A rapid coastal migration along the "southern route" from Africa into southern Asia, some time before 50 kyBP has been strongly suggested by studies on present day world populations (especially those based on mitochondrial DNA) [1, 11, 18, 19–21, 28]. The founder analysis of the mtDNAs in this study suggests 50.0 ± 1.5 kyBP for such arrival which is well within the lower bound range of earlier estimates and perhaps more consistent with the earliest and most pronounced population expansion in southern Asia around 52 kyBP suggested in . Magnitude of this southern Asian growth phase suggests that over half of the global human population lived in Indian subcontinent between ~45 to 20 kyBP and population size peaked at over 60% around 38kyBP . These population expansion estimates are largely in agreement with high mtDNA diversity and star like non-overlapping pattern of numerous lineages of macrohaplogroup M reported previously [4, 6, 9, 7].
Though the stage upto here is clear, the contribution and role of this sizably large earliest settlers' component in the contemporary Indian populations, coupled with later migrations during the last 10 thousand years (ky) from west and east of the subcontinent has been an issue of controversy. Cordaux et al.  based on the non-overlapping pattern of mtDNA phylogeny between India and east Eurasia has supported the argument of Cavalli-Sforza et al.  that in India the genetic traces of early migrations along the southern route were erased by the subsequent migrations, which shaped the present-day mtDNA gene pool of India. However presence of numerous autochthonous lineages in India emerging directly from the root of the founder macrohaplogroups M, N and R [4, 6, 7, 9] during the estimated population growth period in southern Asia (~45 to 20 kyBP) indicates the presence of large component of earliest settlers in the contemporary Indian populations.
In the quest of finding the carriers of the genetic legacy of the earliest settlers among the contemporary Indian populations, some previous studies on mtDNA variation by calculating nucleotide diversity and expansion time (as per methods of Slatkin et al. ) for different linguistic groups of India, distinguished Austro-Asiatic speaking tribes as the oldest and the carriers of the said legacy [31, 32]. Basu et al.  also supported the view by reporting that the frequency of the ancient haplogroup M2 among the Austro-Asiatic tribal populations is as high as 19% and they lack the younger haplogroup M4. However Metspalu et al. , so as this study, rejects such claims as linguistic groups of India do not cluster into distinct branches of the Indian mtDNA tree, [[6, 10, 13], this study] calculating the beginning of expansion for those groupings is problematic, whereas lack of coding region information in Basu et al.  have lead to an over estimation of M2 frequency. Moreover our results indicate that M2 frequency variation among the studied tribes can be better explained by recent population expansion/demographic events than as a function of deep rooting ancestry. The nucleotide diversity though appears better parameter, is also predisposed to influence of past demographic events. The phylogenetic inferences based on such parameters should be strictly viewed in reference to the demographic events, particularly for India.
Our analysis of mtDNA variation in populations of India indicate that the Dravidian tribes extending from southern to central India and tribes of eastern India irrespective of the linguistic affiliation shows equally deep rooted M2 ancestry ~37 ky (Figure 2), comparable nucleotide diversity (Table 2) and similar past demographic history (Figure 3). However Indo-European tribes of western and central India except Kathodi/Katkari and Andh tribes harbour only M2a1 branch representing a time depth of ~8 ky. Kathodi/Katkari and Andh tribe encompasses other braches of M2a, but lacks M2b. All these Indo-European tribes shows appreciable frequency of M2 (Table 1), but they are low on nucleotide diversity (Table 2). Thus it would be highly speculative to tag any one or a group of populations based on linguistics or geography as the representatives of earliest settlers, rather it indicate to the fact that earliest settlers' component is more pronounced in the areas extending from southern to eastern India, and shows decline towards north and northwest India, a cline similar to that of M in general [[5, 11], this study]. However a decline of earliest settlers' component across tribe to higher caste gradient may also be accepted in the respective regions as indicated in .
