Paleoanthropological evidence indicates that modern humans reached South Asia in one of the first dispersals out of Africa, which were later followed by migrations from different parts of the world. The variation of 20 microsatellite and 38 binary polymorphisms on the non-recombining part of the uniparental, hapliod Y-chromosome was examined in 1434 male individual of 87 different populations of India to investigate various hypothesis of migration and peopling of South Asia Sub-continent. This study revealed a total of 24 paternal lineages, of which haplogroups H, R1a1, O2a and R2 portrayed for approximately 70% of the Indian Y-Chromosomes. The high NRY diversity value (0.893) and coalescence age of approx. 45-50 KYA for H and C haplogroups signified an early settlement of the subcontinent by modern humans. Haplogroup frequency and AMOVA results provide similar evidence in support of a common Pleistocene origin of Indian populations, with partial influence of Indo-European gene pool on the Indian society. The differential Y-chromosome and mt DNA pattern in the two Austric speakers of India signaled that an earlier male-mediated exodus from South East Asia largely involved the Austro-Asiatic tribes, while the Tibeto-Burman males migrated with females through two different routes; one from Burma most likely brought the Naga-Kuki-Chin language and O3e Y-chromosomes and the other from Himalayas, which carried the YAP lineages into northern regions of subcontinent. Based on distribution of Y-chromosome haplogroups (H, C, O2a, and R2) and deep coalescing time depths for these paternal lineages, we propose that the present day Dravidian speaking populations of South India are the descendants of earliest Pleistocene settlers while Austro-Asiatic speakers came from SE Asia in a later migration event.

Only rs1426654 is significantly associated with MI in each individual population; however, rs1426654, rs1042602, and rs16891982 are significantly associated with pigmentation in the broader West Maharashtra region after controlling for population and social group, with rs1426654 (SLC24A5) explaining the majority of the observed variation. Am. J. Hum. Biol. 28:610-618, 2016. © 2016 Wiley Periodicals, Inc.

South Asia has a complex history of migrations and is characterized by substantial pigmentary and genetic diversity. For this reason, it is an ideal region to study the genetic architecture of normal pigmentation variation. Here, we present a meta-analysis of two genome-wide association studies (GWASs) of skin pigmentation using skin reflectance (M-index) as a quantitative phenotype. The meta-analysis includes a sample of individuals of South Asian descent living in Canada ( N = 348), and a sample of individuals from two caste and four tribal groups from West Maharashtra, India ( N = 480). We also present the first GWAS of iris color in South Asian populations. This GWAS was based on quantitative measures of iris color obtained from high-resolution iris pictures. We identified genome-wide significant associations of variants within the well-known gene SLC24A5 , including the nonsynonymous rs1426654 polymorphism, with both skin pigmentation and iris color, highlighting the pleiotropic effects of this gene on pigmentation. Variants in the HERC2 gene (e.g., rs12913832) were also associated with iris color and iris heterochromia. Our study emphasizes the usefulness of quantitative methods to study iris color variation. We also identified novel genome-wide significant associations with skin pigmentation and iris color, but we could not replicate these associations due to the lack of independent samples. It will be critical to expand the number of studies in South Asian populations in order to better understand the genetic variation driving the diversity of skin pigmentation and iris color observed in this region.

Our results suggest that various factors may have contributed to pigmentation diversity across the Indian subcontinent. The lack of correlation between UVR and MI suggests that natural selection may not have played a significant role in shaping pigmentation variation across the subcontinent. We discuss other possible explanations, including metabolic conservation and cultural factors such as traditional social hierarchies and strict endogamy that have led to the development of population structure.

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