November 26, 2010

ADMIXTURE on the shores of the Indian Ocean

I have applied Multidimensional Scaling and ADMIXTURE on a dataset of 15 populations:
Cambodians, Papuan, NAN_Melanesian, Gujarati, Malayan, Paniya, North_Kannadi, Sakilli, Singaporean Indians, Singaporean Chinese, Singaporean Malay, Yemenese, Saudis, Maasai, Ethiopians
These were collected from HGDP, Behar et al. (2010), HapMap-3, and the Singapore Genome Variation Project. There are 423 individuals in general (I've used samples of 25 individuals from the HapMap populations).

Here is the MDS plot:



At the bottom are the Papuans, relatively unadmixed Australoids. Close to them, but deviating towards East Eurasians are the NAN Melanesians; these are the Nasioi, Papuan speakers from Bougainville, which they inhabit together with Austronesian speakers.

At the top left are the Singaporean Chinese (CHS) who are Mongoloids. Deviating from them towards Indians are the Cambodians, a Southeast Asian group which according to physical anthropology is a basically Mongoloid population, but admixed with a pre-Mongoloid southern population element similar to that which has been preserved in India. Similar to them are the Singaporean Malay (MAS), another population that is basically Mongoloid but has absorbed Indian-like population elements.

The Singaporean Indians (INS), the North Kannada, the Sakilli and the Gujarati (GIH25) form the third population element in the region of interest.

The other two are the Caucasoids, represented here by the Saudis, with the Yemenese spread toward Africa and the more Caucasoid-admixed Ethiopians and the relatively unadmixed Maasai (MKK25).

These are the main population elements of our region of interest: Ethiopids and Australoids framing the Ocean on the west and east; the South Asians occupying India, and the Mongoloids occupying Southeast Asia, having absorbed the Indian-like former inhabitants of the region.

Here is a blowup of the middle part of the MDS plot, focusing on the Indians:
It's fairly clear that North Kannada and Sakilli (South Indians) occupy a place that is furthest from Caucasoids, while Gujarati and Singaporean Indians are positioned towards Caucasoids (to the top-right).

Let's now turn to ADMIXTURE to confirm the visual impression from the MDS:

Notice the following components:
  1. Light blue, Indian
  2. Dark blue, East African
  3. Light green, Southeast Asian
  4. Dark green, Chinese Mongoloid
  5. Pink, Arabian Caucasoid
  6. Red, Australoid
Finally, here is the table of Fst distances between these 6 inferred components:

Notice the small distance (0.023) between Chinese and Southeast Asian Mongoloids. The Indian component is equidistant between Caucasoids and Mongoloids, but as the MDS plot makes clear, and as the study of Y-chromosome and mtDNA polymorphisms have shown, the distinctive component in Indians is sui generis and not the result of admixture between Caucasoids and Mongoloids. And, finally, the Australoid component is clearly distant from all of the above.

7 comments:

Gui S said...

It's interesting to see how spread out the Malay population is. Some of them must have quite recent Indian admixture, and some recent Chinese admixture. Especially considering urban Malays are must more likely to have admixture like that than ones from the countryside in peninsular Malaysia. Which are more likely to be almost like Cambodians albeit slightly more towards Melanesians and Indians on the plot.
Would be interesting to see a population portrait.

Perahu said...

Interesting analysis dienekes. It's also strange how some Southern Indians resemble East Africans yet there is no genetic similarity.

This Tamil man could have easily been Ethiopian or Somali:

http://d.imagehost.org/0261/tam22.jpg

bobcatstevie said...

The Maasai are not relatively unadmixed. They are actually known for having substantial Cushitic admixture, which is why they are often referred to as "Nilo-Hamitic" rather than simply as "Nilotic" like their relatives in Southern Sudan such as the Dinka. Tishkoff et al. (2009), among others, point this out in that large study of theirs.

This is basically why the Maasai are closer to the Ethiopians in that plot than one would expect, and why in genome-wide studies Yemenis and certain other Middle Eastern populations show greater similarity to the Maasai than they do to the latter's comparatively unmixed Nilotic relatives in southern Sudan as well as other Sub-Saharan Negroid populations. It's not because the Yemenis et al. have a particularly large Negroid component that's specifically related to the Maasai. It's the other way around: the Maasai trace almost half of their ancestry to Cushitic forbears who already had strong West Eurasian affinities.

Aswe said...

You should have included Bantu Africans from East Africa, such as the Luhya. This plot makes it seem like the ancestry of the Maasai is completely East African, which it is not. It is a mix between East African Nilotic/Cushitic and Bantu.

terryt said...

"At the bottom are the Papuans, relatively unadmixed Australoids".

I wonder where the Australian Aborigines would fit?

"Close to them, but deviating towards East Eurasians are the NAN Melanesians; these are the Nasioi, Papuan speakers from Bougainville, which they inhabit together with Austronesian speakers".

The admixture with the Austronesian-speaking people is presumably what drags them towards East Eurasians.

"And, finally, the Australoid component is clearly distant from all of the above".

But there is a widespread Australoid substrate, perhaps an artifact in some cases.

Andrew Oh-Willeke said...

"It's interesting to see how spread out the Malay population is. Some of them must have quite recent Indian admixture, and some recent Chinese admixture. Especially considering urban Malays are must more likely to have admixture like that than ones from the countryside in peninsular Malaysia. Which are more likely to be almost like Cambodians albeit slightly more towards Melanesians and Indians on the plot.
Would be interesting to see a population portrait."

In addition to these factors it is worth recalling that even no, Malaysia is a plural constitutal monarchy, a bit like the UAE. Different populations within Malaysia have enough of an ethnic and national identity to still have their own separate kings without any one of them being pre-eminent.

horacioh said...

Very nice plot.

Dr. H.H.O.C.