The Indian subcontinent is legendary for the cultural, linguistic and genetic diversity of its inhabitants. The contemporary populations of India offer a platform to study the wide range of disciplines viz.
demography, history, linguistics and genetics. Genetic diversity in India can be understood as a result of long term large effective population size, a number of dispersal events and its unique social structure. Maharashtra is the western most state of India inhabited by several caste and tribal populations. It is politically bordered by Gujarat, Madhya Pradesh, Chhattisgarh, Karnataka and Andhra Pradesh in the northwest, northeast, east, south and southeast, respectively. The Arabian Sea makes up Maharashtra's west coast. There are three mountain ranges in this state viz. Sahyadri in west, Satpuda in north and Gondwan in the east. More importantly, the Western Ghats mountain ranges of India is considered as the most densely populated global biodiversity hotspot which has a mosaic of natural, semi-natural and agroecosystems in close proximity to one another 
In India, the Maharashtra state ranks second in population and third in area. It constitutes 9.33 percent of India's population (Census 2001). The tribal populations accounts to about 9.3 percent of the total population of the state (Census 2001). There are 47 scheduled tribal population groups in the state and the majority of them are inhabitants of these geographically difficult topography 
. The major tribal populations of Sahyadri range are the Mahadeo Koli, Thakur, Katkari, Warli, Malhar Koli and Kokana group. Among Satpuda ranges, Bhil, Pawara, Korku and Tadvi are the major groups. The Madia, Gond, Pardhan, Halbi Otkar and Andha are found in the Gondwan range. These tribal groups differ from each other in various aspects, for instance their different cultural practices, marriage pattern and socioeconomic categories. The origin and migration of these groups are uncertain. As majority of these tribal groups living in the remote forest areas remain isolated from each other thus, minimizes the chances of gene flow among them.
Mitochondrial DNA (mtDNA) evidence has been argued to support the model according to which populations of South Asians can trace their origin back to the Out-of-Africa (OoA) dispersal along the southern coastal route approximately 60 KYA 
that is arguably in line with archaeological evidence 
. Based on similarities reported in engraved pieces found at Blombos, South Africa, to those of Patne in India, and cresentic blade and microblade forms reported in India and Sri Lanka to Africa strongly indicated a direct connection between early human colonists in Asia and their ancestors in Africa 
. However, the recent archaeological research has raised question about this dispersal and hypothesized alternative route 
. There is no archaeological evidence concerning the Paleolithic settlement of Western Ghats region by early modern human. It has been suggested that the early human populations in South Asia avoided the Western Ghats region because of high rainfall and thick vegetation 
. Alternatively, it was proposed that such highly rich vegetation zone might have attracted early human because of ease of resources and the lack of corresponding evidence were explained due to various reasons (e.g.
, inadequate surveys or thick vegetation not allowing proper surveys, lithics being transported after use instead of being discarded) 
Previous genetic studies on South Asian populations have identified their genepool as a composite of lineages that have evolved locally since the OoA dispersal and those that have been introduced by a number of more recent dispersal events 
. The analyses of mtDNA, Y chromosome, and autosomal genes have agreed on that the contribution of western Eurasian gene flow to India is more pronounced in the modern populations than that from East and Central Asia whereas, the relative proportions of imported vs
locally differentiated genes appear to be dependent on the particular locus and populations being examined. The geographical location of Maharashtra state makes it quite interesting to study the dispersal of modern humans in South Asia. Besides harboring such an important geographical position in Indian subcontinent, the origin and migration of several populations living in various regions in this state of India and their affinity with other contemporary South Asian population has not been explored, so far, at the high resolution level. The available genetic source of this region is poorly known due to less sample sizes and low resolution 
. Moreover, this state works as a bridge among central, northern and southern parts of India and might give some clues for the peopling of Indian subcontinent, placing it on the way of coastal route migration 
. Therefore, to shed more light on the origin of the Maharashtra population, we first analyzed the control-regions and partial coding-region sequence variations of mtDNA and 20 Y-SNP and 17 Y-STR markers of Y chromosome in two tribal populations (Mahadeo-Koli and Thakur) inhabited in westernmost coastal region of India and compared the results with published sources from contemporary populations 
. Our results not only help to further understand the phylogenetic position of Maharashtra state in South Asia but also provide deeper insights into the origin of Western Ghat populations.