I have applied Multidimensional Scaling and ADMIXTURE on a dataset of 15 populations:
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).
Cambodians, Papuan, NAN_Melanesian, Gujarati, Malayan, Paniya, North_Kannadi, Sakilli, Singaporean Indians, Singaporean Chinese, Singaporean Malay, Yemenese, Saudis, Maasai, Ethiopians
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:
- Light blue, Indian
- Dark blue, East African
- Light green, Southeast Asian
- Dark green, Chinese Mongoloid
- Pink, Arabian Caucasoid
- 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.