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We combined these with other published data from South Asia and neighbouring areas, including a total of 1478 samples (Additional file 1: Table S1).The additional sequences increased substantially the sample size particularly in the West of the Indian Subcontinent, necessitating a re-evaluation of previously inferred phylogeographic patterns [2, 35].
Many recent genetic studies explored different layers of South Asian genetic diversity and population structure [2,14,22,23,24,25,, 13–15, 17, 21–26], but they have tended to focus on one or other marker system and, as a result, decisive results on the details of the settlement process are still lacking.
Whilst current genome-wide analyses conflate all dispersals from Southwest and Central Asia, we were able to tease out from the mitogenome data distinct dispersal episodes dating from between the Last Glacial Maximum to the Bronze Age.
Moreover, we found an extremely marked sex bias by comparing the different genetic systems.
We aimed to provide a refined mt DNA phylogeographic portrait of South Asia, including most crucially an assessment of the extent of genetic influx from other regions (primarily Southwest and Central Asia), in order to assess the impact of immigration during the Late Glacial, postglacial, Neolithic and Bronze Age periods in shaping genetic diversity and structure in South Asia.
For a comprehensive overview across the genome, we have also carried out several fresh analyses of GW patterns across the regions of Southwest, Central and South Asia, and assessed sex-biased gene flow in the region by direct comparison across the same sample sets, using the 1KGP data now available for GW, mt DNA and Y-chromosome diversity.
Moreover, similar analyses can be carried out for the paternally inherited Y-chromosome variation, and comparisons of the two systems can detect sex bias in dispersal patterns.