An important paper was published in September. You can get the paper Reconstructing Indian Population History from the home page of David Reich at Harvard’s Department of Genetics, who was the lead author.
The team analyzed 132 genotypes from 25 groups in India. The findings are quite interesting.
The key finding is that there are two distinct ancestral populations for most Indians
… two ancient populations, genetically divergent, that are ancestral to most Indians today. One, the ‘Ancestral North Indians’ (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, whereas the other, the ‘Ancestral South Indians’ (ASI), is as distinct from ANI and East Asians as they are from each other.
Most Indians have an admixture of the two ancestral genomes. The Onge of Andaman are purely ASI.
The proportion of ANI in the genome is higher for North Indians and upper caste groups. Also, the data indicates a high degree of ‘endogamy’, or marrying within ones group. The jaati boundaries have been rigidly maintained in India for millennia.
The findings are not very surprising for those of us who learned about the Aryan invasion in school. The higher proportion of ANI in the north, ties in with the direction of the invasion/migration. The higher proportion of ANI in upper castes also agrees with the invasion theory. However, the paper makes no conclusions about an Aryan invasion or the timing of any such migration from Central Asia/Europe.
The paper does however go against the Out of India theory that has been promoted lately primarily by Hindu nationalists. This theory says that Indo-Europeans originated in India and migrated from there to the rest of Europe. If that were the case, along with ANI, ASI would also be found in the rest of the Europe. ASI is found only in India.
Razib Khan has written a few posts around the paper and its themes. This search query should get you to the posts quickly, if you are interested. Khan, however, does not jump to the conclusion that ANI equals Aryan invasion. He talks about some his reservations in this video conversation. (Go to 42:10 for the discussion on Indian genetics).
http://static.bloggingheads.tv/maulik/offsite/offsite_flvplayer.swf
Another interesting video conversation is Razib Khan with Greg Cochran (author of The 10,000 Year Explosion). Cochran posits that the mutation that allowed human beings to digest lactase could have been the “killer app” that allowed Central Europeans to spread out and dominate much of Eurasia.
6 am pacific 
I think it's not relevant at this point of time to substantiate the thesis, leave the matter to historians.
Similarly we can argue the roots of most current day Muslims and Christians lie in Hinduism, and the roots of most Hindus like in Buddhism.
I'm expecting frequent posts from you though.
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Whats new about this research finding? Haven't we heard this all the time?
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The findings do agree with what historians and archaeologists believe to be true. However, to use genetics as evidence is new. The use of present day human genotypes to piece together the past is being done around the world. It is exciting and full of potential. I expect many new findings from larger studies of this kind in India in the future.
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