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Phylogenetic relationships between HVR1 haplotypes were estimated by constructing reduced median networks. The size of each node is porportional to the haplotype frequency. Reticulations indicate parallel mutational pathways or multiple mutations. Major subsets of haplogroup M. The frequency of each subset of haplogroup M is indicated. However, most of these Indian West-Eurasian haplotypes belong to an Indian-specific subset of haplogroup U, that is, U2i Kivisild et al.

In addition, the frequency of mtDNA haplogroups with a more recent coalescence estimate i. These haplotypes are derivatives of haplogroups found throughout Europe Richards et al.

Upper castes are more similar to Europeans than to Asians, middle castes are equidistant from the two groups, and lower castes are most similar to Asians.

This pattern is further accentuated by separating the European population into Northern, Southern, and Eastern Europeans; each caste group is most closely related to Eastern Europeans. Moreover, the genetic distance between upper castes and Eastern Europeans is approximately half the distance between Eastern Europeans and middle or lower castes. These results suggest that Indian Y chromosomes, particularly upper caste Y chromosomes, are more similar to European than to Asian Y chromosomes.

This underscores the close affinities between Hindu Indian and Indo-European Y chromosomes based on a previously reported analysis of three Y-chromosome polymorphisms Quintana-Murci et al. Overall, these results indicate that the affinities of Indians to continental populations varies according to caste rank and depends on whether mtDNA or Y-chromosome data are analyzed. However, conclusions drawn from these data are limited because mtDNA and the Y chromosome is each effectively a single haploid locus and is more sensitive to genetic drift, bottlenecks, and selective sweeps compared to autosomal loci.

These limitations of our analysis can be overcome, in part, by analyzing a larger set of independent autosomal loci. Genetic distances estimated from autosomal Alu elements correspond to caste rank, the genetic distance between the upper and lower castes being more than 2.

These trends are the same whether the Kshatriya and Vysya are included in the upper castes, the middle castes, or excluded from the analysis data not shown. Furthermore, a neighbor-joining network of genetic distances between separate castes Fig.

This is similar to the relationship between genetic distances and caste rank estimated from mtDNA Bamshad et al. It is important to note, however, that the autosomal genetic distances are estimated from 40 independent loci. This afforded us the opportunity to test the statistical significance of the correspondence between genetic distance and caste status. Given the resolving power of this autosomal dataset, we next tested whether we could reconcile the results of the analysis of mtDNA and Y-chromosome markers in castes and continental populations.

Neighbor-joining network of genetic distances among caste communities estimated from 40 Alu polymorphisms. Analysis of each caste separately reveals that the genetic distance between the Brahmins and Europeans 0.

Nevertheless, each separate upper caste is more similar to Europeans than to Asians. Because historical evidence suggests greater affinity between upper castes and Europeans than between lower castes and Europeans Balakrishnan , ; Cavalli-Sforza et al. Significance at 0. These results offer statistical support for differences in the genetic affinity of Europeans to caste populations of differing rank, with greater European affinity to upper castes than to lower castes.

Previous genetic studies have found evidence to support either a European or an Asian origin of Indian caste populations, with occasional indications of admixture with African or proto-Australoid populations Chen et al.

Our results demonstrate that for biparentally inherited autosomal markers, genetic distances between upper, middle, and lower castes are significantly correlated with rank; upper castes are more similar to Europeans than to Asians; and upper castes are significantly more similar to Europeans than are lower castes.

This result appears to be owing to the amalgamation of two different patterns of sex-specific genetic variation. A higher proportion of proto-Asian mtDNA restriction-site haplotypes is found in lower castes compared to middle or upper castes, whereas the frequency of West Eurasian haplotypes is positively correlated with caste rank, that is, is highest in the upper castes. For Y-chromosome STR variation the upper castes exhibit greatest similarity with Europeans, whereas the lower caste groups are most similar to Asians.

