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In order to discern migrations into the Subcontinent at different time periods, we also performed a complementary analysis of several “non-autochthonous” N lineages present in South Asia (H2b, H7b, H13, H15a, H29, HV, I1, J1b, J1d, K1a, K2a, N1a, R0a, R1a, R2, T1a, T2, U1, U7, V2a, W and ].

We assessed ML estimations using PAML 4 and the same mitogenome clock assuming the REV mutation model with gamma-distributed rates (discrete distribution of 32 categories) and two partitions, in order to distinguish hypervariable segments I and II (HVS–I and HVS–II) from the rest of the molecule.

This was part of a much wider process of Indo-European expansion, with an ultimate source in the Pontic-Caspian region, which carried closely related Y-chromosome lineages, a smaller fraction of autosomal genome-wide variation and an even smaller fraction of mitogenomes across a vast swathe of Eurasia between 5 and 3.5 ka.

Following the out-of-Africa (OOA) migration, South Asia (or the Indian Subcontinent, here comprising India, Pakistan, Bangladesh, Sri Lanka, Nepal and Bhutan) was probably one of the earliest corridors of dispersal taken by anatomically modern humans (AMH) [].

Moreover, we found an extremely marked sex bias by comparing the different genetic systems.For the autosomal ancestry variation, we considered the mean of each component for the highest likelihood value.The putative origin of the uniparental lineages present in the populations is shown in Additional file Schematic phylogeny of South Asian autochthonous mt DNA haplogroups, based on ML age estimates.India, the second most populous country worldwide, includes a patchwork of different religions and languages, including tribal groups (~8% of the population, speaking over 700 different dialects of the Austro-Asiatic, Dravidian and Tibeto-Burman families) and non-tribal populations, who mostly practice Hinduism, grounded in a strictly hierarchical caste system, and speak Indo-European or Dravidian languages.Indo-European is often associated with northern Indian populations, Pakistan and Bangladesh, and a putative arrival in South Asia from Southwest Asia ~3.5 ka (the so-called “Indo-Aryan invasions”) has been frequently connected with the origins of the caste system [] which, combined with a very complex history, makes the genetic study of Indian populations challenging.India is a patchwork of tribal and non-tribal populations that speak many different languages from various language families.