September 30, 2010

Y-chromosomes of Filipino Negritos and non-Negritos

European Journal of Human Genetics (29 September 2010) | doi:10.1038/ejhg.2010.162

The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups

Frederick Delfin et al.


The Philippines exhibits a rich diversity of people, languages, and culture, including so-called ‘Negrito’ groups that have for long fascinated anthropologists, yet little is known about their genetic diversity. We report here, a survey of Y-chromosome variation in 390 individuals from 16 Filipino ethnolinguistic groups, including six Negrito groups, from across the archipelago. We find extreme diversity in the Y-chromosome lineages of Filipino groups with heterogeneity seen in both Negrito and non-Negrito groups, which does not support a simple dichotomy of Filipino groups as Negrito vs non-Negrito. Filipino non-recombining region of the human Y chromosome lineages reflect a chronology that extends from after the initial colonization of the Asia-Pacific region, to the time frame of the Austronesian expansion. Filipino groups appear to have diverse genetic affinities with different populations in the Asia-Pacific region. In particular, some Negrito groups are associated with indigenous Australians, with a potential time for the association ranging from the initial colonization of the region to more recent (after colonization) times. Overall, our results indicate extensive heterogeneity contributing to a complex genetic history for Filipino groups, with varying roles for migrations from outside the Philippines, genetic drift, and admixture among neighboring groups.

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24 comments:

  1. That map cannot be right: it's full of gray "other", and that means Y(xC,K), what in Eurasia can only mean DE or F(xK), neither of which has been reported at meaningful levels in Island SE Asia, much less Papua.

    There must be an error with the coloring. The Filipino inset seems correct though.

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  2. For what I can see (through the gray goo mist) it looks like:

    C (C2?) and K (MNOPS) are Negrito clades. From what I recall also present in Melanesia and Wallacea and should correspond with the oldest crossing(s) of Wallace Line and the straits West of Philippines, maybe as early as the Middle Paleolithic.

    O1a and O1a2 are specifically Austronesian clades, found in Taiwan Aborigines and Filipinos in great apportions.

    Other O clades, mostly O3, must have other pre-Austronesian origin. In Philippines, O3* in particular is found among Southern Malay Filipinos and two Negrito groups, one of them from further North (Iraya). O3a3b seems related to North Filipinos but not Taiwan Aborigines.

    Malay Filipinos seem divided in three clusters: North, West/Center and South. The Southern cluster looks the less Austronesian because of the high O3* (and some K and C); the Western cluster is dominated by O1a2, except the Hanunuo, who actually appear "Negrito" with all that K, while the Northern cluster is more diverse (O1a*, O1a2 and some "pre-Austronesian" O3a3b).

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  3. Based on the Y-chromosome haplogroup distributions, it seems that the racially purest thus most Negritoid Philippine Negrito group is the Aeta.

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  4. "some Negrito groups are associated with indigenous Australians"

    Which ones are associated with Australians? The author doesn't discriminate between any possible various Cs or Ks, yet these are the most likely haplogroups involved. But the C appears to be mostly South Wallacean, prssumably C2. Is it C2 in the Agta? And What K is spread down the western side of the main island? Admittedly the article deals with the Philippines but if they're going to look at the wider picture it's strange that no C appears anywhere in New Guinea or the islands to the north. Or even stranger still, on the Pacific islands.

    The maps differentiate between an array of Os, yet they're almost certainly relatively recent arrivals in the Philippines. And what is the NO haplogroup shown in Northern Mindanao (Surigaonon and Manobo)?

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  5. "Other O clades, mostly O3, must have other pre-Austronesian origin".

    On what grounds do you claim that to be the case? O3 is certainly part of the Austronesian expansion into the Pacific. So all Os are present in the Austronesian expansion, although some may have been picked up during the expansion.

    "The Southern cluster looks the less Austronesian because of the high O3*"

    Could be more Austronesian if it's associated with the eastward movement.

    "Malay Filipinos seem divided in three clusters: North, West/Center and South".

    That is interesting and warrants further investigation.

    "the racially purest thus most Negritoid Philippine Negrito group is the Aeta".

    But what K haplogroup is represented there?

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  6. I love big beautiful map charts as much as the next guy, but this one comes pretty close to the point of visual overload for me. There must be a better way to present this information visually.

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  7. But what K haplogroup is represented there?

    I think the authors didn't feel need to discriminate between branches of K and C because that they are indigenous to the region, so their intense presence in Negrito groups was no surprise for them. But it would have been better if they had further detailed these haplogroups.

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  8. "On what grounds do you claim that to be the case?"

    Because they do not look Aborigen Taiwanese. As simple as that.

