Kamal900
03-22-2015, 05:23 AM
Ann Hum Biol. Author manuscript; available in PMC 2009 Oct 1.
The genetic structure, affinities, and diversity of the 1 billion Indians hold important keys to numerous unanswered questions regarding the evolution of human populations and the forces shaping contemporary patterns of genetic variation. Although there have been several recent studies of South Indian caste groups, North Indian caste groups, and South Indian Muslims using Y-chromosomal markers, overall, the Indian population has still not been well studied compared to other geographical populations. In particular, no genetic study has been conducted on Shias and Sunnis from North India.
India occupies a unique stage in human population evolution because one of the early waves of migration of modern humans was out of Africa, through West Asia, into India (Cann 2001). More recently, about 15 00010 000 years before present (ybp), when agriculture developed in the Fertile Crescent region that extended from Israel through Northern Syria to Western Iran, there was an eastward wave of human migration (Renfrew 1989; Cavalli-Sforza et al. 1994). It has been postulated that this wave brought the Dravidian language into India (Renfrew 1989). Subsequently, the Indo-European (Aryan) language was introduced into India from the Iranian plateau approximately 40003000 ybp, where this language was probably brought by pastoral nomads from the Central Asian steppes (Renfrew 1989). Therefore, linguistic evidence suggests that West Asia and Central Asia were two major geographical sources contributing to the Indian gene pool.
Indian society predominantly revolves around the concept of caste, or the Caste System, a strong socio-cultural conglomerate of traditions that have created and maintained a great number of hierarchically arranged endogamous groups (Bamshad et al. 2001). This unique social system exists only in India. One impact of the system is that a persons fate, including even the choice of marriage partner, is largely determined at his/her birth. The Hindu caste system plays a major role in social and economic organization of the Indian population. In this system, the society is divided into four broad castes: (from low to high) Sudras, Vaishyas, Kshatriyas and Brahmins. The rules that generally prevent marriages between castes may have contributed to population substructure and the pattern of genetic diversity. Another important feature in Indian population history was the occurrence of four separate or distinct waves of migration into the subcontinent (Cordaux et al. 2004): (i) an ancient Palaeolithic migration by modern humans, (ii) an early Neolithic migration, probably via Proto-Dravidian speakers from the eastern horn of the Fertile Crescent, (iii) an influx of Indo-European speakers, and (iv) a migration from East/Southeast Asians, i.e. Tibeto-Burman speakers.
In this study we examined the genetic compositions of three endogamous North Indian upper caste populations (Brahmins and two sub-populations of Brahmins: Bhargavas and Chaturvedis) and two Muslims sects (Shias and Sunnis). Bhargavas and Chaturvedis practice strict surname endogamy (Agrawal et al. 2005) and Muslims sects (Shias and Sunnis) practice consanguinity. One major aim of the present study is to evaluate the impact of Muslim invasions and their admixturing with upper caste Hindus who otherwise claim to be highly endogamous. We selected Bhargava, Chaturvedis and Brahmins because they are highly homogeneous groups and follow strict endogamy, which does not apply to the lower caste populations.
Results
We investigated 32 Y-chromosome markers in 560 Indian males from five Indian subpopulations. We observed 13 haplogroups (C[large star], E1b1b1, F[large star], G[large star], H1[large star], J2[large star], K[large star], L[large star], O[large star], P[large star], R1a1[large star], R1b1b2[large star] and R2) in these samples. The detailed haplogroups and their frequencies are shown in Figure 1. The common haplogroups included R1a, R2, J2, H1, and C, which accounted for 78.0% of all the Y chromosomes. Four haplogroups (F, K, O and P) had a low frequency in all five populations. Their frequencies ranged from 2.7 to 3.0%. Interestingly, haplogroup E1b1b1 was present only in Shia Muslims (11.0% of the Shia sample). Moreover, none of the Y lineages carried the derived alleles for M174, M170, TAT, M70, M4 and M3 UEPs. This lack of derived alleles of the above SNPs led to an absence of haplogroups D, I, K2, M, N and Q in the North Indian gene pool.
