Genetic Evidence on the Origins of Indian Caste Populations
Genome Research, Vol. 11, Issue 6, 994-1004, June 2001
www.genome.org/ cgi/content/ full/11/6/ 994
Published online before print May 8, 2001, 10.1101/gr.GR- 1733RR
Michael Bamshad,1,10, 12 Toomas Kivisild,2 W. Scott Watkins,3 Mary E.
Dixon,3 Chris E. Ricker,3 Baskara B. Rao,4 J. Mastan Naidu,4 B.V. Ravi
Prasad,4,5 P. Govinda Reddy,6 Arani Rasanayagam, 7 Surinder S. Papiha,8
Richard Villems,2 Alan J. Redd,7 Michael F. Hammer,7 Son V. Nguyen,9
Marion L. Carroll,9 Mark A. Batzer,9,11 and Lynn B. Jorde3
1 Department of Pediatrics, University of Utah, Salt Lake City, Utah
84112, USA; 2 Institute of Molecular and Cell Biology, Tartu University
and Estonian Biocentre, Tartu 51010, Estonia; 3 Department of Human
Genetics, University of Utah, Salt Lake City, Utah 84112, USA; 4
Department of Anthropology, Andhra University, Visakhapatnam, Andhra
Pradesh, India; 5 Anthropological Survey of India, Calcutta, India; 6
Department of Anthropology, University of Madras, Madras, Tamil Nadu,
India; 7 Laboratory of Molecular Systematics and Evolution, University
of Arizona, Tucson, Arizona 85721, USA; 8 Department of Human Genetics,
University of Newcastle-upon- Tyne, UK; 9 Department of Pathology,
Biometry and Genetics, Biochemistry and Molecular Biology, Stanley S.
Scott Cancer Center, Louisiana State University Health Science Center,
New Orleans, Louisiana 70112, USA
ABSTRACT
The origins and affinities of the ~1 billion people living on the
subcontinent of India have long been contested. This is owing, in part,
to the many different waves of immigrants that have influenced the
genetic structure of India. In the most recent of these waves,
Indo-European- speaking people from West Eurasia entered India from the
Northwest and diffused throughout the subcontinent. They purportedly
admixed with or displaced indigenous Dravidic-speaking populations.
Subsequently they may have established the Hindu caste system and placed
themselves primarily in castes of higher rank. To explore the impact of
West Eurasians on contemporary Indian caste populations, we compared
mtDNA (400 bp of hypervariable region 1 and 14 restriction site
polymorphisms) and Y-chromosome (20 biallelic polymorphisms and 5 short
tandem repeats) variation in ~265 males from eight castes of different
rank to ~750 Africans, Asians, Europeans, and other Indians. For
maternally inherited mtDNA, each caste is most similar to Asians.
However, 20%-30% of Indian mtDNA haplotypes belong to West Eurasian
haplogroups, and the frequency of these haplotypes is proportional to
caste rank, the highest frequency of West Eurasian haplotypes being
found in the upper castes. In contrast, for paternally inherited
Y-chromosome variation each caste is more similar to Europeans than to
Asians. Moreover, the affinity to Europeans is proportionate to caste
rank, the upper castes being most similar to Europeans, particularly
East Europeans. These findings are consistent with greater West Eurasian
male admixture with castes of higher rank. Nevertheless, the
mitochondrial genome and the Y chromosome each represents only a single
haploid locus and is more susceptible to large stochastic variation,
bottlenecks, and selective sweeps. Thus, to increase the power of our
analysis, we assayed 40 independent, biparentally inherited autosomal
loci (1 LINE-1 and 39 Alu elements) in all of the caste and continental
populations (~600 individuals) . Analysis of these data demonstrated that
the upper castes have a higher affinity to Europeans than to Asians, and
the upper castes are significantly more similar to Europeans than are
the lower castes. Collectively, all five datasets show a trend toward
upper castes being more similar to Europeans, whereas lower castes are
more similar to Asians. We conclude that Indian castes are most likely
to be of proto-Asian origin with West Eurasian admixture resulting in
rank-related and sex-specific differences in the genetic affinities of
castes to Asians and Europeans.