    "O3 is certainly part of the Austronesian expansion into the Pacific".

    Pointless. I am discussing Philippines not that later stage. Obviously the Malayo-Polynesian branch of Austronesians coalesced in the Philippines (or very close) but what I am talking is about the first arrival of Austronesians to Philippines from Taiwan. A fact strongly supported by linguistics (and after all "Austronesian" is a linguistic concept).

    If the Indoeuropeans that arrived to America were mostly R1b1b2a1a, that does not mean that R1b1b2a1a is originally Indoeuropean. In fact it is surely not the case.

    Can you make a difference between the core population and the expanded population, which may well be very different genetically? Language (and culture, ethnic identity) is much more easy to spread than genes.

    "So all Os are present in the Austronesian expansion, although some may have been picked up during the expansion".

    Pointless. Messing around with words. Arguing about nothing.

    "That is interesting and warrants further investigation".

    I don't know much but I stumbled today on this Wikipedia map on main ethnicities in Philippines and the color code seems to follow that same pattern. However the legend does not help to clarify.

    Maybe someone can illustrate us.

    "But what K haplogroup is represented there?"

    We don't know. Surely MNOPS(xNO,P). MNOPS*... I know it doesn't help.

    "There must be a better way to present this information visually".

    Specially filling in the colors in all cakes. :(

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  9. A rather odd, but intriguing study. You can find it here. http://www.yourfilelink.com/get.php?fid=577370

    On the one hand, they didn't screen for any known sublineages of C and K. On the other hand, they show (Fig. 3) that Negrito and non-Negrito C's are related to Australian and SE Asian ones but apparently not to Polynesian ones. Interestingly, non-Negrito Cs seem to be different from the Negrito C's, coming off from SEAsian C's and BOTH having a connection to Australia. This likely means that Negrito, non-Negrito and Australian aboriginal groups all derive from an ancient SE pool.

    On the one hand, they claim "In particular, some Negrito groups are associated with indigenous Australians" but their Fig. 3 shows that non-Negrito groups also have an Australian connection.

    On the one hand, they claim "We find extreme diversity in the Y-chromosome lineages of Filipino groups with heterogeneity seen in both Negrito and non-Negrito groups, which does not support a simple dichotomy of Filipino groups as Negrito vs non-Negrito." On the other hand, they remark: "Recently, analysis of about 50 000 SNPs in a wide variety of Asian populations, including several FEN groups, found no clear-cut genetic distinction between FEN and FEnN groups, and concluded that, FEN and FEnN groups were part of the same wave of migration.14 This conclusion seems at odds with both the NRY data, which indicate an earlier presence of haplogroups C-RPS4Y and K-M9 in the Philippines that is associated with FEN groups, and with mtDNA data indicating novel and ancient mtDNA lineages in a FEN group (E Gunnarsdottir and M Stoneking, unpublished data)." Their Table 1 shows that virtually all haplogroups detected in the Philippines, including C and K, are shared between Negrito and Non-Negrito groups.

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  10. Surely MNOPS(xNO,P). MNOPS*

    That is for sure of course.

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  11. "I think the authors didn't feel need to discriminate between branches of K and C because that they are indigenous to the region"

    They may not be indigenous to the Philippines though. C2 may have come north from South Wallacea with the Austronesian shuffle, and K may be a back movement from New Guinea (although it does seem to be in the wrong place for this to be so). To me they are the two most interesting haplogroups in the map. The other are all definitely more recent than the Paleolithic, and probably part of the Austronesian shuffle.

    "Because they do not look Aborigen Taiwanese. As simple as that".

    It's not actually simple at all. The Austronesians are by no means exclusively Y-hap O1 and O2. Certainly it looks as though O1 moved south to the Philippines from Taiwan, and kick-started the Austronesian expansion, but beyond the Philippines we find very little O1. To the south the Austronesians are associted with both other O haplogroups.

    "I am talking is about the first arrival of Austronesians to Philippines from Taiwan".

    That is O1. Neither of the others.

    "Can you make a difference between the core population and the expanded population, which may well be very different genetically?"

    Obviously yes. The core Austronesians were Y-hap O1 but other haplogroups were taken up during the expansion. And that expansion is most unlikely to have been uni-directional, especially before it had built up a head of steam.

    "Pointless. Messing around with words. Arguing about nothing".

    No it's not. Both O2 and O3 could easily have been introduced to the Philippines after Y-hap O1. In fact are most likely to have been so. O3 almost certainly does not represent a pre-Austronesian haplogroup in the Philippines.

