Dienekes, David, and Zack, have now integrated the insight from Reconstructing Indian History that the programs which infer population structure, such as STRUCTURE, frappe, and ADMIXTURE, can produce ancestral components which are themselves actually stabilized hybrids. In particular the “South Asian” component in many of these analyses may be an ancient admixture between a European-like population, “Ancestral North Indians,” and an indigenous population with marginally greater affinities to East Asians than Europeans, “Ancestral South Indians.”
Here are the posts of interest: