02-03-2008, 12:57 AM
Another scientific psy ops
http://www.genome.org/cgi/content/full/13/10/2277
Ethnic India: A Genomic View, With Special Reference to Peopling and Structure
Analabha Basu1,4, Namita Mukherjee1,4, Sangita Roy2,4, Sanghamitra Sengupta1,4, Sanat Banerjee1, Madan Chakraborty1, Badal Dey1, Monami Roy1, Bidyut Roy1, Nitai P. Bhattacharyya3, Susanta Roychoudhury2 and Partha P. Majumder1,5
1 Anthropology & Human Genetics Unit, Indian Statistical Institute, Calcutta 700 108, India 2 Human Genetics & Genomics Department, Indian Institute of Chemical Biology, Calcutta, India 3 Crystallography & Molecular Biology Division, Saha Institute of Nuclear Physics, Calcutta, India
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.
<b>
India has served as a major corridor for the dispersal of modern humans (Cann 2001Go). The date of entry of modern humans into India remains uncertain. By the middle Paleolithic period (50,000-20,000 years before present [ybp]), humans appear to have spread to many parts of India (Misra 1992Go). The migration routes of modern humans into India remain enigmatic, and whether there were also returns to Africa from India/Asia is unclear (Maca-Meyer et al. 2001Go; Roychoudhury et al. 2001Go; Cruciani et al. 2002Go). Contemporary ethnic India is a land of enormous genetic, cultural, and linguistic diversity (Karve 1961Go; Beteille 1998Go; Majumder 1998Go).</b> The people of India are culturally stratified as tribals, who constitute 8.08% of the total population (1991 Census of India), and nontribals. There are ~450 tribal communities in India (Singh 1992Go), who speak ~750 dialects (Kosambi 1991Go) that can be classified into one of the following three language families: Austro-Asiatic (AA), Dravidian (DR), and Tibeto-Burman (TB). Most contemporary nontribal populations of India belong to the Hindu religious fold and are hierarchically arranged in four main caste classes, namely, Brahmin (priestly class), Kshatriya (warrior class), Vysya (business class), and Sudra (menial labor class). In addition, there are several religious communities, who practice different religions, namely, Islam, Christianity, Sikhism, Judaism, and so on. The nontribals predominantly speak languages that belong to the Indo-European (IE) or Dravidian families. The IE and DR groups have been the major contributors to the development of Indian culture and society (Meenakshi 1995Go). Indian culture and society are also known to have been affected by multiple waves of migration and gene flow that took place in historic and prehistoric times (Ratnagar 1995Go; Thapar 1995Go). In a recent study conducted on ranked caste populations sampled from one southern Indian State (Andhra Pradesh), Bamshad et al. (2001Go) have found that the genomic affinity to Europeans is proportionate to caste rankâthe upper castes being most similar to Europeans, particularly East Europeans, whereas the lower castes are more similar to Asians. <b>These findings are consistent with the migration of IE groups into India, the establishment of the caste system, and subsequent recruitment of indigenous people into the caste fold.</b> Because the Indian samples for this study were drawn from one geographical area, whether we can safely generalize these findings needs to be investigated.
The tribals are possibly the original inhabitants of India (Thapar 1966Go; Ray 1973Go), although their evolutionary histories and biological contributions to the nontribal populations have been debated (Risley 1915Go; Guha 1935Go; Sarkar 1958Go). Therefore, it is crucial to carry out genetic investigations in geographically and culturally disparate, but ethnically well-defined, populations, using data on a uniform set of mitochondrial (mt), Y-chromosomal, and autosomal DNA markers. Unfortunately, the vast majority of earlier studies on Indian populations have been conducted on ethnically ill-defined populations or have been restricted to a single geographical area or a single set of markersâprimarily either mitochondrial or Y-chromosomal (e.g.,Kivisild et al. 1999aGo; Bamshad et al. 2001Go). The objectives of the present study are to (1) provide a comprehensive view of genomic diversity and differentiation in India, and (2) to draw inferences on the peopling of India, and the origins of the ethnic populations, specifically in relation to the various competing hypotheses, such as whether the Austro-Asiatic or the Dravidian-speaking tribal groups were the original inhabitants of India (Risley 1915Go; Guha 1935Go; Sarkar 1958Go).
We analyzed genetic variation in 44 geographically, linguistically, and socially disparate ethnic populations of India (Table 1). These include 10 restriction site polymorphisms (RSPs), one insertion/deletion (InDel) polymorphism, and hypervariable segment 1 (HVS1) sequences on mtDNA; 11 RSPs, 1 InDel, and 10 short tandem repeat (STR) loci on Y-chromosomal DNA; and 8 InDel and 17 RSPs on autosomal DNA.
