If anyone wants to know about the population genetics of South Asia, I recommend three papers (all are open access):
In the near future ancient DNA will do for South Asia what has been done for Europe, and to a lesser extent the Near East. It will pull back our veil of ignorance. But until then we have genomic inference from larger data sets with a greater number of markers. What can we say now?
– The 2009 work that modern South Asians are broadly a compound of two streams of the out of Africa populations is correct. One is much like other West Eurasians. Another is distantly related to other East Eurasians, with possible affinities to Paleolithic Southeast Asian hunter-gatherers.
– The West Eurasian ancestry of South Asians, the “Ancestral North Indians” (ANI), does likely seem to be a mixture at minimum between two groups. One element is related to the eastern farmers who first adopted agriculture on the slopes of the Zagros ~10,000 year ago. Another stream is closely related to the Yamna people who flourished on the Eurasian steppe north of the Black Sea ~5,000 years ago.
– The Munda peoples seem to have a distinct Southeast Asian component that ties them with other Austro-Asiatic peoples. Their migration was almost certainly tied to the Neolithic migration of rice farmers. They are likely not the primal aboriginals of South Asia.
– The R1a1a-Z93 Y chromosomal lineage found across much of South Asia, and especially the higher castes and the north, increased in frequency within the last 4,000 years. It is almost certainly exogenous to South Asia; ancient DNA from the steppe finds the Z93 in Iranic peoples, but no Indian ancestry in these groups.
As I said, ancient DNA will clarify lots of things. I expect that to happen in the next few years.