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:

Wan Isa Hatin et al, Population Genetic Structure of Peninsular Malaysia Malay Sub-Ethnic Groups. PLoS ONE, 2011. Open access. 

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.

 

More Austronesian genetics: Dayaks are mostly pre-Austronesian (as most other Austronesians)

I just had to mention a paper on Austronesian genetics at one of the great open access publications, Bio Med Central (BMC), and now I have to mention another at the other major open access magazine: Public Library of Science (PLoS):

Tatum S. Simonson et al., Ancestry of the Iban Is Predominantly Southeast Asian: Genetic Evidence from Autosomal, Mitochondrial, and Y Chromosomes. PLoS ONE 2011. Open access.

Because good things always come in batches, right?

Well whatever the case, the Sea Dayaks or Iban people do not cluster well with Taiwan Aborigines or other possible source populations for the fabled Austronesian colonization of Island SE Asia. Nope, they cluster best with mainland SE Asia, notably Vietnamese, Thais and peninsular Malays.

For example, for autosomal DNA, we get the following graph (fig 2):

Where the Iban cluster best with some Indonesian (but not others) and Thais (again some but not others) but not with Taiwan Aborigines (and only poorly with Filipinos).

Not convinced? I cannot blame you because PC analysis suck and specially for autosomal genetics. They also provide a K=3 admixture analysis (fig. S1):

Here we can spot three components, neither of which is too specific. Still the red component seems strongest among Malaysian (not the Iban however), the blue component is most common among some Indonesians, while the green component is widespread by dominant in the mainland if anything (specially Japan/North China). Not too clear anyhow but for deeper clustering you probably want something else, like the HUGO paper.

Let’s see the Y-DNA then (fig. 3):

This is more clear, right: here the Iban are almost like Vietnamese and then like other Sundaland Malays but not like Taiwan Aborigines nor Filipinos. So Y-DNA-wise they do not look particularly Austronesian recent arrivals but older arrivals from Indochina if anything.

MtDNA? Let’s see:

Seems not again: Philippines and Taiwan are far away, while Sundaland, Orang Asli, Thais and Chinese are closer.

The authors conclude:

The majority of mtDNA haplogroups and the greatest proportion of NRY lineages identified in our Iban sample are associated with population movements that occurred prior to this expansion. More NRY haplogroups than mtDNA haplogroups were introduced into this population during the Neolithic expansion, but the proportion of NRY haplogroups attributed to this more recent event is still less than half of the total NRY haplogroups identified. Therefore, it appears that migrations during the Neolithic did not eradicate pre-Neolithic groups.

Another blow against Neolithic replacement nonsense.