Asian Negritos are not one population

By Razib Khan | July 21, 2011 8:39 pm

Negrito, Philippines. Credit: Ken Ilio

In the post below I mentioned that the Malaysian and Philippine Negritos seem to be two very distinct populations. This was something I wanted to explore in more detail, so I naturally decided to poke around the Pan-Asian SNP data set. The aims are made somewhat more difficult by the fact that there are only ~56,000 markers in the data set (as opposed to ~600,000 in the HGDP and more than 1 million in the HapMap). Additionally, the intersection with other data sets is small. For example, only ~20,000 SNPs with the HGDP. With all that in mind I hazarded that something is better than nothing. Relatives and HapMap populations were removed from the data set (thanks Zack). Additionally, I beefed up the South Asian populations with the Gujaratis from the HapMap,which had an intersection of ~32,000 SNPs. After a few test runs I decided to remove the Mlabri. They always shook out very early as a separate population from many others nearby, and, their genetic distances were very high. This tribe is only numbered in the hundreds, and I wouldn’t be surprised if they’ve been subjected to a lot of population bottlenecks, resulting in some very distinctive allele frequencies.

But before I move to the results, let’s back up for a moment. Who are the “Negritos”? As suggested by the term Negrito refers to a range of populations which are characterized by small size and African-like features (very dark skin and frizzy hair). In general their distribution is limited to Southeast Asia (there are suggestions that a Negrito population may only recently have gone extinct in Australia’s rainforests, but that’s speculative. On a more antique scale there are records which may be interpreted to suggest the existence of Negritos in Taiwan as late as 1900, and in southern China within the past 1,000 years). So you can bracket their distribution from the Andaman Islands to the Philippines, with isolated groups in the Malay peninsula. Negritos are presumed to be the original inhabitants of Southeast Asia before the arrival of rice farmers from the north. Like the Pygmies of Africa most of the Negritos speak languages whic hare known in other populations. Those of the Philippines speak Austronesian dialects. Interestingly those of Malaysia speak an Austro-Asiatic language, and so have affinities with many groups to their north linguistically, being surrounded by Austronesian speakers. Only the Andaman Islanders have a distinctive language, which makes sense seeing as how they have been relatively isolated from mainland Asian influences.

I ran ADMIXTURE from K = 4 to K = 12. K = 8 seemed the most informative to me (at higher K’s the major dynamic is that the Philippine Negritos start fragmenting into many distinct clusters). I’ve made a few cosmetic changes. With this East and Southeast Asia heavy data set there’s almost no difference between all the various Indian groups, so I amalgamated them together. I also did the same for related populations geographically adjacent which exhibited no genetic difference (e.g., Central and East Javanese).

The distinctiveness of the two Negrito groups is rather obvious. But what makes it even more obvious are the Fst values across two inferred clusters.

NE AsianP NegritoHmongMelanesianS AsianM NegritoAustro-AsiaticAustronesian
NE Asian00.1010.0460.0990.0950.0980.070.045
Philippines Negrito0.10100.110.1050.1130.1240.1080.096
S Asian0.0950.1130.1070.09900.1040.1030.108
Malaysian Negrito0.0980.1240.0990.1130.10400.0860.098

What’s clearly evident here is that the largest genetic distance across any two inferred populations is between the Malaysian and Philippine Negrito clusters! Let’s visualize the relationships a bit:

Observe that Philippine Negrito cluster tends to have an affinity for Austronesians and the Malaysian Negrito one has one for the Austro-Asiatics. You can tell from the different tribes that there’s varied admixture with Austronesians in the former case, but what about the Malaysian Negritos? (who are of the Jehai and Kensui affiliation) Here’s the individual bar plot:

There’s a substantial Austro-Asiatic admixture in this population. We have seen before that ADMIXTURE’s inferred population clusters are only a rough guide to the real populations which existed in the past. The reality is that the history of the human race has been characterized by repeated fissions and fusions of populations, so all ADMIXTURE clusters are going to be composites anyway depending on the chronology which you are using. The affinity of the Malaysian and Philippine Negrito clusters to the ones geographically close to them suggest to me that they’re telling us about ancient admixture events which have been recombined to the point that a new composite population naturally falls out of the algorithm. It may be that after Taiwan the Philippines was the first major landfall of the original Austronesians, so they may have had a substantial impact on the Negritos very early one. This is already clear in most of the Negrito tribes even with ADMIXTURE. In the case of the Malaysian Negritos the admixture is less extreme, but the fact that they speak an Austro-Asiatic language points to hybridization.

