Interestingly Sanghamitra Sahoo seems to have published a paper on the same topic only two months after Sanghamitra Sengupta did.
It is unfortunate that this paper uses a limited number of UEP markers. Hopefully, future studies will start to seek and test more recently derived markers, which are the only ones that can really address recent events authoritatively.
Moreover, no STR markers were typed, thus further limiting any possible inferences about the time depth of the various Indian lineages.
A real problem with the study is that it performed an "admixture analysis" which considered the modern Central Asians as representative of the prehistoric ones. As it is well known, Central Asians of today have substantial Mongoloid admixture from the proto-historical and historical period and are not representative of the ancient Indo-Iranian groups of the steppe.
In any case, the observations of the authors about the distribution of haplogroups in India are broadly similar to those of the other recent study, and we have to agree that the wholesale assignment of J/R/L Y chromosomes to a recent invasion cannot really be sustained.
From the paper's conclusions:
It is not necessary, based on the current evidence, to look beyond South Asia for the origins of the paternal heritage of the majority of Indians at the time of the onset of settled agriculture. The perennial concept of people, language, and agriculture arriving to India together through the northwest corridor does not hold up to close scrutiny. Recent claims for a linkage of haplogroups J2, L, R1a, and R2 with a contemporaneous origin for the majority of the Indian castes’ paternal lineages from outside the subcontinent are rejected, although our findings do support a local origin of haplogroups F* and H. Of the others, only J2 indicates an unambiguous recent external contribution, from West Asia rather than Central Asia. The current distributions of haplogroup frequencies are, with the exception of the O lineages, predominantly driven by geographical, rather than cultural determinants. Ironically, it is in the northeast of India, among the TB groups that there is clear-cut evidence for large-scale demic diffusion traceable by genes, culture, and language, but apparently not by agriculture.This certainly seems reasonable. J2 is largely restricted to the upper castes in India, and its young age is very suggestive of an external arrival in Neolithic and later times. It is certainly beginning to stand out as the most important exogenous genetic component in the Indian population.
The conclusion that J2 arrived in India from West and not Central Asia is not well-founded, because in the Middle East J*(xJ2) is frequent, but completely lacking in India. But, perhaps, most of Middle Eastern J*(xJ2) expanded recently, with the growth of the Semitic groups and was not present in the parental population from which Indian J2 is derived. Central Asia cannot be rejected so easily though as a source for Indian J2, because the present-day Central Asians have components (within N/C/O/Q) which were probably added by Mongoloid groups recently, and are not representative of the prehistoric populations.
The next step should be to develop informative recent markers in haplogroups J2a and R1a1 to finally establish whether some of these can be unambiguously related to particular Western Eurasian populations. This might be the decisive step to conclude whether Renfrew's hypothesis A (arrival of IE languages to India with early farmers) or hypothesis B (arrival of IE languages to India with IE-ized pastoral nomads) is the correct one.
PNAS (online early)
A prehistory of Indian Y chromosomes: Evaluating demic diffusion scenarios
Sanghamitra Sahoo et al.
Understanding the genetic origins and demographic history of Indian populations is important both for questions concerning the early settlement of Eurasia and more recent events, including the appearance of Indo-Aryan languages and settled agriculture in the subcontinent. Although there is general agreement that Indian caste and tribal populations share a common late Pleistocene maternal ancestry in India, some studies of the Y-chromosome markers have suggested a recent, substantial incursion from Central or West Eurasia. To investigate the origin of paternal lineages of Indian populations, 936 Y chromosomes, representing 32 tribal and 45 caste groups from all four major linguistic groups of India, were analyzed for 38 single-nucleotide polymorphic markers. Phylogeography of the major Y-chromosomal haplogroups in India, genetic distance, and admixture analyses all indicate that the recent external contribution to Dravidian- and Hindi-speaking caste groups has been low. The sharing of some Y-chromosomal haplogroups between Indian and Central Asian populations is most parsimoniously explained by a deep, common ancestry between the two regions, with diffusion of some Indian-specific lineages northward. The Y-chromosomal data consistently suggest a largely South Asian origin for Indian caste communities and therefore argue against any major influx, from regions north and west of India, of people associated either with the development of agriculture or the spread of the Indo-Aryan language family. The dyadic Y-chromosome composition of Tibeto-Burman speakers of India, however, can be attributed to a recent demographic process, which appears to have absorbed and overlain populations who previously spoke Austro-Asiatic languages.