J-M410, which was associated with the first farmer dispersal in Europe [13, 82, 83, 84], shows variance values of 0.346 in the Tharus and 0.339 in Indian groups . These values are lower than those (0.467 and 0.479) observed in Anatolia [13, 82] and (0.410) in Southeast Europe [83, 84] and therefore are compatible with a dispersal of this lineage from somewhere in the Middle East/Asia Minor.Y chromosome frequencies:
Estimates of Western Eurasian/East Asian/Indian area components is below. Note that some haplogroups such as R1a (considered here to be "Indian area") have contested origins, and were widely distributed in Western Eurasia even prehistorically. Thus, it is unclear what proportion of them represents a Western Eurasian vs. an Indian area origin.
The latest Y-STR diversity estimates (incl. this paper for Tharus from Eastern Terai and Indians) do suggest a substantially greater antiquity of R1a1 in the Indian subcontinent than in most of West Eurasia, but, as of yet, there is no sign that the R1a1 monolith will be broken by phylogeographically interesting downstream markers which would allow us to make a better sense of it.
UPDATE (July 6)
A reader points me to a fairly nuanced description of R1a1 in the paper.
Actually, the high frequency of the R1-M17 haplogroup found in the Central Eurasian territory, together with its gradient of diffusion that was associated with the Indo-European expansion [74, 75, 76], would leave some uncertainty about its geographic origin. However, the high microsatellite variation supports an ancient presence, dated in our samples over 14 ky [see Additional file 3] of the M17 marker in the Indian subcontinent, as suggested by Kivisild et al. , and sustained by Sengupta et al.  and Thanseem et al. , who consider the Indo-European M17 only a contribution to a local Early Holocene pre-existing Indian M17.This is also what I consider the most likely scenario (although I disagree on the date of 14ky, which was calculated with the "evolutionary mutation rate"): that the exogenous Indo-Aryans included R-M17 Y-chromosomes, but the totality of South Asian R-M17 Y-chromosomes cannot be ascribed to them.
The Tharus themselves are actually speakers of an Indo-Aryan language, and the presence in them of the J-M172/R-M17 combination as the major West Eurasian element in their gene pool is noteworthy. In my opinion it is precisely this combination that dominated early Indo-Aryans, although it may have met in India earlier J/R variants.
(Paper by Thanseem et al. referenced in the above quote; interestingly, according to that paper, J2 and R-related lineages occur at twice the frequency in upper than in lower castes, which seems consistent with my hypothesis, and other evidence.)
BMC Evolutionary Biology doi:10.1186/1471-2148-9-154
Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation
Simona Fornarino et al.
Central Asia and the Indian subcontinent represent an area considered as a source and a reservoir for human genetic diversity, with many markers taking root here, most of which are the ancestral state of eastern and western haplogroups, while others are local. Between these two regions, Terai (Nepal) is a pivotal passageway allowing, in different times, multiple population interactions, although because of its highly malarial environment, it was scarcely inhabited until a few decades ago, when malaria was eradicated. One of the oldest and the largest indigenous people of Terai is represented by the malaria resistant Tharus, whose gene pool could still retain traces of ancient complex interactions. Until now, however, investigations on their genetic structure have been scarce mainly identifying East Asian signatures.
High-resolution analyses of mitochondrial-DNA (including 34 complete sequences) and Y-chromosome (67 SNPs and 12 STRs) variations carried out in 173 Tharus (two groups from Central and one from Eastern Terai), and 104 Indians (Hindus from Terai and New Delhi and tribals from Andhra Pradesh) allowed the identification of three principal components: East Asian, West Eurasian and Indian, the last including both local and inter-regional sub-components, at least for the Y chromosome.
Although remarkable quantitative and qualitative differences appear among the various population groups and also between sexes within the same group, many mitochondrial-DNA and Y-chromosome lineages are shared or derived from ancient Indian haplogroups, thus revealing a deep shared ancestry between Tharus and Indians. Interestingly, the local Y-chromosome Indian component observed in the Andhra-Pradesh tribals is present in all Tharu groups, whereas the inter-regional component strongly prevails in the two Hindu samples and other Nepalese populations. The complete sequencing of mtDNAs from unresolved haplogroups also provided informative markers that greatly improved the mtDNA phylogeny and allowed the identification of ancient relationships between Tharus and Malaysia, the Andaman Islands and Japan as well as between India and North and East Africa. Overall, this study gives a paradigmatic example of the importance of genetic isolates in revealing variants not easily detectable in the general population.