We performed an AMOVA using the 32 Y-chromosomal markers in the five populations from North India. The results provided quantitative support of the genetic affiliations of these populations (Table I). The five populations were in principle divided into two groups (upper caste and Muslims). We further divided the upper caste group into two subgroups: Brahmins who follow endogamy and Bhargavas and Chaturvedis who follow surname endogamy (i.e. marriage is only allowed within the same sub-population). The fraction of variation among the upper caste populations was moderately high (1.08%). We then compared each upper caste population with Muslims. Bhargavas had the highest fraction of variation (1.54%) with the Muslim group, while Brahmins had the smallest fraction of variation (0.18%). Overall, the fraction of variance between the upper caste as a whole group and Muslims was low (0.86%).
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755252/table/T1/
Central Asian (or west Eurasian lineage)
The Central Asian or west Eurasian Y-lineages are depicted in terms of presenting a similar high frequency of sibling clades of R haplogroups (R1a1[large star] and R2) in the studied populations. A total of 256 of the 560 individuals (45.7%) in this study belonged to European Y-lineages, i.e. R1a1[large star] (M173/M17), R1b1b2[large star] (M173) and R2 (M124) clades (Figure 1). Similar results were reported in a previous study of the Indian subcontinent (Kivisild et al. 2003). Haplogroup R reflects the impact of expansion and migration of Indo-European pastoralists from Central Asia, thus linking haplogroup frequency to specific historical events (Sengupta et al. 2006). Haplogroup R is widely spread in central Asian Turkic-speaking populations and in eastern European Finno-Ugric and Slavic speakers and is less frequent in populations from the Middle East and Sino-Tibetan regions of northern China (Karafet et al. 1999; Underhill et al. 2000).
Interestingly, the high frequency of the R1a1[large star] haplogroup seems to be concentrated around the elevated terrain of central and western Asia. This haplogroup is mainly found in Indian, Iranian, and Central Asian populations and has been postulated to have a Central Asian origin (Quintana-Murci et al. 2001; Wells et al. 2001; Kivisild et al. 2003). However, our results have shown that high incidence of R2 clade was also observed in other North Indian populations, which was similarly reported in other studies (Cordaux et al. 2004; Cavalli-Sforza 2005). Overall, we suggest that Central Asia is the most likely source of North Indian Y lineage considering the historical and genetic background of North India (Karve 1968; Balakrishnan 1978).
Middle East (West Asian) lineages
The Y-lineages observed in the present study may suggest two major episodes of migrations: One carried J2 and to some extent L and G with the Neolithic farmers (Underhill et al. 2001) and the other arrived with the Muslims carrying E1b1b1 and a few more haplogroups such as J2[large star] and G[large star]. Kivisild et al. (2003) also reported the presence of a J2 clade and postulated that the origin of the J2 clade in India was probably Central Asia. The major Middle Eastern lineage present in our study was J2[large star] with an average frequency of 13.8% and its frequency among Shias was the highest (19.5%).
This might have been due to two different episodes of migrations, one concomitant with the development and spread of agriculture ~800010 000 years ago (Renfrew 1989; Cavalli-Sforza 2005), and the other more recent migration being the arrival of Muslim rulers 1000 years ago. The supporting evidence of the Middle East or West Asian migrations in Indian Muslims was demonstrated by the presence of 11.0% of haplogroup E1b1b1 in Shia Muslims. Our results revealed that Shia Muslims are different from Sunnis and other upper caste populations. They possess a relatively high frequency of the E1b1b1 haplogroup which was not observed in any other population selected for the present study. It appears that gene pool of extant Shia Muslims reflects the contributions of earlier Islamic invaders who might have maintained the founder population features. Zerjal et al. (2007) have also recently reported the low frequency of E3b3a[large star] (old nomenclature in YCC2002) in lower caste populations, i.e. Panchamas and Vaishyas populations of Uttar Pradesh, India.
In our study, the frequency of haplogroup G[large star] was 4.1% in the total sample. However, its frequency varied greatly among the populations we studied. It was 9.7% in Shias, supporting the genetic signature of the Middle East in Shias. In contrast to the Muslims, haplogroup G[large star] was absent in Chaturvedis and Bhargavas and in low frequency in Brahmins (1.7%).