INTRODUCTION
Shared Indo-European languages (i.e., Hindi and most European languages)
suggested to linguists of the nineteenth and twentieth centuries that
contemporary Hindu Indians are descendants of primarily West Eurasians
who migrated from Europe, the Near East, Anatolia, and the Caucasus
3000-8000 years ago (Poliakov 1974; Renfrew 1989a,b). These nomadic
migrants may have consolidated their power by admixing with native
Dravidic-speaking (e.g., Telugu) proto-Asian populations who controlled
regional access to land, labor, and resources (Cavalli-Sforza et al.
1994), and subsequently established the Hindu caste hierarchy to
legitimize and maintain this power (Poliakov 1974; Cavalli-Sforza et al.
1994). It is plausible that these West Eurasian immigrants also
appointed themselves to predominantly castes of higher rank. However,
archaeological evidence of the diffusion of material culture from
Western Eurasia into India has been limited (Shaffer 1982). Therefore,
information on the genetic relationships of Indians to Europeans and
Asians could contribute substantially to understanding the origins of
Indian populations.
Previous genetic studies of Indian castes have failed to achieve a
consensus on Indian origins and affinities. Various results have
supported closer affinity of Indian castes either with Europeans or with
Asians, and several factors underlie this inconsistency. First, erratic
or limited sampling of populations has limited inferences about the
relationships between caste and continental populations (i.e., Africans,
Asians, Europeans). These relationships are further confounded by the
wide geographic dispersal of caste populations. Genetic affinities among
caste populations are, in part, inversely correlated with the geographic
distance between them (Malhotra and Vasulu 1993), and it is likely that
affinities between caste and continental populations are also
geographically dependent (e.g., different between North and South Indian
caste populations) . Second, it has been suggested that castes of
different rank may have originated from or admixed with different
continental groups (Majumder and Mukherjee 1993). Third, the size of
caste populations varies widely, and the effects of genetic drift on
some small, geographically isolated castes may have been substantial.
Fourth, most of the polymorphisms assayed over the last 30 years are
indirect measurements of genetic variation (e.g., ABO typing), have been
sampled from only a few loci, and may not be selectively neutral.
Finally, only rarely have systematic comparisons been made with
continental populations using a large, uniform set of DNA polymorphisms
(Majumder 1999).
To investigate the origin of contemporary castes, we compared the
genetic affinities of caste populations of differing rank (i.e., upper,
middle, and lower) to worldwide populations. We analyzed mtDNA
(hypervariable region 1 [HVR1] sequence and 14 restriction- site
polymorphisms [RSPs]), Y-chromosome (5 short-tandem repeats [STRs] and
20 biallelic polymorphisms) , and autosomal (1 LINE-1 and 39 Alu inserts)
variation in ~265 males from eight different Telugu-speaking caste
populations from the state of Andhra Pradesh in South India (Bamshad et
al. 1998). Comparisons were made to ~400 individuals from tribal and
Hindi-speaking caste and populations distributed across the Indian
subcontinent (Mountain et al. 1995; Kivisild et al. 1999) and to ~350
Africans, Asians, and Europeans (Jorde et al. 1995, 2000; Seielstad et
al. 1999).
