Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans

BACKGROUND:Recent advances in the understanding of the maternal and paternal heritage of south and southwest Asian populations have highlighted their role in the colonization of Eurasia by anatomically modern humans. Further understanding requires a deeper insight into the topology of the branches of the Indian mtDNA phylogenetic tree, which should be contextualized within the phylogeography of the neighboring regional mtDNA variation. Accordingly, we have analyzed mtDNA control and coding region variation in 796 Indian (including both tribal and caste populations from different parts of India) and 436 Iranian mtDNAs. The results were integrated and analyzed together with published data from South, Southeast Asia and West Eurasia.RESULTS:Four new Indian-specific haplogroup M sub-clades were defined. These, in combination with two previously described haplogroups, encompass approximately one third of the haplogroup M mtDNAs in India. Their phylogeography and spread among different linguistic phyla and social strata was investigated in detail. Furthermore, the analysis of the Iranian mtDNA pool revealed patterns of limited reciprocal gene flow between Iran and the Indian sub-continent and allowed the identification of different assemblies of shared mtDNA sub-clades.CONCLUSIONS:Since the initial peopling of South and West Asia by anatomically modern humans, when this region may well have provided the initial settlers who colonized much of the rest of Eurasia, the gene flow in and out of India of the maternally transmitted mtDNA has been surprisingly limited. Specifically, our analysis of the mtDNA haplogroups, which are shared between Indian and Iranian populations and exhibit coalescence ages corresponding to around the early Upper Paleolithic, indicates that they are present in India largely as Indian-specific sub-lineages. In contrast, other ancient Indian-specific variants of M and R are very rare outside the sub-continent.This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at [email protected]

Genetic Evidence on the Origins of Indian Caste Populations

This is the published version, also available here: http://www.dx.doi.org/10.1101/gr.173301.The origins and affinities of the ∼1 billion people living on the subcontinent of India have long been contested. This is owing, in part, to the many different waves of immigrants that have influenced the genetic structure of India. In the most recent of these waves, Indo-European-speaking people from West Eurasia entered India from the Northwest and diffused throughout the subcontinent. They purportedly admixed with or displaced indigenous Dravidic-speaking populations. Subsequently they may have established the Hindu caste system and placed themselves primarily in castes of higher rank. To explore the impact of West Eurasians on contemporary Indian caste populations, we compared mtDNA (400 bp of hypervariable region 1 and 14 restriction site polymorphisms) and Y-chromosome (20 biallelic polymorphisms and 5 short tandem repeats) variation in ∼265 males from eight castes of different rank to ∼750 Africans, Asians, Europeans, and other Indians. For maternally inherited mtDNA, each caste is most similar to Asians. However, 20%–30% of Indian mtDNA haplotypes belong to West Eurasian haplogroups, and the frequency of these haplotypes is proportional to caste rank, the highest frequency of West Eurasian haplotypes being found in the upper castes. In contrast, for paternally inherited Y-chromosome variation each caste is more similar to Europeans than to Asians. Moreover, the affinity to Europeans is proportionate to caste rank, the upper castes being most similar to Europeans, particularly East Europeans. These findings are consistent with greater West Eurasian male admixture with castes of higher rank. Nevertheless, the mitochondrial genome and the Y chromosome each represents only a single haploid locus and is more susceptible to large stochastic variation, bottlenecks, and selective sweeps. Thus, to increase the power of our analysis, we assayed 40 independent, biparentally inherited autosomal loci (1 LINE-1 and 39 Alu elements) in all of the caste and continental populations (∼600 individuals). Analysis of these data demonstrated that the upper castes have a higher affinity to Europeans than to Asians, and the upper castes are significantly more similar to Europeans than are the lower castes. Collectively, all five datasets show a trend toward upper castes being more similar to Europeans, whereas lower castes are more similar to Asians. We conclude that Indian castes are most likely to be of proto-Asian origin with West Eurasian admixture resulting in rank-related and sex-specific differences in the genetic affinities of castes to Asians and Europeans

PGM1 Subtypes in Populations of the Indian Subcontinent

Isoelectric focusing was performed to analyze PGM1 polymorphism in six tribal, five caste, and five Muslim populations from the Indian subcontinent. Although a considerable range of allele frequencies was observed in certain caste and Muslim groups, the phenotypic distribution showed significant genetic heterogeneity only among the tribal groups. Discriminant analysis suggests that the PGM locus provides useful anthropogenetic information to differentiate the populations of the subcontinent in terms of their social structure. In the three population groups studied the variation in the heterozygosity levels suggests that the genetic diversity at the PGM1 locus maybe the result of the structure of various population groups

Chapter 17 The Genetics of Language and Farming Spread in India

Most maternal lineages of present-day Indians derive from a common ancestor in mtDNA haplogroup M that split into Indian, eastern Asian, Papuan, and Australian subsets 40,000-60,000 mtDNA-years ago. The second major component in Indian maternal heredity lines traces back to the split of haplogroup U into Indian, western Eurasian and northern African variants approximately at the same time. The variation in these two ancient Indian-specific sets of lineages is the main modifier in the heterogeneity landscape of Indian populations, defining the genetic differences between caste groups and geographic regions in the sub-continent. The difference between regional caste groups is accentuated furthermore by the presence of a northwest to sout

The distribution of the 3' VNTR polymorphism in human dopamine transporter gene (DAT1) in world populations

This is the published version, also available here: http://www.jstor.org/stable/41465826

A deletion polymorphism in the human COL1A2 gene. Genetic evidence for a non-African population whose descendants spread to all continents

This is the published version, also available here: http://www.jstor.org/stable/41465791