Of particular interest is the fact that Indian populations have little influence by the pink (main Mongoloid) cluster. As I have stated before on numerous occasions, whatever similarity between Indians and East Asians is due to ancient common ancestry (evidenced e.g., in their common possession of mtDNA macrohaplogroup M), rather than any significant "East Asian" ancestry. From the paper:
We found that allele frequencies in India showed detectably greater similarity to populations in Europe and the Middle East than to those in East Asia (Figure 4). This result is consistent with the fact that the cluster corresponding to India in Figure 2A subdivides a previously obtained cluster corresponding to Europe, the Middle East, and Central/South Asia .The genetic homogeneity of Indians may be resolved with more markers:
This observation, together with the reasonably strong support in the neighbor-joining tree for particular groupings within India, suggests that a detectable amount of population structure does exist in the Indian data and that the addition of more loci might cause clusters corresponding to specific subsets of the Indian sample to become distinguishable. It is noteworthy, however, that in previous analyses of other geographic regions [19,28] using smaller numbers of markers, subclusters have been more easily identifiable elsewhere than was seen here for India with 1,200 markers.PLoS Genetics
Low Levels of Genetic Divergence across Geographically and Linguistically Diverse Populations from India
Noah A. Rosenberg et al.
Ongoing modernization in India has elevated the prevalence of many complex genetic diseases associated with a western lifestyle and diet to near-epidemic proportions. However, although India comprises more than one sixth of the world's human population, it has largely been omitted from genomic surveys that provide the backdrop for association studies of genetic disease. Here, by genotyping India-born individuals sampled in the United States, we carry out an extensive study of Indian genetic variation. We analyze 1,200 genome-wide polymorphisms in 432 individuals from 15 Indian populations. We find that populations from India, and populations from South Asia more generally, constitute one of the major human subgroups with increased similarity of genetic ancestry. However, only a relatively small amount of genetic differentiation exists among the Indian populations. Although caution is warranted due to the fact that United States–sampled Indian populations do not represent a random sample from India, these results suggest that the frequencies of many genetic variants are distinctive in India compared to other parts of the world and that the effects of population heterogeneity on the production of false positives in association studies may be smaller in Indians (and particularly in Indian-Americans) than might be expected for such a geographically and linguistically diverse subset of the human population.