A reader points me to a talk given by David Reich at the Center for Human Genetic Research 2013 Retreat. One of the issues Reich brought up is old, but perhaps worth reemphasizing: due to endogamy many South Asians carry a higher load of recessive ailments. This is not due to recent inbreeding (which is barred by custom in many South Asian groups, which enforce kin-level exogamy), but long term genetic isolation. Over time even a moderate sized population can be affected by drift. This was one of the major points in the 2009 paper Reconstructing Indian History, but not one particularly emphasized in the press follow up. A major implication is that a relatively simple public health measure for South Asians would be to marry outside of their jati. The social or genetic distance need not be great. But one generation of outbreeding should “mask” many of the deleterious alleles. If this model is correct one should be able to track decreases in morbidity within the American South Asian population, where there are many inter-caste and inter-regional marriages (yes, this is between people of putative high status, but this doesn’t matter).
Second, Reich agrees that the ANI (West Eurasian, “Ancestral North India”) admixture into the India population exhibits at least two admixture events. There were hints of this in the original 2009 paper, and looking more closely at the South Asian data others have suggested this more explicitly. This seems the best explanation for why non-Brahmin upper castes in South India do exhibit distance on the ANI-ASI cline from lower castes, but without clear connection to many ancestral components with a “northern” affinity present at non-trivial levels in Indo-European speaking groups and South Indian Brahmins (or those groups which have admixed with Brahmins, such as Nairs).
The hypothesis I prefer is that there was an initial wave of West Asian agriculturalists who arrived in the Indian subcontinent <10,000 years B.P., and admixed with the ASI ("Ancestral South Indian") substrate. Then, there was at least one further substantial demographic wave of West Eurasians, probably bringing the Indo-European languages. This population had more northern affinities (though not exclusively; the Basque vs. non-Basque difference in European seems to be a West Asian element), which explains the subsidiary minor explicitly European-like element found in many upper caste populations, and to a lesser extent Indo-European speaking South Asians generally. Finally, I do suspect that some groups in the Northwest, such as Jatts, were shaped by later migrations.