Ethnic India: A Genomic View, With Special Reference to Peopling and Structure
We report a comprehensive statistical analysis of data on 58 DNA markers (mitochondrial [mt], Y-chromosomal, and autosomal) and sequence data of the mtHVS1 from a large number of ethnically diverse populations of India. Our results provide genomic evidence that (1) there is an underlying unity of female lineages in India, indicating that the initial number of female settlers may have been small; (2) the tribal and the caste populations are highly differentiated; (3) the Austro-Asiatic tribals are the earliest settlers in India, providing support to one anthropological hypothesis while refuting some others; (4) a major wave of humans entered India through the northeast; (5) the Tibeto-Burman tribals share considerable genetic commonalities with the Austro-Asiatic tribals, supporting the hypothesis that they may have shared a common habitat in southern China, but the two groups of tribals can be differentiated on the basis of Y-chromosomal haplotypes; (6) the Dravidian tribals were possibly widespread throughout India before the arrival of the Indo-European-speaking nomads, but retreated to southern India to avoid dominance; (7) formation of populations by fission that resulted in founder and drift effects have left their imprints on the genetic structures of contemporary populations; (8) the upper castes show closer genetic affinities with Central Asian populations, although those of southern India are more distant than those of northern India; (9) historical gene flow into India has contributed to a considerable obliteration of genetic histories of contemporary populations so that there is at present no clear congruence of genetic and geographical or sociocultural affinities.
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Fundamental genomic unity of ethnic India is revealed by analysis of mitochondrial DNA
Mitochondrial DNA (mtDNA) profiles of 23 ethnic populations of India drawn from diverse cultural, linguistic and geographical backgrounds are presented. There is extensive sharing of a small number of mtDNA haplotypes, reconstructed on the basis of restriction fragment length polymorphisms, among the populations. This indicates that Indian populations were founded by a small number of females, possibly arriving on one of the early waves of out-of-Africa migration of modern humans; ethnic differentiation occurred subsequently through demographic expansions and geographic dispersal. The Asian-specific haplogroup M is in high frequency in most populations, especially tribal populations and Dravidian populations of southern India. Populations in which the frequencies of haplogroup M are relatively lower show higher frequencies of haplogroup U; such populations are primarily caste populations of northern India. This finding is indicative of a higher Caucasoid admixture in northern Indian populations. By examining the sharing of haplotypes between Indian and south-east Asian populations, we have provided evidence that south-east Asia was peopled by two waves of migration, one originating in India and the other originating in southern China. These findings have been examined and interpreted in the light of inferences derived from previous genomic and historical studies.
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Distinctive KIR and HLA diversity in a panel of north Indian Hindus
HLA and KIR are diverse and rapidly evolving gene complexes that work together in human immunity mediated by cytolytic lymphocytes. Understanding their complex immunogenetic interaction requires study of both HLA and KIR diversity in the same human population. Here a panel of 72 unrelated north Indian Hindus was analyzed. HLA-A, B, C, DRB1, DQA1, and DQB1 alleles and their frequencies were determined by sequencing or high-resolution typing of genomic DNA; KIR genotypes were determined by gene-specific typing and by allele-level DNA typing for KIR2DL1, 2DL3, 2DL5, 3DL1, and 3DL2. From HLA analysis, the north Indian population is seen to have several characteristics shared either with Caucasian or East Asian populations, consistent with the demographic history of north India, as well as specific features, including several alleles at high frequency that are rare or absent in other populations. A majority of the north Indian KIR gene profiles have not been seen in Caucasian and Asian populations. Most striking is a higher frequency of the B group of KIR haplotypes, resulting in equal frequencies for A and B group haplotypes in north Indians. All 72 members of the north Indian panel have different HLA genotype and different KIR genotype.
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Genetic variation of ApoB 3'hyper variable region polymorphism among Brahmins of North India
ApoB 3'hyper variable region (ApoB 3'HVR) is highly polymorphic and hence an informative marker. It could be an ideal candidate to study the genetic heterogeneity among different population groups of the Indian subcontinent. It is one of the markers for which population data are available. This makes the ApoB 3'HVR an ideal locus for a pilot study to investigate the relationships between different populations and the microevolutionary processes leading to their present-day distribution. In the present investigation, we have studied ApoB 3'HVR in three endogamous groups of North India and have compared these populations on the basis of inter- and intra-group diversity. The sub-populations chosen were Bhargavas, Chaturvedis, and non-Bhargava non-Chaturvedi Brahmins of Uttar Pradesh. Nineteen segregating alleles were detected in our population groups. The average observed heterozygosity was quite high (0.717), suggesting high diversity at the ApoB 3'HVR locus. Low value of average GST (0.0126) and FST (0.002) reflects non-significant deviation of heterozygosity between the three subgroups. On comparing the three study groups with ApoB 3'HVR of other Indian and world populations, it was clear that greater diversity was observed for Africans followed by Europeans and Asians. There was relative homogeneity among the continental groups. In our study it was observed that there was high heterozygosity, an extended range of allele size, a quasi unimodal allele size distribution, centred on HVE 37. These findings indicate that our populations may be characterized as ancestral, since similar features are observed in the African population. ApoB 3'HVR polymorphism suggests that despite practising restricted marital patterns, these groups or castes do not significantly differ from each other at the genetic level. This may be because of the fact that divergence time may not be enough to cause genetic variation in these groups. However, it may not be ruled out that the ApoB 3'HVR polymorphism probably predates the divergence of these sub-castes. We are further testing this observation, using mtDNA for maternal lineages and Y-chromosome markers for paternal lineages.