Indigenous Indian lineage
The putative earliest inhabitants of India have been postulated to be tribal populations and more specifically, Austro-Asiatic tribes (Majumder 1998). These original inhabitants of India carry some of the Y-lineages dispersed from Africa (Underhill et al. 2000, 2001) that include unresolved F[large star], H1[large star], C[large star] (without M217 transversion) and O[large star] (Cordaux et al. 2004). Of these four haplogroups, H1[large star] was found at a higher frequency among Indian tribes (30%) (Cordaux et al. 2004) and represents the major indigenous Indian haplogroup. Haplogroup H1[large star] has rarely been seen in Central Asian or West Asian populations (Wells et al. 2001). In our study, we found haplogroup H1[large star] in all five populations and it represented one of the major Indian haplogroups. Haplogroups C[large star] (without M217) and O[large star] are distributed widely in Southeast Asia and in earlier inhabitants of India.
Conclusions
The synthesis of Y-genealogy and estimated diversity of several clades demonstrated that North Indians carry three Y-lineages, one derived from Central Asia or West Eurasia (R1a1[large star], R1b1b2[large star] and R2 haplogroups), one derived from the Middle East (J2[large star], Shia-specific E1b1b1, and to some extent G[large star] and L[large star] haplogroups), and the indigenous Indian Y-lineage marked by H1[large star], F[large star], O[large star] and C[large star] without the M217 transversion. Our data revealed that there may have been admixture between Sunni Muslims and Brahmins in North India. However, a recent study has shown the presence of the YAP + element in lower caste groups, namely Panchamas and Vaishyas of North India (Uttar Pradesh) (Zerjal et al. 2007). It may be postulated that there was admixture between Shia Muslims with both higher and lower caste groups from Uttar Pradesh in the past. Our previous results based on mtDNA analysis (Terreros et al. 2007) revealed that the two Muslim sects (Shia and Sunni) appeared to lack significant levels of the haplogroups (M2, U2, R5) which are believed to represent the proto-Indians involved in the initial migration out of Africa along the southern Asian coast 60 00080 000 ybp. This suggests that admixture between Islamic travellers who introduced their religion, culture, and language into Indian groups might have also shaped the social status and geographical proximity of the existing Indian populations. Interestingly, results on both mtDNA and Y chromosome indicate rather similar findings.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755252/
The genetic structure, affinities, and diversity of the 1 billion Indians hold important keys to numerous unanswered questions regarding the evolution of human populations and the forces shaping contemporary patterns of genetic variation. Although there have been several recent studies of South Indian caste groups, North Indian caste groups, and South Indian Muslims using Y-chromosomal markers, overall, the Indian population has still not been well studied compared to other geographical populations. In particular, no genetic study has been conducted on Shias and Sunnis from North India.
India occupies a unique stage in human population evolution because one of the early waves of migration of modern humans was out of Africa, through West Asia, into India (Cann 2001). More recently, about 15 00010 000 years before present (ybp), when agriculture developed in the Fertile Crescent region that extended from Israel through Northern Syria to Western Iran, there was an eastward wave of human migration (Renfrew 1989; Cavalli-Sforza et al. 1994). It has been postulated that this wave brought the Dravidian language into India (Renfrew 1989). Subsequently, the Indo-European (Aryan) language was introduced into India from the Iranian plateau approximately 40003000 ybp, where this language was probably brought by pastoral nomads from the Central Asian steppes (Renfrew 1989). Therefore, linguistic evidence suggests that West Asia and Central Asia were two major geographical sources contributing to the Indian gene pool.
Indian society predominantly revolves around the concept of caste, or the Caste System, a strong socio-cultural conglomerate of traditions that have created and maintained a great number of hierarchically arranged endogamous groups (Bamshad et al. 2001). This unique social system exists only in India. One impact of the system is that a persons fate, including even the choice of marriage partner, is largely determined at his/her birth. The Hindu caste system plays a major role in social and economic organization of the Indian population. In this system, the society is divided into four broad castes: (from low to high) Sudras, Vaishyas, Kshatriyas and Brahmins. The rules that generally prevent marriages between castes may have contributed to population substructure and the pattern of genetic diversity. Another important feature in Indian population history was the occurrence of four separate or distinct waves of migration into the subcontinent (Cordaux et al. 2004): (i) an ancient Palaeolithic migration by modern humans, (ii) an early Neolithic migration, probably via Proto-Dravidian speakers from the eastern horn of the Fertile Crescent, (iii) an influx of Indo-European speakers, and (iv) a migration from East/Southeast Asians, i.e. Tibeto-Burman speakers.