I also ran some principal component analyses. Basically each dimension represents an independent axis of variation in the genetic data set. The first component of variation is clearly the west-east one ins Eurasia. Note that it’s 5 times larger than the second dimension. I’ve highlighted the two Negrito populations. Observe that in general they don’t manifest a particular close relationship:

So what’s the moral of this story? Don’t judge a book by its cover! Up until the waters rose with the end of the last Ice Age ~12,000 years ago the southeast region of Eurasia, and out toward Oceania, were far less fragmented. Biogeographically you have Sundaland where Malaysia and western Indonesia are today. To the east there was Sahul, which combined Australia and New Guinea. Expanding out to India and southeast to Australia physical anthropologists in the 20th century posited the Australoid race. Using ADMIXTURE and PCA you can see shadows of an Ice Age Southeast Eurasian race which extended from India to Australia. Shadows because outside of Australia and Melanesia it is either a thin submerged layer, or it persists as residual tribes such as the Ati of the Philippines or the Semang of Malaysia.

Malaysian Negritos ~1900

But these populations had their own population structure and distinctions. My bet would be that the Malaysian Negritos are closer to the Onge of the Andaman Islanders, and that these two groups emerged out of a western branch of Sundalanders. The Philippine Negritos are from an eastern branch, and their closer affinity to Melanesians may be due to longstanding gene flow across the two populations (another option is that very old Austronesian admixture in both has shifted their non-Austronesian components closer together in allele frequency). Overall, I suspect that the past ~10,000 years have been radically different from the past insofar as population replacement and expansion has occurred on a scale never before seen due to the demographic impact of agriculture. The remaining Negritos may be the tip of the iceberg in terms of the genetic diversity which disappeared as the hunters gave way to the farmers.

Image credit: Maximilian Dörrbecker


Comments (37)

  1. Sandgroper

    People can make of that what they like – word of caution, be very wary of anything coming out of the History Wars, on either side.

  2. Joe

    It’s an interesting result, but not overly surprising. In my mental narrative of demographic changes across ancient east Asia, the first modern humans came out of Africa and into Asia, following the sea route, and then multiplied and disbursed. The northerners evolved culturally and genetically differently from the southerners. Conditions changed a few thousand years ago and that precipitated major demographic changes. Small groups of northerners migrated south (austro-asiatics, then Austronesian, then Chinese) and rapidly expanded, permanently changing the demographics. Since the negritos of the south were there for a long time, but the northerners are recent, small groups that quickly expanded, we should expect big differences between geographically separated negritos, they shouldn’t cluster that closely.

  3. Here is Colin Groves’ rejoinder to the Quadrant article:

    And here is another response:

    Both papers refer to my theory on the cause of low stature in rainforest peoples. In my opinion, the so-called Negritos in North Queensland, Australia were simply a local, forest-adapted group of Aborigines. They did not go extinct. Some are still around, although they have bred into the white population and with taller Aborigines. They are discussed in Peter McAllister’s recent book, Pygmonia.

  4. In my opinion, the so-called Negritos in North Queensland, Australia were simply a local, forest-adapted group of Aborigines.

    these results support the repeated origination of this phenotype.

  5. Pavlova

    The purple component is modal among Indonesians, important in Malay Negritos and nearly absent among Phillipine Negritos. Perhaps the Malay Negritos got their purple components from the Malay populations, including proto-Malay.

    Also the Fst distances look weird. NE Asians are closer to Melanesians than SE Asians are to Melanesians? Your results tell me that Northern Chinese, Koreans and Japanese are closer to Melanesians than the SE Asians are to Melanesians.

    Perhaps this NE Asian cluster needs to be separated by higher K’s. This is only speculation, but I have a suspicion that part of the “NE Asian” cluster among Ryukyuans can be split into another cluster that has affinities with Papuans, while the other part of the “NE Asian” cluster is more of a Northern Mongoloid cluster (aka Korean, Tungusic, Yayoi). This is because Ryukyuans are largely Jomon descendants who are, as some claim, Australoid.

