Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia

Abstract

South Asia harbors one of the highest levels genetic diversity in Eurasia, which could be interpreted as a result of its long-term large effective population size and of admixture during its complex demographic history. In contrast to Pakistani populations, populations of Indian origin have been underrepresented in previous genomic scans of positive selection and population structure. Here we report data for more than 600,000 SNP markers genotyped in 142 samples from 30 ethnic groups in India. Combining our results with other available genome-wide data, we show that Indian populations are characterized by two major ancestry components, one of which is spread at comparable frequency and haplotype diversity in populations of South and West Asia and the Caucasus. The second component is more restricted to South Asia and accounts for more than 50% of the ancestry in Indian populations. Haplotype diversity associated with these South Asian ancestry components is significantly higher than that of the components dominating the West Eurasian ancestry palette. Modeling of the observed haplotype diversities suggests that both Indian ancestry components are older than the purported Indo-Aryan invasion 3,500 YBP. Consistent with the results of pairwise genetic distances among world regions, Indians share more ancestry signals with West than with East Eurasians. However, compared to Pakistani populations, a higher proportion of their genes show regionally specific signals of high haplotype homozygosity. Among such candidates of positive selection in India are MSTN and DOK5, both of which have potential implications in lipid metabolism and the etiology of type 2 diabetes.

Genome-Wide Analysis of Cold Adaptation in Indigenous Siberian Populations

“…The level of iHS signal sharing among Siberian groups (18–47%; Figure S7 in File S1) was, in fact, comparable to that observed among distinct geographic regions, e.g. between Europe and South Asia (37–55%), and between Europe and East Asia (21–22%) [49]. These results are meaningful in the light of the low effective population sizes and vast geographic areas inhabited by the Siberian populations.…”

A Complete Absence of Missense Mutation in Myosin Regulatory and Essential Light Chain Genes of South Indian Hypertrophic and Dilated Cardiomyopathies

“…Thus, the MYL2 and MYL3 mutations are rare and the least cause of cardiomyopathies in Indians. Our data provide important information regarding the frequencies of MYL2 and MYL3 variations in Indians, as well as in south Asians, as about 50% of south Asian ancestry is from India [28]. …”

A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals

“…For example, Metspalu et al [28] argued cogently that the GW pattern in South Asia was the result of a complex series of processes, but they also suggested that an East Asian component, common in extant Central Asians, should be evident in the Subcontinent if it had experienced large-scale Bronze Age immigration from Central Asia. In fact, however, aDNA evidence shows that this element was not present in the relevant source regions in the Early Bronze Age [76].…”