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Citation: Seguin-Orlando, Andaine, et al. “Genomic structure in Europeans dating back at least 36,200 years.” Science (2014): aaa0114.
The above is a plot of shared drift (ergo, history) between Mal’ta, the 24,000 year old Siberian boy, and various world populations. As per Lazaridis et al. you see a north to south gradient in Europe. As per Raghavan et al. you see the evidence of a lot of contribution to Native American ancestry. The rest of the world tells an interesting story. Recall that the highest fraction of Ancestral North Eurasia (ANE) outside of the New World is among the peoples of the North Caucasus. Their shared drift statistic is depressed in comparison to Europeans because of their high fraction of Basal Eurasians (BEu). What I want you to focus on is a secondary mode of shared drift in northwest South Asia. The reddish tinged circle are the Kalash I am rather sure from what I have heard/seen. The Ancestral North Indian (ANI) ancestors of South Asians seem to resemble the people of the South Caucasus (Georgians/Armenians) from what I have read/seen (I’ve run a few f-stats and D-stats myself). If this means that have a fair share of BEu then their yellowish shading might be misleading in terms of their total ANE ancestry.
Just something to think about.
Addendum: Everything I’ve seen suggests that there were two movements into South Asia from the north/west. The Brahui/Baloch are very distinctive in comparison to the Kalash/Pathan/Burusho. This might be a function of continuous gene flow from distinct regions to the west as well, especially in the case of the Brahui/Baloch, who have had associations as far afield as Oman due to their geographic proximity.
There’s a fairly good archeological/linguistic model of how ANE might have entered the Hindu Kush, and it’s show in this lecture at 58:56 minutes.
http://www.youtube.com/watch?v=HliaR2Ep24s&list=PLAXoDomeFLX90fTHi0W8lYBtEoZHSBH2i&index=6
This gels very well with the split in R1a-Z645 into “European” R1a-Z282 and “South Asian” R1a-Z93, probably during the Copper Age.
Also, from what I’ve seen the actual level of ANE in the Hindu Kush, especially among the Kalash and many Pashtuns, is probably higher than 30%, and thus higher than in the Northeast Caucasus (~29%) and significantly higher than in the South Caucasus (~15%). The MA1 shared drift stats for the Kalash are, as you say, probably depressed by Basal Eurasian admixture, but maybe also ASI. Many of the Makrani and some of the others have non-trivial SSA ancestry, which depresses their stats even more.