    "which indicate an earlier presence of haplogroups C-RPS4Y and K-M9 in the Philippines"

    Maybe not. That is why I consider those haplogroups to be the most interesting in the study. They may be pre-Austronesian there, but they may not be. They too may be outsiders.

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  12. They may not be indigenous to the Philippines though. C2 may have come north from South Wallacea with the Austronesian shuffle, and K may be a back movement from New Guinea (although it does seem to be in the wrong place for this to be so).

    By region, I meant the wider region consisting of Oceania, Australia, New Zealand and parts of Southeastern Asia including all of the Malay Archipelago, shortly all of the regions that more or less carry the genetic imprint of Australoid and/or Negritoid populations.

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  13. "beyond the Philippines we find very little O1".

    I've checked my data and see I was wrong there. Y-hap O1 does indeed spread down to Tenggara. It then swings east to a little bit in the Moluccas, and even a small amount out as far as Western Polynesia, and west to Borneo, Java and Sumatra.

    "To the south the Austronesians are associted with both other O haplogroups".

    The main O haplogroup in the Austronesian-speaking people of the Pacific is O3a. O3 is the most common haplogroup all through China, Vietnam, Malaysia and Sumatra. Therefore it's unlikely to be early, pre-Austronesian, to the Philippines. The O haplogroup in Madagascar, and which presumably carried the Austronesian language there, is O2a.

    "By region, I meant the wider region consisting of Oceania, Australia, New Zealand and parts of Southeastern Asia including all of the Malay Archipelago, shortly all of the regions that more or less carry the genetic imprint of Australoid and/or Negritoid populations".

    So you agree that Y-hap O is an immigrant to the region?

    By the way Maju. I was studying evolution, genes and subspecies formation long before you were born.

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  14. So you agree that Y-hap O is an immigrant to the region?

    It most probably arrived the region later than K and C, but I think it isn't clear when.

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  15. I think the "C-RPS4Y" in the charts of this paper is actually C*. We can see that the majority of Polynesian Y-DNA shown in the map are "Others" which should be C2, and "Others" in Australia are mostly C4.

    Negrito K-M9 could be k-M526* and Filipino O3* could be mostly O3a3-P201*, according to Karafet's 2010 paper on Indonesian Y-DNA.

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  16. to terryt:

    According to Karafet et al. 2010, the main O haplogroup of Austronesian people of the Pacific is O3a3-P201*.

    http://konglong.5d6d.com/userdirs/8/6/konglong/attachments/month_1003/100310061232b28285bd8a61b3.png

    http://konglong.5d6d.com/userdirs/8/6/konglong/attachments/month_1006/1006301937fb1a1dd6c6fb34f7.jpg

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  17. The full paper is here if you haven't read it:

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

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  18. "I think the "C-RPS4Y" in the charts of this paper is actually C*."

    And C* is most likely an unclassified C lineage, for which SNPs are unknown, right? This means SEAsia has something like C7 distinct from C2 and C4 in the South and C5, C1 and C3 in the North.

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  19. To German Dziebel:

    I agree with you, that's what I think, we can also see C* (C-RPS4Y*) widespread in ISEA from Karafet's paper and chart.

    Please see this:

    http://konglong.5d6d.com/userdirs/8/6/konglong/attachments/month_1003/1003100612c0a6320d06a3206c.png

    http://konglong.5d6d.com/userdirs/8/6/konglong/attachments/month_1006/1006301937fb1a1dd6c6fb34f7.jpg

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  20. "This means SEAsia has something like C7 distinct from C2 and C4 in the South and C5, C1 and C3 in the North".

    That's a valid way of looking at it I suppose.

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  21. I am confused by the mention in some comments about 'malay Filipinos' which I interpret to indicate mainstream Filipinos. The Philippine map is showing information ONLY from what we call "cultural minorities" or "indigenous communities".

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  22. 'Malay Filipinos' means non-Negrito Filipinos generally. The Malays almost certainly are associated in the Philippines with Austronesian-speaking people. As you say, they are now a majority, mainstream if you like.

    "The Philippine map is showing information ONLY from what we call 'cultural minorities' or 'indigenous communities'".

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  23. There are no data for the 'Malay Filipinos' in the map, are there? I do not see data for Tagalogs, Ilocanos, or Visayans. I am presuming that the discussion here is limited to Philippine ethnic minorities who actually moved into the archipelago much earlier.

    The ethnic minorities represent early inhabitants of the archipelago and are understandably genetically diverse. I came across this looking for mainstream Filipino haplogroups and the diversity between regions.

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  24. Malay Filipinos would be entirely Y-DNA O of some sort except for very minor (if any) uptake of older haplogroups.

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