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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.
PDF file
We report a comprehensive statistical analysis of data on 58 DNA markers (mitochondrial [mt], Y-chromosomal, and autosomal) and sequence data of the mtHVS1 from a large number of ethnically diverse populations of India. Our results provide genomic evidence that (1) there is an underlying unity of female lineages in India, indicating that the initial number of female settlers may have been small; (2) the tribal and the caste populations are highly differentiated; (3) the Austro-Asiatic tribals are the earliest settlers in India, providing support to one anthropological hypothesis while refuting some others; (4) a major wave of humans entered India through the northeast; (5) the Tibeto-Burman tribals share considerable genetic commonalities with the Austro-Asiatic tribals, supporting the hypothesis that they may have shared a common habitat in southern China, but the two groups of tribals can be differentiated on the basis of Y-chromosomal haplotypes; (6) the Dravidian tribals were possibly widespread throughout India before the arrival of the Indo-European-speaking nomads, but retreated to southern India to avoid dominance; (7) formation of populations by fission that resulted in founder and drift effects have left their imprints on the genetic structures of contemporary populations; (8) the upper castes show closer genetic affinities with Central Asian populations, although those of southern India are more distant than those of northern India; (9) historical gene flow into India has contributed to a considerable obliteration of genetic histories of contemporary populations so that there is at present no clear congruence of genetic and geographical or sociocultural affinities.
PDF file
Fundamental genomic unity of ethnic India is revealed by analysis of mitochondrial DNA
Mitochondrial DNA (mtDNA) profiles of 23 ethnic populations of India drawn from diverse cultural, linguistic and geographical backgrounds are presented. There is extensive sharing of a small number of mtDNA haplotypes, reconstructed on the basis of restriction fragment length polymorphisms, among the populations. This indicates that Indian populations were founded by a small number of females, possibly arriving on one of the early waves of out-of-Africa migration of modern humans; ethnic differentiation occurred subsequently through demographic expansions and geographic dispersal. The Asian-specific haplogroup M is in high frequency in most populations, especially tribal populations and Dravidian populations of southern India. Populations in which the frequencies of haplogroup M are relatively lower show higher frequencies of haplogroup U; such populations are primarily caste populations of northern India. This finding is indicative of a higher Caucasoid admixture in northern Indian populations. By examining the sharing of haplotypes between Indian and south-east Asian populations, we have provided evidence that south-east Asia was peopled by two waves of migration, one originating in India and the other originating in southern China. These findings have been examined and interpreted in the light of inferences derived from previous genomic and historical studies.
PDF file
Distinctive KIR and HLA diversity in a panel of north Indian Hindus
HLA and KIR are diverse and rapidly evolving gene complexes that work together in human immunity mediated by cytolytic lymphocytes. Understanding their complex immunogenetic interaction requires study of both HLA and KIR diversity in the same human population. Here a panel of 72 unrelated north Indian Hindus was analyzed. HLA-A, B, C, DRB1, DQA1, and DQB1 alleles and their frequencies were determined by sequencing or high-resolution typing of genomic DNA; KIR genotypes were determined by gene-specific typing and by allele-level DNA typing for KIR2DL1, 2DL3, 2DL5, 3DL1, and 3DL2. From HLA analysis, the north Indian population is seen to have several characteristics shared either with Caucasian or East Asian populations, consistent with the demographic history of north India, as well as specific features, including several alleles at high frequency that are rare or absent in other populations. A majority of the north Indian KIR gene profiles have not been seen in Caucasian and Asian populations. Most striking is a higher frequency of the B group of KIR haplotypes, resulting in equal frequencies for A and B group haplotypes in north Indians. All 72 members of the north Indian panel have different HLA genotype and different KIR genotype.
PDF file
Genetic variation of ApoB 3'hyper variable region polymorphism among Brahmins of North India
ApoB 3'hyper variable region (ApoB 3'HVR) is highly polymorphic and hence an informative marker. It could be an ideal candidate to study the genetic heterogeneity among different population groups of the Indian subcontinent. It is one of the markers for which population data are available. This makes the ApoB 3'HVR an ideal locus for a pilot study to investigate the relationships between different populations and the microevolutionary processes leading to their present-day distribution. In the present investigation, we have studied ApoB 3'HVR in three endogamous groups of North India and have compared these populations on the basis of inter- and intra-group diversity. The sub-populations chosen were Bhargavas, Chaturvedis, and non-Bhargava non-Chaturvedi Brahmins of Uttar Pradesh. Nineteen segregating alleles were detected in our population groups. The average observed heterozygosity was quite high (0.717), suggesting high diversity at the ApoB 3'HVR locus. Low value of average GST (0.0126) and FST (0.002) reflects non-significant deviation of heterozygosity between the three subgroups. On comparing the three study groups with ApoB 3'HVR of other Indian and world populations, it was clear that greater diversity was observed for Africans followed by Europeans and Asians. There was relative homogeneity among the continental groups. In our study it was observed that there was high heterozygosity, an extended range of allele size, a quasi unimodal allele size distribution, centred on HVE 37. These findings indicate that our populations may be characterized as ancestral, since similar features are observed in the African population. ApoB 3'HVR polymorphism suggests that despite practising restricted marital patterns, these groups or castes do not significantly differ from each other at the genetic level. This may be because of the fact that divergence time may not be enough to cause genetic variation in these groups. However, it may not be ruled out that the ApoB 3'HVR polymorphism probably predates the divergence of these sub-castes. We are further testing this observation, using mtDNA for maternal lineages and Y-chromosome markers for paternal lineages.
PDF file
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.
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