tell me how all this correlate with data that, at best, can only be interpreted as SA→AA direction and never vice versa.

       

    Leave a Reply

    Fill in your details below or click an icon to log in:

    WordPress.com Logo

    You are commenting using your WordPress.com account. Log Out / Change )

    Twitter picture

    You are commenting using your Twitter account. Log Out / Change )

    Facebook photo

    You are commenting using your Facebook account. Log Out / Change )

    Google+ photo

    You are commenting using your Google+ account. Log Out / Change )

    Connecting to %s

     
    %d bloggers like this: