Mixing populations

Reconstructing Indian population history has been commented on By Dienekes
560K SNP study reveals dual rigin of Indian populations (Reich et al. 2009), Rajib Khan Indians as hybrids (a.k.a Aryan invasion in the house!) , John Hawks SNPtastic India and others. John Hawks is somewhat skeptical but the other two are more positive with some reservations and so it is probably an important paper. Dienekes says:
"The paper does demolish some theories that have been popular in some circles:
There is no evidence of caste as simply social division of labor. This thesis is inconsistent with differential ANI admixture (and distance from Western Eurasians) across the caste hierarchy.
There is no evidence that Indo-Aryan and Dravidian speakers differ only in language. It is now clear that they are different from each other genetically as well, and this difference is not an "internal affair" of India, but is related to populations outside it. Indo-Aryan speakers differ precisely in having a larger ANI component.
There is no evidence that Indo-European languages originated in India. Let us consider what this would entail:
Suppose postulated ancient Indian PIE speakers had a similar genetic makeup as modern Indians (i.e., a mix of ANI and ASI). Then, the absence of the ASI component outside South Asia cannot be explained.
If ancient Indian PIE speakers had a purely ANI makeup, then the absence of the ASI component outside South Asia -as in (1)- can be explained. However, this would entail that sharply differentiated populations (ANI and ASI) co-existed in India without mixing for thousands of years; ANI-like PIEs spread from India with their languages; ANI and ASI admixed afterwards. To say that this scenario is not parsimonious would be charitable.
The only way in which PIE languages may have originated in India would be if they spread without the spread of people. However, before the advent of writing and modern means of transportation and communication, the only way to spread languages was by migration of people."
As far as I can see ASI, ANI are mathematical constructs. From the Supplementary Information which is available online:
"In our data, the hypothesis of mixture emerges naturally from
PCA (Figure 3), which shows that nearly all the Indo-European and Dravidian speaking groups spread out on a one dimensional gradient in a plot of the first versus the second PC.

Modeling the history of many Indian groups as a mixture of two ancestral populations is an oversimplification. In reality, even if ancient mixture did occur, it is likely to have been between substructured populations instead of homogeneous populations, and it is likely to have occurred at multiple times and at multiple geographic locations. However, approximating the history of many Indian groups as a simple mixture of two homogeneous ancestral populations provides a good fit to the summary statistics of allele frequency differentiation, and we believe that in this
sense it is a useful starting point for future analyses that can detect more subtle events."
Rajib says " generally agree with the gist of this. The main issue I would also highlight is that these results only clarify and solidify what was likely from previous analyses of worldwide genetic variation. That is, the populations of Northwest India are closer to those of the Middle East & Europe than those of Southeast India are. It was rather awesome that they confirm that the Onge, who are almost extinct, are a relatively unadmixed ancient population. The Onge branch seems to descend from an ancestral population which also gave rise what is termed in the paper "Ancestral South Indian" (ASI). They exhibit no admixture with "Ancestral North Indians" (ANI). This paper confirmed and clarified as well as that the proportion of West Eurasian related lineages increases both as a function of geography and caste. That is, there is a SE-NW and lower-to-upper caste gradient whereby West Eurasian related lineages become more prevalent. This has long been known, but this paper did it with more SNPs across the genome."
There is some more discussion in Rajib's post The politics of genetic history in India : "Now, let me state something clearly: on average an individual from an Indo-Aryan or Dravidian speaking group in South Asia is going to be more closely related genetically in terms of total genome content to anyone in the Indian subcontinent from Indo-Aryan or Dravidian speaking groups than they are to some from outside the Indian subcontinent."
Law and Other Things wonders in The origins of caste :
"For lawyers, it does. International law and legal institutions have developed to deal with racism. Caste, seen as a one-region problem, has not received similar attention. The issue became controversial in 2001, when the International Conference on Racism in Durban took place. Many dalit groups insisted that casteism was a form of racism; while the government, in keeping with its approach to all international monitoring of human rights, strongly refuted the claim. If caste was indeed race, India would be pulled up by the international institutions that deal with racism."
From Rajib's first post:"Note that upper caste South Indian groups clearly have more ANI than lower caste South Indians, but they have a lower proportion than some North Indian lower castes, and are in the range of one North Indian tribal group." It all seems to be a matter of proportion and perspective.
P.S. The original paper of Reich et all is currently available online:
http://www.law.harvard.edu/faculty/faculty-workshops/reich.paper.pdf
The supplements are available at the Nature link. Rajib Khan has two more posts on the topic. In this post he links to a write up by an Indian geologist Suvrat Kher.
P.S. Rajib has given a link to the pdf file of the paper:
http://scienceblogs.com/gnxp/indiapaper.pdf
Link to the supplentary information is abve:
http://www.nature.com/nature/journal/v461/n7263/extref/nature08365-s1.pdf
and supplementary appendix:
http://www.nature.com/nature/journal/v461/n7263/extref/nature08365-s2.pdf