April 6, 2011

Malaysians fall in diverse genetic clusters

A paper of some interest on Malay autosomal genetics and their relations with other Asian peoples has just been published:


Most interesting is fig. 1, which displays a neighbor-joining of the various Malaysian populations (four Malay, one Proto-Malay and two Orang Asli or Negrito populations) and other populations studied here (see table 1 for details). Here goes my annotated version of this tree (all color elements are my addition):

click to expand

The authors go to some quite incredible speculations to explain the various clusterings of Malays (Melayu, boxed populations in graph), notably imaginary massive admixture with Indians and Chinese. 

I understand that they are very wrong and that what the tree is crying out loud is the following:
  • Cluster I represents more or less genuine Austronesians by blood. I say this because the Thoraja (ID-TR) have in the past been shown to be quite archetypal Austronesians in autosomal studies.
  • Cluster II represents more or less genuine pre-Austronesians, proto-Malay or whatever you wish to call them. They cluster well with "Chinese"... from Yunnan (SE Asian Tibeto-Burman and Mon-Khmer speaking peoples), which are the only "Chinese" in this paper. Yunnanese, Proto-Malay, Melayu Jawa and Javanese Indonesians cluster too tightly to be any admixture: they are one single stock.
  • The so called cluster III is no cluster (it needs at least two elements to be called that way) but an isolate. It may indicate an even older stock than proto-Malay but it may also indicate admixture with either Indians or Negritos.
There is also a 3D PC analysis but, besides showing that the same dual clustering among SE Asian Mongoloids, it is very difficult to read. I'd say that it is suggestive of both Melayu Minang and Melayu Kelantan showing a slight tendency towards Indians along dimension 3 rather than towards Negritos but it may well be an optical illusion. It does place these two populations somewhat apart within the region anyhow.

10 comments:

  1. Malaysia is not anywhere close to monoethnic event today (50% Malay, 24% Chinese, 11% indigeneous, 7% Indian); has many religions that intersect with ethnicity (60% Muslim, 19% Buddhist, 9% Christian, 6% Hindi); has many languages (including Bahasa Malaysia, English, multiple Chinese dialects, Panjabi and Thai); has subnational monarchies still exist who elect a first among equals to be head of state, and was cobbled together by the British from at least four predecessor states by the British in 1963, Singapore left in 1965 because there was too much factional tension) and has a geographically factured territory that is small enough to allow ready admixture to the extent that local culture permits it.

    Given all of that, lots of clusters are to be expected.

    The Austronesian and Negrito clusters you discuss are straight forward and make a lot of sense. Negrito are, of course, the oldest, Austronesians, of course, the youngest, and both extremes are well understood.

    The two groups in Cluster II and the one in Cluster III are the interesting ones. A Chinese aligned cluster makes lot of sense. One ought to be a Thai/Austroasiatic aligned cluster. One ought to align more or less with oldest layer non-Negrito Indonesians.

    The descriptions of the categories, as is so often the case, are a bit opaque to make out.

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  2. Following up, on closer examination:

    The Bugis in Cluster I are an ethnicity that crosses national boundaries into Indonesia and speak an Austronesian language.

    The Minang in Cluster I are a strongly identified Austronesian ethnicity.

    The Jawa in Cluster II (MN-JV) are ethnically affiliated with the Javans of Indonesia, and would be old layer pre-Austronesian Sunda Indonesian, and cluster most tightly with the Indonesian co-ethnics. Their current language appears to be Austronesian, but was probably not in ancient times.

    The Temuan in Cluster II (MN-TM) are identifed as indigeneous and would be old layer pre-Austronesian Sunda people. Their language appears to be Austronesian, but was probably not in ancient times.

    The Chinese Wa in Yunnan province in Cluster II are Mon-Khmer linguistically and ethnically, rather than Tibeto-Burmese. The clustering of the Jinuo of Yunnan province would suggest that their Tibeto-Burmese linguistic affiliation is probably a case of language switch without demic replacement and that they were probably Mon-Khmer population sometime back far enough to be lost to history.

    The Cluster III appears to be Thai aligned by recent admixture, historic origin traditions and geography (the far Northern edge).

    It is interesting that the Negritos are intermediate between the Clusters I-III with East/Southeast Asian affinities and the cluster from India proper.

    Chinese and Indian populations appear to be excluded from the sample as being non-Malaysians.

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  3. They only analyzed "native" populations in Malaysia: Malays, Proto-Malays and Orang Asli. "Immigrant" populations like Chinese, Indians, etc. are not considered. Also 3-generation ancestry in the community was demanded so no recent hybridation is believed to be at play.

    "The Chinese Wa in Yunnan province in Cluster II are Mon-Khmer linguistically and ethnically, rather than Tibeto-Burmese".

    Thanks for that tip. I did not expect that (and have not checked myself as I did not know of any Mon-Khmer in Yunnan).

    "The clustering of the Jinuo of Yunnan province would suggest that their Tibeto-Burmese linguistic affiliation is probably a case of language switch without demic replacement and that they were probably Mon-Khmer population sometime back far enough to be lost to history".

    As I often say: languages change, genes remain.

    "The Cluster III appears to be Thai aligned by recent admixture, historic origin traditions and geography (the far Northern edge)".

    That's something I did consider but in that case I would have expected proximity with Cluster II ("old SE Asian" apparently) and in no case to be out of the "Mongoloid" set (clusters I+II). So the admixture with either Indians or Negritos is a real possibility.

    "It is interesting that the Negritos are intermediate between the Clusters I-III with East/Southeast Asian affinities and the cluster from India proper".

    That's normal if you consider:

    (1) the Eurasian expansion process, when the division between South Asians and Eastern Eurasians happened first of all (according to what I gather from mtDNA and Y-DNA).

    (2) that Negritos may have some "Mongoloid" admixture and vice-versa.

    But even in the Hugo paper Papuans clearly clustered with East Asians (in contrast to South and West Eurasians). They stem from the same stock even if the root of that stock is twice or even thrice older than uncle Cro-Magnon (more or less).

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  4. The clustering show in the tree-like chart (which is not drawn to scale and doesn't indicate which secondary branches are closest to separate primary branchings) doesn't seem like a very good fit for the relationships shown in the 3D-PCA chart where MY-KN (cluster three) is involved. MY-KN seems quite close to MY-MN, and both MY-KN and MY-MN are a bit removed from the overall cluster, so the case for make it a deeply rooted different branch of the phylogenetic tree is not too clear.

    Cluster Three is fairly close to Clusters One and Two but quite remote from the samples from India and the Negrito samples and Cluster Three is not intermediate between the main Cluster One and Cluster Two group on one hand and the Negrito sample on the other. So Negrito admixture is not supported and Indian admixture doesn't look particularly plausible from the MY-KN position either.

    The seeming lack of closeness is exaggerated by the lack of East Asian samples such as Han Chinese or Japanese or Korean or Tibetan or even Hmong-Mien in the analysis, and by the fact that the Chinese samples are probably not genetically typical of Chinese populations.

    If those reference populations were included, I think that you would find that everyone in Clusters I-III would fit in Southeast Asian cluster distinct from East Asian/Northest Asin clusters.

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  5. "The authors go to some quite incredible speculations to explain the various clusterings of Malays (Melayu, boxed populations in graph), notably imaginary massive admixture with Indians and Chinese. I understand that they are very wrong"

    Of course you do. You have refused to accept any substantial prehistoric movement into SE Asia from further north for as long as I've been commenting on your blog. Seems (as I already knew) that I am not the only one to accept such southward movement. As for the India element, I'm not so sure. However certainly many Thais and Camdodians certainly look more 'Indian' than they do 'East Asian'.

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  6. Regardless: the authors fail to demonstrate in any meaningful way such ideas of admixture. What we see is two different stocks, plus the third one of the Negritos, and an anomalous isolate (Melayu Kelantan) that might or not represent admixture.

    If the MK position in the NJ tree represents admixture, it is not clear with whom. It may also just represent another layer of the Paleolithic ethnogenesis of Eastern Eurasia: a stage between Negritos and Mongoloids, so to say. Or more precisely a proto-Mongoloid stage.

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  7. You can imagine (real or not) migrations of clusters I and II. Cluster II has at least a "northern" (Yunnan) component while cluster I is surely the Austronesian (Malay) one (from Philippines or Taiwan?) because of the Thoraja inclusion.

    But "cluster III" (Melayu Kelantan) would if anything speak of at least partial local roots prior to these alleged migrations, because it's closer to Negritos, Indians and Yorubans, standing out of the shared I+II Mongoloid-specific double cluster.

    I'm not taking a stand but attributing admixture "just because", without even checking it (as simple as taking HapMap control samples and running Admixture or whatever of the like) is nonsensical, unscientific and speculative.

    "Religious" in other words.

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  8. If you want to let your imagination speculate based on phenotypes also:

    - Kelantan football team
    - Minang ladies from Negeri Sembilan
    - Bugis girls from Johor in dancing clothes
    - Jawa men dancer-percusionists from Johor

    The Minang look very much Thoraja to me (even the hats remind of Thoraja boat-shaped homes), even if the Bugis should cluster closer - they are related to the Bugis of Sulawesi, who are neighbors of the Thoraja.

    The Jawa instead give a "Chinese" vibe in their clothing and arguably their looks, even if their closest relative are Javanese (no idea how are Javanese dances, sorry).

    One could well say that some of the Kelantan individuals look vaguely South Asian instead. Is this because of admixture of because they retain more of the unmodified original pan-Eurasian roots? I'd say the second but I'm not sure.

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  9. "Malaysia is not anywhere close to monoethnic event today"

    And it's basically two separate regions: peninsular Malaya and the Northwest Borneo. I'd expect the two regions to have a reasonably separate history and prehistory.

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