<b>
Austro-Asiatic-Speaking Tribals May Be the Earliest Inhabitants of India</b>
Sociocultural and linguistic evidence indicates (Risley 1915Go; Thapar 1966Go; Pattanayak 1998Go) that the AA tribals are the original inhabitants of India. Some other scholars have, however, argued that tribal groups speaking DR and AA languages have evolved from an older original substrate of proto-Australoids (Keith 1936Go), whereas the TB tribals are later immigrants from Tibet and Myanmar (Guha 1935Go). Our findings strongly support the hypothesis that AA tribals are the earliest inhabitants of India. They possess the highest frequencies of the ancient east-Asian mtDNA HG-M and exhibit the highest HVS1 nucleotide diversity (Table 4). They also have the highest frequency of subHG M2 (19%), which had the highest HVS1 nucleotide diversity compared with other subHGs and therefore possibly the earliest settlers (the estimated coalescence time is 63,000 ± 6000 ybp; Kivisild et al. 1999aGo). Although all sociolinguistic groups seem to have undergone significant population expansions as evidenced by the unimodality of the HVS1 mismatch distributions (data not shown) and by the values of the relevant statistics (small values of the "raggedness" statistic and significantly large negative values of Fu's Fs statistic; Table 4), the AA tribals show the highest value of the estimated expansion time, ~55,000 years, which is ~15,000 years larger than the estimates for the other groups. Although we cannot be sure that this expansion took place in India, in conjunction with the other findings, it appears that this group of tribals may be the earliest inhabitants of India.
<b>
Dravidian Speakers, Now Confined to Southern India, May Have Earlier Been Widespread Throughout India: Genetic Signatures of "Elite Dominance"?</b>
The IE and DR speakers share a significantly larger number of HVS1 sequences (Fig. 8A) compared with those between other groups. The number of individuals sharing these sequences is also the largest between IE and DR groups (Fig. 8B). These facts are striking, especially because the geographical regions presently inhabited by them are virtually disjoint. To explore in further detail the presence of cryptic population structure and the relationships among the various subgroups of populations, we have carried out a "population structure" analysis (Pritchard et al. 2000Go). In this analysis, an unknown number (K) of hypothetical ancestral populations is assumed to have contributed to the genetic profiles of contemporary populations. The number of hypothetical ancestral populations and their relative genetic contributions are statistically estimated from allele frequency data of contemporary populations. The results of population structure analysis based on our autosomal data also show (Fig. 9) that the DR and IE speakers are the most similar, in the sense that the proportional contributions of the five estimated hypothetical ancestral populations to these two groups are the most similar. These findings are consistent with the historical view that the DR speakers were possibly widespread throughout India (Thapar 2003Go). When the ranked caste system was formed after the arrival of the IE speakers ~3500 ybp, many indigenous people of India, who were possibly DR speakers, embraced (or were forced to embrace) the caste system, together with the IE language and admixture. In fact, Renfrew (1992Go) has suggested that the elite dominance model, which envisages the intrusion of a relatively small but well-organized group that takes over an existing system by the use of force, may be appropriate to explain the distribution of the IE languages in north India and Pakistan. As the IE speakers, who entered India primarily through the northwest corridor, advanced into the Indo-Gangetic plain, indigenous people, especially the DR speakers, may have retreated southward to avoid linguistic dominance, after an initial period of admixture and adoption of the caste system. As evidenced by their strong genetic similarities (data not shown), the IE-speaking Halba tribals were most probably a DR-speaking tribal group, which is consistent with IE dominance over DR tribals.
<b>
Central Asian Populations Have Contributed to the Genetic Profiles of Upper Castes, More in the North Than in the South</b>
Central Asia is supposed to have been a major contributor to the Indian gene pool, particularly to the north Indian gene pool, and the migrants had supposedly moved to India through Afghanistan and Pakistan. From mtHVS1 data, we have estimated FST values between the populations of the Central Asia and Pakistan regions (data were collated from Calafell et al. 1996Go; Comas et al. 1998Go; Kivisild et al. 1999aGo) and those belonging to various geographical regions of India. Populations of Central Asia and Pakistan show the lowest (0.017) coefficient of genetic differentiation with the north Indian populations, higher (0.042) with the south Indian populations, and the highest (0.047) with the northeast Indian populations. The Central Asian populations are genetically closer to the upper-caste populations than to the middle- or lower-caste populations, which is in agreement with Bamshad et al.'s (2001Go) findings. Among the upper-caste populations, those of north India are, however, genetically much closer (FST = 0.016) than those of south India (FST = 0.031). Phylogenetic analysis of Y-HG data collated from various sources (Hammer et al. 2000Go; Nebel et al. 2000Go; Rosser et al. 2000Go; Qamar et al. 2002Go) and with those generated in the present study also showed a similar picture (data not shown). One explanation, consistent with those of the previous section, is that even after the DR speakers retreated to the south to avoid elite dominance, there has been admixture between Central and West Asians and northern Indian populations.