RESULTS
Analysis of mtDNA Suggests a Proto-Asian Origin of Indians
MtDNA HVR1 genetic distances between caste populations and Africans,
Asians, and Europeans are significantly different from zero (p < 0.001)
and reveal that, regardless of rank, each caste group is most closely
related to Asians and is most dissimilar from Africans (Table 1). The
genetic distances from major continental populations (e.g., Europeans)
differ among the three caste groups, and the comparison reveals an
intriguing pattern. As one moves from lower to upper castes, the
distance from Asians becomes progressively larger. The distance between
Europeans and lower castes is larger than the distance between Europeans
and upper castes, but the distance between Europeans and middle castes
is smaller than the upper caste-European distance. These trends are the
same whether the Kshatriya and Vysya are included in the upper castes,
the middle castes, or excluded from the analysis. This may be owing, in
part, to the small sample size (n = 10) of each of these castes. Among
the upper castes the genetic distance between Brahmins and Europeans
(0.10) is smaller than that between either the Kshatriya and Europeans
(0.12) or the Vysya and Europeans (0.16). Assuming that contemporary
Europeans reflect West Eurasian affinities, these data indicate that the
amount of West Eurasian admixture with Indian populations may have been
proportionate to caste rank.
Table 1. MtDNA (HVR1 Sequence) Genetic Distances between Caste Groups
from Andhra Pradesh and Continental Populations
Conventional estimates of the standard errors of genetic distances
assume that polymorphic sites are independent of each other, that is,
unlinked. Because mtDNA polymorphisms are in complete linkage
disequilibrium (as are polymorphisms on the nonrecombining portions of
the Y chromosome), this assumption is violated. Alternatively, the mtDNA
genome can be treated as a single locus with multiple haplotypes.
However, even if this assumption is made, mtDNA distances do not differ
significantly from one another even at the level of the three major
continental populations (Nei and Livshits 1989), the standard errors
being greater than the genetic distances. Considering that the distances
between castes and continental populations are less than those between
different continental populations, the estimated mtDNA genetic distances
between upper castes and Europeans versus lower castes and Europeans
would not be significantly different from each other. Therefore, to
resolve further the relationships of Europeans and Asians to
contemporary Indian populations, we defined the identities of specific
mtDNA restriction- site haplotypes.
The presence of the mtDNA restriction sites DdeI10,394 and AluI10,397
defines a haplogroup (a group of haplotypes that share some sequence
variants), M, that was originally identified in populations that
migrated from mainland Asia to Southeast Asia and Australia (Ballinger
et al. 1992; Chen et al. 1995; Passarino et al. 1996) and is found at
much lower frequency in European and African populations. Most of the
common haplotypes found in Telugu- and Hindi- speaking caste populations
belong to haplogroup M (Table 2) and do not differentiate into
language-specific clusters in a phylogenetic reconstruction (Fig. 1).
Furthermore, these Indian haplogroup-M haplotypes are distinct from
those found in other Asian populations (Fig. 2) and indicate the
existence of Indian-specific subsets of haplogroup M (e.g., M3). As
expected if the lower castes are more similar to Asians than to
Europeans, and the upper castes are more similar to Europeans than to
Asians, the frequencies of M and M3 haplotypes are inversely
proportional to caste rank (Table 2).
Table 2. MtDNA Haplogroup Frequencies in Dravidic and Hindi-Speaking
Indians
Figure 1 Phylogeny of haplogroup M in India. 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. The identities of HVR1 mutations (numbered according
to the Cambridge reference sequence +16000; Anderson et al. 1981) that
define major haplogroup subsets are depicted along selected internodes.
The coalescence estimate of Indian haplogroup-M haplotypes is 48,000 ±
1500 yr, suggesting that Indian-specific mtDNA haplotypes split from a
proto- Asian ancestor in the late Pleistocene.
Figure 2 Major subsets of haplogroup M. Phylogenetic relationships of
HVR1 haplotypes assigned to haplogroup M were estimated for: (a) 343
Indians (Quintana-Murci et al. 1999a; this study); (b) 16 Turks and 78
Central Asians (Comas et al. 1998; this study); (c) 60 Mongolians
(Kolman et al. 1996); (d) 25 Ethiopians (Quintana-Murci et al. 1999a);
(e) 56 Chinese (Horai et al. 1996; this study); (f) 103 Japanese (Horai
et al. 1996; Seo et al. 1998). The founding node of each network (M*)
differs from the CRS (Anderson et al. 1981) by transitions at np 10398,
10400, and 16223. The frequency of each subset of haplogroup M is
indicated. Each phylogenetic network was pruned by eliminating branches
containing haplotypes summing to a frequency of <5% (these branches were
binned with the founder haplotype, M*). The identities of HVR1 mutations
(numbered according to the CRS 16,000; Anderson et al. 1981) that define
major haplotype subsets are depicted along selected internodes.