In this study we examined the genetic compositions of three endogamous North Indian upper caste populations (Brahmins and two sub-populations of Brahmins: Bhargavas and Chaturvedis) and two Muslims sects (Shias and Sunnis). Bhargavas and Chaturvedis practice strict surname endogamy (Agrawal et al. 2005) and Muslims sects (Shias and Sunnis) practice consanguinity. One major aim of the present study is to evaluate the impact of Muslim invasions and their admixturing with upper caste Hindus who otherwise claim to be highly endogamous. We selected Bhargava, Chaturvedis and Brahmins because they are highly homogeneous groups and follow strict endogamy, which does not apply to the lower caste populations.
Results
We investigated 32 Y-chromosome markers in 560 Indian males from five Indian subpopulations. We observed 13 haplogroups (C[large star], E1b1b1, F[large star], G[large star], H1[large star], J2[large star], K[large star], L[large star], O[large star], P[large star], R1a1[large star], R1b1b2[large star] and R2) in these samples. The detailed haplogroups and their frequencies are shown in Figure 1. The common haplogroups included R1a, R2, J2, H1, and C, which accounted for 78.0% of all the Y chromosomes. Four haplogroups (F, K, O and P) had a low frequency in all five populations. Their frequencies ranged from 2.7 to 3.0%. Interestingly, haplogroup E1b1b1 was present only in Shia Muslims (11.0% of the Shia sample). Moreover, none of the Y lineages carried the derived alleles for M174, M170, TAT, M70, M4 and M3 UEPs. This lack of derived alleles of the above SNPs led to an absence of haplogroups D, I, K2, M, N and Q in the North Indian gene pool.
We performed an AMOVA using the 32 Y-chromosomal markers in the five populations from North India. The results provided quantitative support of the genetic affiliations of these populations (Table I). The five populations were in principle divided into two groups (upper caste and Muslims). We further divided the upper caste group into two subgroups: Brahmins who follow endogamy and Bhargavas and Chaturvedis who follow surname endogamy (i.e. marriage is only allowed within the same sub-population). The fraction of variation among the upper caste populations was moderately high (1.08%). We then compared each upper caste population with Muslims. Bhargavas had the highest fraction of variation (1.54%) with the Muslim group, while Brahmins had the smallest fraction of variation (0.18%). Overall, the fraction of variance between the upper caste as a whole group and Muslims was low (0.86%).
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755252/table/T1/
Central Asian (or west Eurasian lineage)
The Central Asian or west Eurasian Y-lineages are depicted in terms of presenting a similar high frequency of sibling clades of R haplogroups (R1a1[large star] and R2) in the studied populations. A total of 256 of the 560 individuals (45.7%) in this study belonged to European Y-lineages, i.e. R1a1[large star] (M173/M17), R1b1b2[large star] (M173) and R2 (M124) clades (Figure 1). Similar results were reported in a previous study of the Indian subcontinent (Kivisild et al. 2003). Haplogroup R reflects the impact of expansion and migration of Indo-European pastoralists from Central Asia, thus linking haplogroup frequency to specific historical events (Sengupta et al. 2006). Haplogroup R is widely spread in central Asian Turkic-speaking populations and in eastern European Finno-Ugric and Slavic speakers and is less frequent in populations from the Middle East and Sino-Tibetan regions of northern China (Karafet et al. 1999; Underhill et al. 2000).
Interestingly, the high frequency of the R1a1[large star] haplogroup seems to be concentrated around the elevated terrain of central and western Asia. This haplogroup is mainly found in Indian, Iranian, and Central Asian populations and has been postulated to have a Central Asian origin (Quintana-Murci et al. 2001; Wells et al. 2001; Kivisild et al. 2003). However, our results have shown that high incidence of R2 clade was also observed in other North Indian populations, which was similarly reported in other studies (Cordaux et al. 2004; Cavalli-Sforza 2005). Overall, we suggest that Central Asia is the most likely source of North Indian Y lineage considering the historical and genetic background of North India (Karve 1968; Balakrishnan 1978).