The time depth of M2 lineage and diversity indices in Indo-European speakers of western region extending up to central India posits the expansion of earliest settlers' component into these areas during the post Last Glacial Maximum(LGM) growth (~12 to 7 kyBP) of population (Figure 3) or perhaps little later (Figure 3 -pannel 'F'). However this requires further investigation. It is only during this rapid growth; regional and population specific branching patterns appear on the more or less homogenous M2 phylogeny. The possible explanation would be the earliest settlers of India prior to this rapid population growth had lived in an extended enclave and there had been continuous gene flow across population boundaries. The second but more plausible reason of such homogeneity could be that earliest settlers by virtue of large population size during ~45 to 20 kyBP  and Indian ecological setting which, favoured tendency to isolate and subjugate  might have been differentiated into populations distributed far apart as suggested in recent studies [4, 9]. But during the LGM and late glacial aridity, climate across India and south Asia generally seems to have been much more arid than present. Geomorphological indicators from the landmass of India suggest dune mobility in the northwest , and greatly reduced river flow in north central India during the span of time that covered the full glacial . Offshore indicators of salinity (due to runoff from the land) suggest that LGM aridity was substantially greater than at present. Indicators of upwelling intensity in the Indian Ocean suggest that the summer monsoon was much weaker than present at the LGM, but reaching its weakest at around 15,800 – 12,500 C14 years ago, that is 17,800-13,800 calibrated or 'real' years ago . During this period of cold and more arid conditions rainforest retreated and was replaced by dry grasslands. However, some monsoon forests and woodlands in southern India and scrub, open woodland in eastern India probably existed in presently moist forest climates. This appears to be harsh conditions for an hunting gathering based subsistence, thus to fight the adverse, probably shrinking populations might have come close to each other in a more habitable area allowing a free gene flow between populations, whereas ancestral population of the Kathodi/Katkari M2a2 lineage appears to have remained isolated during this period. In the post LGM growth period, though population spread over wide geographical regions. Maternal gene flow is evident in the geographical neighbors suggesting fluidic population specific boundaries until recently at least among the tribes.
The next important event on the Indian scene is the beginnings of agriculture and use of pottery [36–41]. Cultivation of plants/agriculture diffused from the Fertile Crescent within the past 10,000 years. The steady advance beyond this stage seems however to have been primarily driven by the crop-animal complex derived from the mid-east, reaching the tip of southern India around 3 to 2 kyBP [42, 43]. The diffusion of pottery traditions, which arise in response to the need to store and cook grains, shows evidence of the influences from northwest and northeast, with the western influence predominating over much of the country. Thus the Black and Red ware reflects western, while the Corded ware Chinese influence [44–46]. Two other technological innovations, known to have originated outside of India, the domestication of horse, around 6 kyBP on the shores of Black Sea in present Ukraine, and the use of iron around 5 kyBP in Anatolia in present day Turkey, appears in the Indian archeological records (around 2 kyBP) soon after the agriculture . The recent study investigating the cultural or demic diffusion model of agriculture in India supported the demic diffusion model which predicts a substantial genetic input from migrating agriculturalists . The advent of agriculture and perhaps migrating agriculturists brought about dramatic changes in the economy, technology and demography of human societies. Human habitat in the hunting-gathering stage was essentially on hilly, rocky and forested regions, which had ample wild plant and animal food resources. Agriculture led to the emergence of villages and towns and perhaps brought with it the division of society into occupational groups. . Crop cultivation resulted in the loss of the traditional habitat of hunter-gatherers by deforestation, fragmenting and marginalizing numerous such populations, many of whom were assimilated into agriculturally based subsistence economies , thereby catalyzing some sort of regional similarities across tribe caste continuum. Our results on reconstructed past population demography indicating decline of earliest settlers' population (female population here) during this period in almost all the geographical regions except western (Figure 3) is consistent with the above proposition and suggests that demic diffusion of these technologies were rapid, perhaps involving large migrating populations with these technologies.
The highest frequency of east Eurasian- specific mtDNA haplogroups [11, 22] and absence of M2 an earliest settlers component (Table 1) among Tibeto-Burman speaking tribes of northeastern states of India suggests that, despite the more recent migrations to India, these populations remained relatively isolated, explaining the close correlation between genetic and linguistic results [49, 50]. This contrasts with the situation observed in other regions of India, where linguistic structure shows very little concordance with the genetic structures.