http://www.genome.org/cgi/content/full/13/10/2277
Ethnic India: A Genomic View, With Special Reference to Peopling and Structure
Analabha Basu1,4, Namita Mukherjee1,4, Sangita Roy2,4, Sanghamitra Sengupta1,4, Sanat Banerjee1, Madan Chakraborty1, Badal Dey1, Monami Roy1, Bidyut Roy1, Nitai P. Bhattacharyya3, Susanta Roychoudhury2 and Partha P. Majumder1,5
1 Anthropology & Human Genetics Unit, Indian Statistical Institute, Calcutta 700 108, India 2 Human Genetics & Genomics Department, Indian Institute of Chemical Biology, Calcutta, India 3 Crystallography & Molecular Biology Division, Saha Institute of Nuclear Physics, Calcutta, India
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.
<b>
India has served as a major corridor for the dispersal of modern humans (Cann 2001Go). The date of entry of modern humans into India remains uncertain. By the middle Paleolithic period (50,000-20,000 years before present [ybp]), humans appear to have spread to many parts of India (Misra 1992Go). The migration routes of modern humans into India remain enigmatic, and whether there were also returns to Africa from India/Asia is unclear (Maca-Meyer et al. 2001Go; Roychoudhury et al. 2001Go; Cruciani et al. 2002Go). Contemporary ethnic India is a land of enormous genetic, cultural, and linguistic diversity (Karve 1961Go; Beteille 1998Go; Majumder 1998Go).</b> The people of India are culturally stratified as tribals, who constitute 8.08% of the total population (1991 Census of India), and nontribals. There are ~450 tribal communities in India (Singh 1992Go), who speak ~750 dialects (Kosambi 1991Go) that can be classified into one of the following three language families: Austro-Asiatic (AA), Dravidian (DR), and Tibeto-Burman (TB). Most contemporary nontribal populations of India belong to the Hindu religious fold and are hierarchically arranged in four main caste classes, namely, Brahmin (priestly class), Kshatriya (warrior class), Vysya (business class), and Sudra (menial labor class). In addition, there are several religious communities, who practice different religions, namely, Islam, Christianity, Sikhism, Judaism, and so on. The nontribals predominantly speak languages that belong to the Indo-European (IE) or Dravidian families. The IE and DR groups have been the major contributors to the development of Indian culture and society (Meenakshi 1995Go). Indian culture and society are also known to have been affected by multiple waves of migration and gene flow that took place in historic and prehistoric times (Ratnagar 1995Go; Thapar 1995Go). In a recent study conducted on ranked caste populations sampled from one southern Indian State (Andhra Pradesh), Bamshad et al. (2001Go) have found that the genomic affinity to Europeans is proportionate to caste rankâthe upper castes being most similar to Europeans, particularly East Europeans, whereas the lower castes are more similar to Asians. <b>These findings are consistent with the migration of IE groups into India, the establishment of the caste system, and subsequent recruitment of indigenous people into the caste fold.</b> Because the Indian samples for this study were drawn from one geographical area, whether we can safely generalize these findings needs to be investigated.
The tribals are possibly the original inhabitants of India (Thapar 1966Go; Ray 1973Go), although their evolutionary histories and biological contributions to the nontribal populations have been debated (Risley 1915Go; Guha 1935Go; Sarkar 1958Go). Therefore, it is crucial to carry out genetic investigations in geographically and culturally disparate, but ethnically well-defined, populations, using data on a uniform set of mitochondrial (mt), Y-chromosomal, and autosomal DNA markers. Unfortunately, the vast majority of earlier studies on Indian populations have been conducted on ethnically ill-defined populations or have been restricted to a single geographical area or a single set of markersâprimarily either mitochondrial or Y-chromosomal (e.g.,Kivisild et al. 1999aGo; Bamshad et al. 2001Go). The objectives of the present study are to (1) provide a comprehensive view of genomic diversity and differentiation in India, and (2) to draw inferences on the peopling of India, and the origins of the ethnic populations, specifically in relation to the various competing hypotheses, such as whether the Austro-Asiatic or the Dravidian-speaking tribal groups were the original inhabitants of India (Risley 1915Go; Guha 1935Go; Sarkar 1958Go).
We analyzed genetic variation in 44 geographically, linguistically, and socially disparate ethnic populations of India (Table 1). These include 10 restriction site polymorphisms (RSPs), one insertion/deletion (InDel) polymorphism, and hypervariable segment 1 (HVS1) sequences on mtDNA; 11 RSPs, 1 InDel, and 10 short tandem repeat (STR) loci on Y-chromosomal DNA; and 8 InDel and 17 RSPs on autosomal DNA.