Middle East (West Asian) lineages
The Y-lineages observed in the present study may suggest two major episodes of migrations: One carried J2 and to some extent L and G with the Neolithic farmers (Underhill et al. 2001) and the other arrived with the Muslims carrying E1b1b1 and a few more haplogroups such as J2[large star] and G[large star]. Kivisild et al. (2003) also reported the presence of a J2 clade and postulated that the origin of the J2 clade in India was probably Central Asia. The major Middle Eastern lineage present in our study was J2[large star] with an average frequency of 13.8% and its frequency among Shias was the highest (19.5%).
This might have been due to two different episodes of migrations, one concomitant with the development and spread of agriculture ~800010 000 years ago (Renfrew 1989; Cavalli-Sforza 2005), and the other more recent migration being the arrival of Muslim rulers 1000 years ago. The supporting evidence of the Middle East or West Asian migrations in Indian Muslims was demonstrated by the presence of 11.0% of haplogroup E1b1b1 in Shia Muslims. Our results revealed that Shia Muslims are different from Sunnis and other upper caste populations. They possess a relatively high frequency of the E1b1b1 haplogroup which was not observed in any other population selected for the present study. It appears that gene pool of extant Shia Muslims reflects the contributions of earlier Islamic invaders who might have maintained the founder population features. Zerjal et al. (2007) have also recently reported the low frequency of E3b3a[large star] (old nomenclature in YCC2002) in lower caste populations, i.e. Panchamas and Vaishyas populations of Uttar Pradesh, India.
In our study, the frequency of haplogroup G[large star] was 4.1% in the total sample. However, its frequency varied greatly among the populations we studied. It was 9.7% in Shias, supporting the genetic signature of the Middle East in Shias. In contrast to the Muslims, haplogroup G[large star] was absent in Chaturvedis and Bhargavas and in low frequency in Brahmins (1.7%).
Indigenous Indian lineage
The putative earliest inhabitants of India have been postulated to be tribal populations and more specifically, Austro-Asiatic tribes (Majumder 1998). These original inhabitants of India carry some of the Y-lineages dispersed from Africa (Underhill et al. 2000, 2001) that include unresolved F[large star], H1[large star], C[large star] (without M217 transversion) and O[large star] (Cordaux et al. 2004). Of these four haplogroups, H1[large star] was found at a higher frequency among Indian tribes (30%) (Cordaux et al. 2004) and represents the major indigenous Indian haplogroup. Haplogroup H1[large star] has rarely been seen in Central Asian or West Asian populations (Wells et al. 2001). In our study, we found haplogroup H1[large star] in all five populations and it represented one of the major Indian haplogroups. Haplogroups C[large star] (without M217) and O[large star] are distributed widely in Southeast Asia and in earlier inhabitants of India.
Conclusions
The synthesis of Y-genealogy and estimated diversity of several clades demonstrated that North Indians carry three Y-lineages, one derived from Central Asia or West Eurasia (R1a1[large star], R1b1b2[large star] and R2 haplogroups), one derived from the Middle East (J2[large star], Shia-specific E1b1b1, and to some extent G[large star] and L[large star] haplogroups), and the indigenous Indian Y-lineage marked by H1[large star], F[large star], O[large star] and C[large star] without the M217 transversion. Our data revealed that there may have been admixture between Sunni Muslims and Brahmins in North India. However, a recent study has shown the presence of the YAP + element in lower caste groups, namely Panchamas and Vaishyas of North India (Uttar Pradesh) (Zerjal et al. 2007). It may be postulated that there was admixture between Shia Muslims with both higher and lower caste groups from Uttar Pradesh in the past. Our previous results based on mtDNA analysis (Terreros et al. 2007) revealed that the two Muslim sects (Shia and Sunni) appeared to lack significant levels of the haplogroups (M2, U2, R5) which are believed to represent the proto-Indians involved in the initial migration out of Africa along the southern Asian coast 60 00080 000 ybp. This suggests that admixture between Islamic travellers who introduced their religion, culture, and language into Indian groups might have also shaped the social status and geographical proximity of the existing Indian populations. Interestingly, results on both mtDNA and Y chromosome indicate rather similar findings.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755252/