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1.  Y-chromosomal insights into the genetic impact of the caste system in India 
Human genetics  2006;121(1):137-144.
The caste system has persisted in Indian Hindu society for around 3,500 years. Like the Y chromosome, caste is defined at birth, and males cannot change their caste. In order to investigate the genetic consequences of this system, we have analysed male-lineage variation in a sample of 227 Indian men of known caste, 141 from the Jaunpur district of Uttar Pradesh and 86 from the rest of India. We typed 131 Y-chromosomal binary markers and 16 microsatellites. We find striking evidence for male substructure: in particular, Brahmins and Kshatriyas (but not other castes) from Jaunpur each show low diversity and the predominance of a single distinct cluster of haplotypes. These findings confirm the genetic isolation and drift within the Jaunpur upper castes, which are likely to result from founder effects and social factors. In the other castes, there may be either larger effective population sizes, or less strict isolation, or both.
doi:10.1007/s00439-006-0282-2
PMCID: PMC2590678  PMID: 17075717
Y chromosome; haplotype; human population substructure; Indian caste system
2.  Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA 
BMC Genetics  2006;7:42.
Background
India is a country with enormous social and cultural diversity due to its positioning on the crossroads of many historic and pre-historic human migrations. The hierarchical caste system in the Hindu society dominates the social structure of the Indian populations. The origin of the caste system in India is a matter of debate with many linguists and anthropologists suggesting that it began with the arrival of Indo-European speakers from Central Asia about 3500 years ago. Previous genetic studies based on Indian populations failed to achieve a consensus in this regard. We analysed the Y-chromosome and mitochondrial DNA of three tribal populations of southern India, compared the results with available data from the Indian subcontinent and tried to reconstruct the evolutionary history of Indian caste and tribal populations.
Results
No significant difference was observed in the mitochondrial DNA between Indian tribal and caste populations, except for the presence of a higher frequency of west Eurasian-specific haplogroups in the higher castes, mostly in the north western part of India. On the other hand, the study of the Indian Y lineages revealed distinct distribution patterns among caste and tribal populations. The paternal lineages of Indian lower castes showed significantly closer affinity to the tribal populations than to the upper castes. The frequencies of deep-rooted Y haplogroups such as M89, M52, and M95 were higher in the lower castes and tribes, compared to the upper castes.
Conclusion
The present study suggests that the vast majority (>98%) of the Indian maternal gene pool, consisting of Indio-European and Dravidian speakers, is genetically more or less uniform. Invasions after the late Pleistocene settlement might have been mostly male-mediated. However, Y-SNP data provides compelling genetic evidence for a tribal origin of the lower caste populations in the subcontinent. Lower caste groups might have originated with the hierarchical divisions that arose within the tribal groups with the spread of Neolithic agriculturalists, much earlier than the arrival of Aryan speakers. The Indo-Europeans established themselves as upper castes among this already developed caste-like class structure within the tribes.
doi:10.1186/1471-2156-7-42
PMCID: PMC1569435  PMID: 16893451
4.  In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India 
BMC Genomics  2006;7:151.
Background
Macrohaplogroups 'M' and 'N' have evolved almost in parallel from a founder haplogroup L3. Macrohaplogroup N in India has already been defined in previous studies and recently the macrohaplogroup M among the Indian populations has been characterized. In this study, we attempted to reconstruct and re-evaluate the phylogeny of Macrohaplogroup M, which harbors more than 60% of the Indian mtDNA lineage, and to shed light on the origin of its deep rooting haplogroups.
Results
Using 11 whole mtDNA and 2231 partial coding sequence of Indian M lineage selected from 8670 HVS1 sequences across India, we have reconstructed the tree including Andamanese-specific lineage M31 and calculated the time depth of all the nodes. We defined one novel haplogroup M41, and revised the classification of haplogroups M3, M18, and M31.
Conclusion
Our result indicates that the Indian mtDNA pool consists of several deep rooting lineages of macrohaplogroup 'M' suggesting in-situ origin of these haplogroups in South Asia, most likely in the India. These deep rooting lineages are not language specific and spread over all the language groups in India. Moreover, our reanalysis of the Andamanese-specific lineage M31 suggests population specific two clear-cut subclades (M31a1 and M31a2). Onge and Jarwa share M31a1 branch while M31a2 clade is present in only Great Andamanese individuals. Overall our study supported the one wave, rapid dispersal theory of modern humans along the Asian coast.
doi:10.1186/1471-2164-7-151
PMCID: PMC1534032  PMID: 16776823
5.  Global Patterns in Human Mitochondrial DNA and Y-Chromosome Variation Caused by Spatial Instability of the Local Cultural Processes 
PLoS Genetics  2006;2(4):e53.
