I believe the problem lies with the tree model which are inadequate to represent human variation. A look at Indian Y & Mt DNA tells us that the most Indian Paternal lineages are Western Eurasian while the reverse is true with maternal lineages. Our plotting close to Siberian/N American Populations is on account of both groups possessing a combination of Eastern and non-Eastern Eurasian Ancestry and both groups being rich in ANE like ancestry. Have you seen the recent Lazaridis paper on Neolithic Iran? If New findings are to be believed we are essentially a combination of an ancient East Eurasian population (ASI), Neolithic Iranians and a Steppe population