Dienekes points out yet another study that uses autosomal SNP microarray data to infer population structure, which finds :
South Indian upper- and lower-caste populations have ∼30% and 10% membership in the inferred European group, respectively.
Social stratification based on "European" (more properly extra-Indian Cauasoid) ancestry in South Indian populations is not surprising; see my post on the Origin of Hindu Brahmins. Differential -based on caste- admixture with an exogenous element is not really compatible with an indigenous creation of the caste system, and is more in accord with the traditional theory of an exogenous origination of the upper caste populations.
 Jinchuan Xing et al. Fine-scaled human genetic structure revealed by SNP microarrays. Genome Research doi:10.1101/gr.085589.108