  6. carpetanuiq

    If Negrito look is adaptation to rainforest (very likely) we must explain why there are rainnforests ( without
    Negrito-like peoples: I refer for instance places such as New Guinea or America where we know peoples are ancient enough. ¿maybe you need a special kind of rainforest for these traits to evolve (New Guinea is a mountaneous area) ? ¿ maybe not enough time to develop ? ¿ maybe peoples of America had lost genes needed for these traits ?

  7. Ian

    If Negrito look is adaptation to rainforest (very likely) we must explain why there are rainnforests without Negrito-like peoples

    There are two sets of traits that make “Negrito-like peoples” – short stature and curly hair with “African-like” features. Dark skin, I think, is widespread enough outside of the rainforest zone that it can be ignored here.

    The latter combination of features are present in Indian tribals, Papuans, Melanesians and Australians, in addition to Africans, so my guess would be that would just be the retention of ancestral traits, with the ‘European’ and ‘East Asian’ type features representing adaptations to colder climates.

    As for short stature – many ‘rainforest’ groups in the New World are fairly short in stature. And they haven’t been in that sort of an environment nearly as long as these other groups.

    New Guinea may be something of an outlier here, but much of the island is actually quite high elevation – it’s not low elevation tropical rainforest. So the environment may not be equivalent at all. Added to that, of course, is the fact that evolution is not deterministic. Short stature may be one way to deal with a certain set of environmental constraints, but it may not be the only solution the presents itself.

  8. highland new guinea is also not dominated by hunter-gatherers.

  9. Does archaeology provide any insight into how long modern humans have been in either the Philippines or Malaysia?

  10. I think where you have rainforest people who are not of short stature, two things may obtain. Either the people are relatively light-skinned or they are agriculturalists. Or both. People in New Guinea are mostly agriculturalists.

    My theory explains the “negrito” or “pygmy” type on the basis of low ultraviolet light in the rainforest and dark skin. This leads to a lack of capacity to make vitamin D. I wrote this up in “Homo” in 1994.

  11. Sandgroper

    Agriculturalists should get less Vitamin D from diet, not more. But they do clear forest to grow crops.

    Something that stands out with African pygmies, aside from small stature, is shortened life span – they stop growing early, reproduce early and die early.

    Does that happen with any of the peoples labelled as ‘negrito’? I have not seen it referred to in anything I have read about them.

  12. Sandgroper, that sounds like the Migliano life history theory. Reference to tables of ages at menarche and age at first child do not indicate that Pygmies or Negritos are unusual in this regard. That is, they do not become sexually mature any earlier than other human groups.

  13. Pavlova

    These FST results show that NE Asians are closer to Negritos than SE Asians are to Negritos. The results are inaccurate and flawed, unless the NE Asian cluster can be split into different clusters at a higher K, which seems likely since Okinawans should NOT have more “NE Asian” than Koreans and Japanese. It doesn’t make any logical sense. Perhaps the “NE Asian” label should be called “Okinawan” rather than “NE Asian” (which also wouldn’t make much sense since Uyghurs should not have Okinawan admixture, but rather, should have Northern Mongoloid admixture). Higher K’s should be used to split this “NE Asian” cluster to different clusters, such as “Okinawan” and “Northern Mongoloid”.

  14. Sandgroper

    Julian, yes, that’s what I’m referring to. Thanks for reminding me.

    I’m wrong – I see Andrea Migliano also referred specifically to two Filipino groups as well, and generally to “pygmies around the world” as having low life expectancy, typically 16-24 years, as reported on by Ed Yong here:

  15. Sandgroper

    More here, but I can’t access it.

    The abstract refers to early onset of reproduction.

  16. See this:

    See Table 2 for example. I can’t see any evidence that Pygmies and Negritos are unusual in terms of age at menarche or first reproduction.

  17. Sandgroper


    No, neither can I.

  18. The Asmat and the Yanomamo seem to have similar life expectancy to the Pygmies and Negritos, according to the table.

  19. Sandgroper

    Yeah. The Yanomami are pretty small, though.

  20. If Pygmy and Negrito women were actually having babies quickly in response to excessive general mortality, that would make sense. But there is no evidence for that. The authors say that menarche and first reproduction occur “relatively early (given their adult body size)” which is true, but it is not the same as having babies earlier than normal.

  21. Sandgroper

    Reproduction is not the same as having babies? 🙂

    Damn, no wonder I only managed to father one of them.

  22. The authors are saying that Pygmy women have babies while they are small. Well, yes, they are pygmies. But the data show that they are not reproducing (having babies) younger than other groups.

    It is a nice theory, but the data don’t support it.

  23. Sandgroper

    Yeah, I had gained the impression that it’s a dramatic difference, but it’s not, not from those data.

  24. Sandgroper, there has been a lot of uncritical support for the life history theory in the media. From your screenname, you may be an Australian. You may have heard Peter McAllister, an Australian, on the Robin Williams radio program. Peter and I have chatted. I was grateful he covered my UV light theory in his book “Pygmonia”, but I think he is pushing the Migliano theory too hard. I told him that I have been to the area where the Australian “Negritos” lived and I find it hard to credit that it was tougher than other Aboriginal environments.

  25. Sandgroper

    Julian, yes, born in south west. Noongar country.

    I don’t live in Australia much now, but I’m familiar with Peter’s book.

    I agree.

  26. Has anybody out there actually met sizable numbers of different kinds of negritos? If you have, can you tell them apart by looking at them fairly easily, or do the different kinds really do look alike even after you are familiar with them?

    By way of analogy, I’ve looked at enough pictures of Melanesian to reach the point where I could tell them apart from sub-Saharan Africans with, say, about a 90% accuracy rate just from pictures. That’s not a terribly impressive capability, however, because they aren’t closely related at all.

    What about the various flavors of negritos? Do they seem similar to those who know them, or is their similarity mostly just the obvious things: stature, skin, hair?

  27. I think the life history theory is just a “sexier” theory than mine. Mine is pure physiology (UV light, vitamin D, etc.) The life history theory makes for more of a human interest story.

    By the way, the area where Australia’s “Negritos” lived is tropical rainforest. I have not met many of the Aborigines from that area. I did meet one older man who fitted the usual descriptions: short, relatively light skin, “rainforest hair” IIRC. The local doctor (GP, family doctor) showed me around the area and I met some of the people.

  28. Sandgroper

    Julian, I am not too familiar with a lot of Queensland. I was astonished when I first saw those photographs.

    Yeah, I don’t have any ideology or set of priors that I filter stuff through. But it’s certainly not my field, so I tend to accept people’s analysis of data less questioningly than maybe I should, while trying to filter out the extraneous stuff.

    Steve, I have encountered people in peninsular Malaysia who I am pretty sure were Semang – they looked very different from everyone else there – very much darker (except for some Tamils), skinnier and smaller in stature. But in real life, those crude indicators are really not too helpful – e.g. skin is not a colour, it’s a spectrum, has texture, etc; hair varies a lot. People vary a lot in darkness of skin just through UV exposure – e.g. Thai farmers go very dark in the sun. Really, it was the smallness and skinniness that hit me the most, among a general population that are not huge to begin with.

    If you encountered Melanesians in real life, I doubt you would ever confuse them with sub saharan Africans, they are very different. But in real life, you have a lot more inputs – e.g. when I see someone, I don’t really mentally separate out the visual inputs from the aural or behavioural cues, it’s a package. Plus there’s context. But it never did occur to me that Melanesians would be closely related to Africans, there was never I time when I ever thought that. I can’t imagine why anyone would, unless they were just trying to fit everyone onto a very simple racial framework, using a few very crude classifiers. I read some of that stuff as a kid, but it was never credible to me.

  29. occamseraser

    There is a critique of Migliano et al (2007) in Human Biology (Feb, 2010) by Becker et al. Migliano et al. respond in a letter to the editor in the same journal and defend there model for Asian “pygmies”.

    There is a recently described toe bone from the Philippines (Callao Cave) that pushes human arrival there back to at least ~67 ka. (published at length in the Journal of Human Evolution).

  30. Sandgroper

    Steve, spot the similarities. I can’t.

    They’re probably all small. I’d say that’s about it.

    Some of those don’t have black hair, either.

  31. carpetanuiq

    Sandgroper, excelent link !.

    After reading the thread I´m confused about what to consider “Negrito traits” and how to explain the origin of these traits.

    Negrito traits: for me a summary of negrito physical traits, if such a thing exists is: low stature (lower than the average of surounding peoples); curly hair; dark skin (black not brown); I would include also nose shape and maybe mouth and skull shape.
    While New Guineans have some of this traits, I would not label them Negritos.

