The paper does not appear to be live yet, so I cannot comment on the specifics. However, judging from the abstract I see no reason to agree with the authors' conclusions. My most recent observations on the topic can be found in Origin of Hindu Brahmins. The authors' observation of paragroup R1a* Y-chromosomes in India is in itself unremarkable, as such chromosomes have been found outside India, e.g., in North Iran, Crete, and Greek Macedonia (and I'm sure elsewhere). The argument about the presence of R1a1 in tribals does not carry force, as its presence there (at much lower frequencies than in Brahmin groups) can be explained as the result of occasional admixture. Moreover, India is exceptionally notable for its lack (except in a few erratics) of the related haplogroup R1b, which once again argues against the emergence of R1a in India itself.
See also another recent study which considers R1a1 extraneous in India, and which includes links to various other blog posts on the topic.
Perhaps I will have more on this when I read the paper (feel free to send me a copy to my e-mail address).
J Hum Genet. 2009 Jan 9. [Epub ahead of print]
The Indian origin of paternal haplogroup R1a1(*) substantiates the autochthonous origin of Brahmins and the caste system.
Sharma S. et al.
Many major rival models of the origin of the Hindu caste system co-exist despite extensive studies, each with associated genetic evidences. One of the major factors that has still kept the origin of the Indian caste system obscure is the unresolved question of the origin of Y-haplogroup R1a1(*), at times associated with a male-mediated major genetic influx from Central Asia or Eurasia, which has contributed to the higher castes in India. Y-haplogroup R1a1(*) has a widespread distribution and high frequency across Eurasia, Central Asia and the Indian subcontinent, with scanty reports of its ancestral (R(*), R1(*) and R1a(*)) and derived lineages (R1a1a, R1a1b and R1a1c). To resolve these issues, we screened 621 Y-chromosomes (of Brahmins occupying the upper-most caste position and schedule castes/tribals occupying the lower-most positions) with 55 Y-chromosomal binary markers and seven Y-microsatellite markers and compiled an extensive dataset of 2809 Y-chromosomes (681 Brahmins, and 2128 tribals and schedule castes) for conclusions. A peculiar observation of the highest frequency (up to 72.22%) of Y-haplogroup R1a1(*) in Brahmins hinted at its presence as a founder lineage for this caste group. Further, observation of R1a1(*) in different tribal population groups, existence of Y-haplogroup R1a(*) in ancestors and extended phylogenetic analyses of the pooled dataset of 530 Indians, 224 Pakistanis and 276 Central Asians and Eurasians bearing the R1a1(*) haplogroup supported the autochthonous origin of R1a1 lineage in India and a tribal link to Indian Brahmins. However, it is important to discover novel Y-chromosomal binary marker(s) for a higher resolution of R1a1(*) and confirm the present conclusions.