A close reading of the recent Thangaraj paper, referenced below, indicates that there are primarily two West Asian y-haplogroups that entered the Indian subcontinent by a western coastal route during the Neolithic: J2a4 and L1. It notes that the R1a y-haplogroup is not strongly associated with this coastal Neolithic expansion. The described J2a4 and L1 Neolithic expansion is consistent with the findings of Sengupta et al.
Neither the Thangaraj paper or the Sengupta paper support the notion of a single Iron Age expansion of Indo-Aryans. The Thangaraj paper specifically suggests an approximate age of paternal gene flow from West Asia of approximately 10,000 years.
These results are consistent with earlier posts on the y-haplogroup distribution maps for J2 and L.
Eurogenes ADMIXTURE K=10 results run on the Eurogenes dataset help to illustrate the process of West Asian admixture into the South Indian genetic background:
Georgians, Armenians, Assyrians, Iranians, Sindhis and Gujaratis indicates a diffusion process between West Asia and Western Coastal India.
The fact that there is a very low contribution to Sindhis and Gujaratis from the Southwest Asian component is consistent with the Thangaraj assertion that the age of J2 and L paternal gene flow into India occured approximately 10,000 years ago. The Southwest Asian component is associated with the J1 y-haplogroup. The J1 y-haplogroup has a pre-Holocene expansion time in the Zagros Mountains, but its rapid growth is associated with the J1 expansion into the Arabian peninsula in the last 9000 years.
The Influence of Natural Barriers in Shaping the Genetic Structure of Maharashtra Populations
Thangaraj et al
Results and Discussion:
"The Y chromosome analysis identified nine major haplogroups in Maharashtra populations (Table 2), of which South Asian specific haplogroup H is most frequent in caste and tribal populations. Second most frequent haplogroup is hg R1a present in caste as well as tribal populations. Some of the studies considered hg H as a tribal and hg R1a as caste specific marker previously , , . In contrast to them, the present study supports the occurrence of these haplogroups in both caste and tribal populations of India , . The discrepancy of frequency distribution of these haplogroups in caste and tribal populations can be explained by their different population sizes where evolutionary forces act in a different way and diverse social customs that involve practicing endogamy at different levels ."
"Near Eastern specific hg J2 is also significantly present in both of the studied populations (Table 2 and Table S2). This haplogroup thought to be associated with the intrusion from Near East during Neolithic agricultural expansion . Further dissection of this hg revealed most of the samples to be derived for marker M410 (hg. J2a). The further genotyping of M410 derived samples remained ancestral to M67 marker (hg. J2a4). The worldwide phylogeographic distribution of hg J2a suggests its entry in Indian subcontinent through northwestern corridor and an abrupt drop further south due to Western Ghat mountain ranges (Fig. 3). The rooted Y-STR network of different Y chromosomal haplogroups provided a diverse haplotype distribution in Maharashtra populations (Fig. 4)."
"By using the Y-STR data from both of the populations, we have calculated the variance and coalescent ages for different haplogroups (Table 4). The age of microsatellites variation in all of the major haplogroups ranges from 7–35 KYA (Table 4). The South Asian specific haplogroups F*, H1a and R2 show pre-Neolithic, while hg L1 shows Neolithic expansion time. The age of haplogroup R1a ranges from 10–17 KYA which is consistent with previous large scale study on this haplogroup . The network analysis of R1a with other Indian populations failed to provide any regional or linguistic clustering (Fig. S2)."
"In conclusion, our results on Maharashtra populations are consistent with other Indian populations suggest that the tribal as well as caste populations of Indian subcontinent practice a strict endogamy even though they live in a close proximity and share the ritual and social customs. The mtDNA results dissected and increased the clarity of South Asian mtDNA phylogeny. The colonization of western part of Western Ghat is facilitated mainly through migration of populations via western coast rather than mainland where Western Ghat-Vindhya mountains and Narmada-Tapti rivers worked as a natural barrier. Our data is in congruent with the other observations that Indian populations including Maharashtra state are largely derived from Paleolithic ancient settlers, however, a more recent (~10 Ky older) detectable paternal gene flow from west Asia is well reflected in present genetic study."