For Y biallelic polymorphism variation, each caste group is more similar to Europeans than to Asians, and the affinity to Europeans is proportional to caste rank, that is, is highest in the upper castes. Genetic distances from Asian populations become larger as one moves from lower to middle to upper caste populations. It is especially noteworthy that the analysis of Y biallelic polymorphisms, which involved an independent set of comparative Asian, European, and African populations, again indicated the same pattern.

Additional support is offered by the fact that the autosomal polymorphisms yielded a statistically significant difference between the upper-caste—European and lower-caste—European genetic distances. With additional loci, other differences e. The most likely explanation for these findings, and the one most consistent with archaeological data, is that contemporary Hindu Indians are of proto-Asian origin with West Eurasian admixture.

However, admixture with West Eurasian males was greater than admixture with West Eurasian females, resulting in a higher affinity to European Y chromosomes.

This supports an earlier suggestion of Passarino et al. Furthermore, the degree of West Eurasian admixture was proportional to caste rank. This explanation is consistent with either the hypothesis that proportionately more West Eurasians became members of the upper castes at the inception of the caste hierarchy or that social stratification preceded the West Eurasian incursion and that West Eurasians tended to insert themselves into higher-ranking positions.

One consequence is that shared Indo-European languages may not reflect a common origin of Europeans and most Indians, but rather underscores the transfer of language mediated by contact between West Eurasians and native proto-Indians. West Eurasian admixture in Indian populations may have been the result of more than one wave of immigration into India. Kivisild et al. It is also possible that haplotypes with an older coalescence were introduced by Dravidians, whereas haplotypes with a more recent coalescence belonged to Indo-Europeans.

Alternatively, the coalescence dates of these haplotypes may predate the entry of West Eurasians populations into India. Regardless of their origin, West Eurasian admixture resulted in rank-related differences in the genetic affinities of castes to Europeans and Asians. Furthermore, the frequency of West Eurasian haplotypes in the founding middle and upper castes may be underestimated because of the upward social mobility of women from lower castes Bamshad et al.

These women were presumably more likely to introduce proto-Asian mtDNA haplotypes into the middle and upper castes. Our analysis of 40 autosomal markers indicates clearly that the upper castes have a higher affinity to Europeans than to Asians.

The high affinity of caste Y chromosomes with those of Europeans suggests that the majority of immigrating West Eurasians may have been males. As might be expected if West Eurasian males appropriated the highest positions in the caste system, the upper caste group exhibits a lower genetic distance to Europeans than the middle or lower castes.

This is underscored by the observation that the Kshatriya an upper caste , whose members served as warriors, are closer to Europeans than any other caste data not shown. Furthermore, the bp deletion polymorphism in CC chemokine receptor 5, whose frequency peaks in populations of Eastern Europe, is found only in two Brahmin males M.

Bamshad and S. Ahuja, unpubl. The stratification of Y-chromosome distances with Europeans could also be caused by male-specific gene flow among caste populations of different rank. However, we and others have demonstrated that there is little sharing of Y-chromosome haplotypes among castes of different rank Bamshad et al.

The affinity of caste populations to Europeans is more apparent for Y-chromosome biallelic polymorphisms than Y-chromosome STRs. This could be attributed to the use of different European populations in comparisons using STRs and biallelic polymorphisms.

Alternatively, it may reflect, in part, the effects of high mutation rates for the Y-chromosome STRs, which would tend to obscure relationships between caste and continental populations. A lack of consistent clustering at the continental level has been observed in several studies of Y-chromosome STRs Deka et al.

The autosomal Alu and biallelic Y-chromosome polymorphisms, in contrast, have a slower rate of drift than Y-chromosome STRs because of a higher effective population size, and their mutation rate is very low.

Thus, the Y-chromosome biallelic polymorphisms and autosomal Alu markers may serve as more stable markers of worldwide population affinities.

Our analysis may help to explain why estimates of the affinities of caste groups to worldwide populations have varied so widely among different studies.


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