    Negrito traits origin. Imo there are three competing hypothesis:
    –negrito look is an adaptation to tropical rainforest: no matter how the original surounding populations looked, if you introduce a large enough group in a tropical rainforest, given enough time (how much is enough ?) you will get the full negrito traits package. Some consequences: poeples with Negrito looks can be unrelated; you expect to find Negrito looks wherever you find tropical rainforest and ancient peoples living there; you expect to not find Negrito look peoples outside tropical rainforest.
    –negrito look is a remaining of the first Ooa population. The common traits are explained by descent and adaptation: the original Ooa population was living in tropical rainforest, migrated Ooa through a tropical rainforest or similar biome route and those populations that has been living in a tropical rainforest and isolated since then, has conserved the traits.
    –negrito look explained by descent alone. Same as before but the original Ooa population looked like this even without living in a tropical rainforest and some of their isolated descendants Ooa has mantained their traits. Consequences: we would not be surprised to find negrito traits in isolated populations not living in tropical rainforest (any known case ?).

    One key piece of information is what happened to the areas where we find Negritos today under extreme (cold) climate conditions, that is LGM:

    The match is almost exact: we find Negritos today exactly where we find tropical rainforest during LGM (I could not discern if the light brown color in the corn of Australia refers to tropical rain forest; the same regarding New Guinea north-east coast). We do not find them in places in SA and SEA where there are today tropical rain forest but not during LGM.
    I think this rule out third hypothesis but let open first and second. If first is correct, present Negritos distribution says nothing about Ooa route. If second is correct it may say something.

    P.s. An interesting link regarding the origin of another phenotype: fair eye and hair. In this case the explanation is sexual selection:

  32. The “Negritos” in Queensland, Australia, were once known as Barrineans under a scheme proposed by Norman Tindale and Joseph Birdsell, anthropologists, which had Australia being populated by three waves of migration. The Barrineans were supposedly a short-statured initial group, with remnants in the Queensland rainforests and in Tasmania. The evidence is weak for this theory and most Australian anthropologists would now dismiss the idea. I have seen original diaries by Tindale in which he investigates the rainforest Aborigines and develops his ideas about Barrineans and the supposed Tasmanian connection. (Lake Barrine is a body of water in the rainforest area.)

    The oldest settlement in the Queensland rainforest known to archaeology is at Jiyer Cave, dated to 4,000 years BP.

  33. Sorry, more recent review gives 8,000 years BP for human occupation of Queensland rainforests:

  34. Sandgroper

    Excellent paper.

    So, far from being a remnant of a very early wave of ‘negrito’ migration to Australia, the rain forest people were actually pretty recent occupants adapting to changing environment. Which pretty much shoots giant holes through Birdsell’s theory. Not completely, maybe, but it makes it look increasingly very unlikely.

    I’m always fascinated by Aboriginal toxic plant processing – I try to imagine the process of discovery, and always find it difficult. I mean, some of the processes were fairly complex, and seemingly not intuitive.

  35. Justin Giancola

    “shadows of an Ice Age Southeast Eurasian race which extended from India to Australia. ”

    I would lean towards Arabia through southern Iran through… But there it could be more genetically submerged, or underwater or desert now.

  36. “These FST results show that NE Asians are closer to Negritos than SE Asians are to Negritos. The results are inaccurate and flawed, unless the NE Asian cluster can be split into different clusters at a higher K, which seems likely since Okinawans should NOT have more “NE Asian” than Koreans and Japanese. It doesn’t make any logical sense. Perhaps the “NE Asian” label should be called “Okinawan” rather than “NE Asian” (which also wouldn’t make much sense since Uyghurs should not have Okinawan admixture, but rather, should have Northern Mongoloid admixture). Higher K’s should be used to split this “NE Asian” cluster to different clusters, such as “Okinawan” and “Northern Mongoloid”.”

    There was a major influx of population to Okinawa in the fist millenium from Japan, which was some combination of NE Asian (Yaoyi), Ainu (not clear how that shows up in the ancestral population analysis) and Northern Chinese (mostly at the tail end of this time period). We have very little information about the extent to which Okinawa was virgin territory or experienced population replacement at this time. It is certainly plausible that any prior population mixed with Yaoyi immigrants in proportions similar enough to those of Japan’s main islands that the original inhabitants became geneticall indistinguishable from the other Japanese except that they lacked the same amount of Northern Chinese immigration.


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


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