Because of the widespread phenomenon of patrilocality, it is hypothesized that Y-chromosome variants tend to be more localized geographically than those of mitochondrial DNA (mtDNA). Empirical evidence confirmatory to this hypothesis was subsequently provided among certain patrilocal and matrilocal groups of Thailand, which conforms to the isolation by distance mode of gene diffusion. However, we expect intuitively that the patterns of genetic variability may not be consistent with the above hypothesis among populations with different social norms governing the institution of marriage, particularly among those that adhere to strict endogamy rules. We test the universality of this hypothesis by analyzing Y-chromosome and mtDNA data in three different sets of Indian populations that follow endogamy rules to varying degrees. Our analysis of the Indian patrilocal and the matrilocal groups is not confirmatory to the sex-specific variation observed among the tribes of Thailand. Our results indicate spatial instability of the impact of different cultural processes on the genetic variability, resulting in the lack of universality of the hypothesized pattern of greater Y-chromosome variation when compared to that of mtDNA among the patrilocal populations.
Synopsis
In most human societies, women traditionally move to their husband's home after marriage, and these societies are thus “patrilocal,” but in a few “matrilocal” societies, men move to their wife's home. These social customs are expected to influence the patterns of genetic variation. They should lead to a localization of male-specific Y-chromosomal variants and wide dispersal of female-specific mitochondrial DNA variants in patrilocal societies and vice versa in matrilocal societies. These predicted patterns have indeed been observed in previous studies of populations from Thailand. Indian societies, however, are endogamous, so marriage should always take place within a population, and these different patterns of genetic variation should not build up. The authors have now analyzed ten patrilocal and five matrilocal Indian populations, and find that there is indeed little difference between the patrilocal and matrilocal societies. The authors therefore conclude that patterns of genetic variation in humans are not universal, but depend on local cultural practices.
doi:10.1371/journal.pgen.0020053
PMCID: PMC1435684  PMID: 16617372
6.  Global Patterns in Human Mitochondrial DNA and Y-Chromosome Variation Caused by Spatial Instability of the Local Cultural Processes 
PLoS Genetics  2006;2(4):e53.
Because of the widespread phenomenon of patrilocality, it is hypothesized that Y-chromosome variants tend to be more localized geographically than those of mitochondrial DNA (mtDNA). Empirical evidence confirmatory to this hypothesis was subsequently provided among certain patrilocal and matrilocal groups of Thailand, which conforms to the isolation by distance mode of gene diffusion. However, we expect intuitively that the patterns of genetic variability may not be consistent with the above hypothesis among populations with different social norms governing the institution of marriage, particularly among those that adhere to strict endogamy rules. We test the universality of this hypothesis by analyzing Y-chromosome and mtDNA data in three different sets of Indian populations that follow endogamy rules to varying degrees. Our analysis of the Indian patrilocal and the matrilocal groups is not confirmatory to the sex-specific variation observed among the tribes of Thailand. Our results indicate spatial instability of the impact of different cultural processes on the genetic variability, resulting in the lack of universality of the hypothesized pattern of greater Y-chromosome variation when compared to that of mtDNA among the patrilocal populations.
Synopsis
In most human societies, women traditionally move to their husband's home after marriage, and these societies are thus “patrilocal,” but in a few “matrilocal” societies, men move to their wife's home. These social customs are expected to influence the patterns of genetic variation. They should lead to a localization of male-specific Y-chromosomal variants and wide dispersal of female-specific mitochondrial DNA variants in patrilocal societies and vice versa in matrilocal societies. These predicted patterns have indeed been observed in previous studies of populations from Thailand. Indian societies, however, are endogamous, so marriage should always take place within a population, and these different patterns of genetic variation should not build up. The authors have now analyzed ten patrilocal and five matrilocal Indian populations, and find that there is indeed little difference between the patrilocal and matrilocal societies. The authors therefore conclude that patterns of genetic variation in humans are not universal, but depend on local cultural practices.
doi:10.1371/journal.pgen.0020053
PMCID: PMC1435684  PMID: 16617372

Results 1-6 (6)