<b>
Austro-Asiatic-Speaking Tribals May Be the Earliest Inhabitants of India</b>
Sociocultural and linguistic evidence indicates (Risley 1915Go; Thapar 1966Go; Pattanayak 1998Go) that the AA tribals are the original inhabitants of India. Some other scholars have, however, argued that tribal groups speaking DR and AA languages have evolved from an older original substrate of proto-Australoids (Keith 1936Go), whereas the TB tribals are later immigrants from Tibet and Myanmar (Guha 1935Go). Our findings strongly support the hypothesis that AA tribals are the earliest inhabitants of India. They possess the highest frequencies of the ancient east-Asian mtDNA HG-M and exhibit the highest HVS1 nucleotide diversity (Table 4). They also have the highest frequency of subHG M2 (19%), which had the highest HVS1 nucleotide diversity compared with other subHGs and therefore possibly the earliest settlers (the estimated coalescence time is 63,000 ± 6000 ybp; Kivisild et al. 1999aGo). Although all sociolinguistic groups seem to have undergone significant population expansions as evidenced by the unimodality of the HVS1 mismatch distributions (data not shown) and by the values of the relevant statistics (small values of the "raggedness" statistic and significantly large negative values of Fu's Fs statistic; Table 4), the AA tribals show the highest value of the estimated expansion time, ~55,000 years, which is ~15,000 years larger than the estimates for the other groups. Although we cannot be sure that this expansion took place in India, in conjunction with the other findings, it appears that this group of tribals may be the earliest inhabitants of India.
<b>
Dravidian Speakers, Now Confined to Southern India, May Have Earlier Been Widespread Throughout India: Genetic Signatures of "Elite Dominance"?</b>
The IE and DR speakers share a significantly larger number of HVS1 sequences (Fig. 8A) compared with those between other groups. The number of individuals sharing these sequences is also the largest between IE and DR groups (Fig. 8B). These facts are striking, especially because the geographical regions presently inhabited by them are virtually disjoint. To explore in further detail the presence of cryptic population structure and the relationships among the various subgroups of populations, we have carried out a "population structure" analysis (Pritchard et al. 2000Go). In this analysis, an unknown number (K) of hypothetical ancestral populations is assumed to have contributed to the genetic profiles of contemporary populations. The number of hypothetical ancestral populations and their relative genetic contributions are statistically estimated from allele frequency data of contemporary populations. The results of population structure analysis based on our autosomal data also show (Fig. 9) that the DR and IE speakers are the most similar, in the sense that the proportional contributions of the five estimated hypothetical ancestral populations to these two groups are the most similar. These findings are consistent with the historical view that the DR speakers were possibly widespread throughout India (Thapar 2003Go). When the ranked caste system was formed after the arrival of the IE speakers ~3500 ybp, many indigenous people of India, who were possibly DR speakers, embraced (or were forced to embrace) the caste system, together with the IE language and admixture. In fact, Renfrew (1992Go) has suggested that the elite dominance model, which envisages the intrusion of a relatively small but well-organized group that takes over an existing system by the use of force, may be appropriate to explain the distribution of the IE languages in north India and Pakistan. As the IE speakers, who entered India primarily through the northwest corridor, advanced into the Indo-Gangetic plain, indigenous people, especially the DR speakers, may have retreated southward to avoid linguistic dominance, after an initial period of admixture and adoption of the caste system. As evidenced by their strong genetic similarities (data not shown), the IE-speaking Halba tribals were most probably a DR-speaking tribal group, which is consistent with IE dominance over DR tribals.
<b>
Central Asian Populations Have Contributed to the Genetic Profiles of Upper Castes, More in the North Than in the South</b>
Central Asia is supposed to have been a major contributor to the Indian gene pool, particularly to the north Indian gene pool, and the migrants had supposedly moved to India through Afghanistan and Pakistan. From mtHVS1 data, we have estimated FST values between the populations of the Central Asia and Pakistan regions (data were collated from Calafell et al. 1996Go; Comas et al. 1998Go; Kivisild et al. 1999aGo) and those belonging to various geographical regions of India. Populations of Central Asia and Pakistan show the lowest (0.017) coefficient of genetic differentiation with the north Indian populations, higher (0.042) with the south Indian populations, and the highest (0.047) with the northeast Indian populations. The Central Asian populations are genetically closer to the upper-caste populations than to the middle- or lower-caste populations, which is in agreement with Bamshad et al.'s (2001Go) findings. Among the upper-caste populations, those of north India are, however, genetically much closer (FST = 0.016) than those of south India (FST = 0.031). Phylogenetic analysis of Y-HG data collated from various sources (Hammer et al. 2000Go; Nebel et al. 2000Go; Rosser et al. 2000Go; Qamar et al. 2002Go) and with those generated in the present study also showed a similar picture (data not shown). One explanation, consistent with those of the previous section, is that even after the DR speakers retreated to the south to avoid elite dominance, there has been admixture between Central and West Asians and northern Indian populations.