The Cham People and why the genetic structure of SE Asia is mostly not the product of Austronesian expansion

09 May
Cham girls
There’s a new interesting paper on the haploid genetics of SE Asians, with some focus on the Cham People, who are an enclave of Austronesian speakers in the middle of pre-Austronesian peoples (Austroasiatic specially).


Cham people are the major Austronesian speakers of Mainland Southeast
Asia (MSEA) and the reconstruction of the Cham population history can
provide insights into their diffusion. In this study, we analyzed
non-recombining region of the Y chromosome markers of 177 unrelated
males from four populations in MSEA, including 59 Cham, 76 Kinh, 25 Lao,
and 17 Thai individuals. Incorporating published data from
mitochondrial DNA (mtDNA), our results indicated that, in general, the
Chams are an indigenous Southeast Asian population. The origin of the
Cham people involves the genetic admixture of the Austronesian
immigrants from Island Southeast Asia (ISEA) with the local populations
in MSEA. Discordance between the overall patterns of Y chromosome and
mtDNA in the Chams is evidenced by the presence of some Y chromosome
lineages that prevail in South Asians. Our results suggest that
male-mediated dispersals via the spread of religions and business trade
might play an important role in shaping the patrilineal gene pool of the
Cham people.


Fig. 5 (click for the original)
Just some of the Cham patrilineages seem to be attributable to Austronesian origins from Island SE Asia (ISEA). In this regard, I suggest to take a look with due care to figure 5 (click on thumb at the right), which shows the median-joining networks of the relevant Cham lineages in the context of the wider SE Asian context.
Some detail in brief (see also fig. 2 for the details, n(Cham)=59):
  • P(xO) is all actually R and better observed in fig. 6, where it becomes obvious that it’s all linked to South Asia (R1a1a and R2a).
  • C is mostly C3-P217 but there is also one individual with C* (C2?). It seems mostly related to Mainland SE Asia (MSEA) rather than ISEA, as seems logical for a lineage with the greatest concentration in far NE Asia. The C* single case is probably of Austronesian origin.
  • F(xK) is found in two Cham individuals and some others. One of them is H, which is surely also of “recent” arrival from South Asia (Hindu and Muslim religion, trade).
  • K(xNO,P) is found in 10% of the surveyed Cham men. It may have arrived from ISEA and most is concentrated in a single haplotype among the Cham (further reinforcing the idea of a possible Austronesian founder effect).
  • O* (P191): found in one Cham and obviously from MSEA
  • O1a (M119): found in 3 Cham and I’d say that related to South China (2) and MSEA (1).
  • O2a1* (M95): this paragroup is way too common in MSEA for all branches to have anything to do with Austronesians (Cham: 30.5%, what is a major component)
  • O2a1a (M88): this lineage is not found at all in ISEA but only MSEA and South China (Cham 8.5%).
  • O3a* (P200): the Cham individuals are clearly haplotypes as their MSEA neighbors (Cham: 6.8%).
  • O3a2b (M7): it also looks very much MSEA (Cham: 5.1%)
  • O3a2c1 (M134): a single Cham man sits on a branch derived from South China.
This leaves the count of male-mediated origin:
  • MSEA & South China: 67.9% (all O and C3)
  • ISEA (likely Austronesian): 13.6% (K*, C* and F*)
  • Taiwan & Philippines (core Austronesian): nothing at all
  • South Asia (Hindu/Muslim historical networks): 18.7% (R, H)
Can we stretch a bit the  Austronesian influence? Maybe but not really much. I am probably as surprised as you may be. It’s also quite surprising that almost 20% of the Cham patrilineages are from South Asia. 
Fig. 3 – Principal Component analysis based on Y-DNA haplogroups

Cham apart, it is interesting that, in the above PCA chart, we can see two more clear clusters: (1) Wallaceans (regardless of language) and (2) a core Austronesian group made up of Taiwan, Mentawai and Nias (and to lesser extent Borneo). 
This “Taiwanese Aboriginal” identity in the Y-DNA of the small and peculiar Indonesian islands of Nias and Mentawai (located West of Sumatra) has been observed before and seem to describe these two populations as the only “pure” Austronesian colonies in all ISEA.
However it is also true that Borneo does approach this cluster (although it may depend on the particular samples considered). By contrast, Java and Bali are a whole dimension apart, much closer to MSEA populations than to the “true Austronesians” of Aboriginal Taiwan and their genetic neighborhood. 

Mitochondrial DNA

There is much less emphasis of the paper on mtDNA but at least there is a pie chart of the frequencies among the Cham and the Kinh (from North Vietnam, Austroasiatic speakers):
Fig. 7 – haplogroup apportions in two populations from Vietnam
Something that quickly strikes the eye is that the Cham do not have much more B4 than the Kinh, somewhat dispelling the “myth” of this matrilineage being associated with Austronesian expansion everywhere (a subclade, B4a1a1a, is an important founder effect among Polynesians however: the so-called “Polynesian motif” but that’s about it).
Also the Kinh may have a slightly more “Northerner” affinity for some haplogroups: low N9a, high M8. 
I wonder if the R* among the Cham is made up of South Asian clades (like some of the abundant M* maybe) or it hides something else.

Update (may 12): Fig. 7 clearly states that: For mtDNA haplogroups, M* includes M17, M20, M21d, M22, M33c, M50, M51,
M71, M72, M73, and M77; N* includes N21 and N23; R* includes R22 and R23. I had not noticed this before (h/t Terry). 

Posted by on May 9, 2012 in East Asia, mtDNA, population genetics, SE Asia, Y-DNA


7 responses to “The Cham People and why the genetic structure of SE Asia is mostly not the product of Austronesian expansion

  1. John Yhemon

    February 23, 2013 at 8:57 pm

    Hi – I come to this with no knowledge of the discussion so far. Any chance you could, in very simple terms, explain the relation of this paper and this discussion to other austronesian groups of Mainland SEA? I'd be grateful.

  2. Maju

    February 24, 2013 at 12:17 am

    The Cham speak an Austronesian language, being the main (only?) Austronesian group established in the mainland other than peninsular Malays. Other than that, Terry almost invariably goes a bit (or a lot) off-topic and loves arguing everything, especially everything Austronesian.

  3. terryt

    February 24, 2013 at 12:21 am

    There are few Austronesian-speaking groups on the mainland. It is mainly an island language group although see it as being related to the Tai-Kradai group of the mainland. The Austronesian language looks to have originated in Taiwan and spread from there through the Philippines and east into the Pacific and west to Madagascar. Maju has numerous posts on the subject and I'm sure he will be able to link you to at least some of them. You will find some by clicking on 'labels' at the bottom of his post here.

  4. John Yhemon

    February 24, 2013 at 4:32 pm

    I'm thinking of the Ede (Rhade) and Jarai of Vietnam's Central Highlands. I think there must be 1 million or more non-Cham Austronesian speakers there. They have historical memories of their own connection to the Cham as "brothers". Wondering if the research you discuss might have bearing on those remembered histories, and if there is additional research that might shed light on similarities or differences in those early histories, the origins of the groups, etc.

  5. Maju

    February 24, 2013 at 4:43 pm

    No idea. Maybe Terry can tell you something?

  6. terryt

    February 24, 2013 at 7:38 pm

    Sorry. I have no idea. I do think that the Cham are not the only Austronesian-speaking Vietnamese though, so it makes sense that members originally connected with the Cham would have moved north.

  7. kartika huic

    April 17, 2013 at 1:26 pm

    This comment has been removed by the author.


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