Of the non-Asian mtDNA haplotypes found in Indian populations, most are
of West Eurasian origin (Table 2; Torroni
et al. 1994; Richards et al. 1998). However, most of these Indian
West-Eurasian haplotypes belong to an Indian- specific subset of
haplogroup U, that is, U2i (Kivisild et al. 1999), the oldest and second
most common mtDNA haplogroup found in Europe (Torroni et al. 1994). In
agreement with the HVR1 results, the frequency of West Eurasian mtDNA
haplotypes is significantly higher in upper castes than in lower castes
(p < 0.05), the frequency of U2i haplotypes increasing as one moves from
lower to higher castes. In addition, the frequency of mtDNA haplogroups
with a more recent coalescence estimate (i.e., H, I, J, K, T) was
fivefold higher in upper castes (6.8%) than in lower castes (1.4%).
These haplotypes are derivatives of haplogroups found throughout Europe
(Richards et al. 1998), the Middle East (Di Rienzo and Wilson 1991), and
to a lesser extent Central Asia (Comas et al. 1998). Collectively, the
mtDNA haplotype evidence indicate that contemporary Indian mtDNA evolved
largely from proto- Asian ancestors with Western Eurasian admixture
accounting for 20%-30% of mtDNA haplotypes.
Y-Chromosome Variation Confirms Indo-European Admixture
Genetic distances estimated from Y-chromosome STR polymorphisms differ
significantly from zero (p < 0.001) and reveal a distinctly different
pattern of population relationships (Table 3). In contrast to the mtDNA
distances, the Y- chromosome STR data do not demonstrate a closer
affinity to Asians for each caste group. 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. The genetic
distance between caste populations and Africans is progressively larger
moving from lower to middle to upper caste groups (Table 3).
Table 3. Y Chromosome (STRs) Genetic Distances between Caste Groups
from Andhra Pradesh and Continental Populations
Genetic distances estimated from Y-chromosome biallelic polymorphisms
differ significantly from zero (p < 0.05), and the patterns differ from
the mtDNA results even more strikingly than the Y-chromosome STRs. For
Y- chromosome biallelic polymorphism data, each caste group is more
similar to Europeans (Table 4), and as one moves from lower to middle to
higher castes the genetic distance to Europeans diminishes
progressively. 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. 1999b).
Table 4. Y Chromosome (Bi-Allelic Polymorphisms) Genetic Distances
between Caste Groups from Andhra Pradesh and Continental Populations
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. Consequently, we assayed 1
LINE-1 and 39 unlinked Alu polymorphisms.
Affinities to Europeans and Asians Stratified by Caste Rank
Genetic distances estimated from autosomal Alu elements correspond to
caste rank, the genetic distance between the upper and lower castes
being more than 2.5 times larger than the distance between upper and
middle or middle and lower castes (upper to middle, 0.0069; upper to
lower, 0.018; middle to lower, 0.0071). 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. 3) clearly differentiates castes of different rank
into separate clusters. This is similar to the relationship between
genetic distances and caste rank estimated from mtDNA (Bamshad et al.
1998). 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. The Mantel correlation
between interindividual genetic distances and distances based on social
rank was low but highly significant for individuals ranked into upper,
middle, and lower groups (r = 0.08; p < 0.001) and into eight separate
castes (r = 0.07; p < 0.001). 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.
Figure 3 Neighbor-joining network of genetic distances among caste
communities estimated from 40 Alu polymorphisms. Distances between upper
castes (U; Brahmin, Vysya, Kshatriya), middle castes (M; Yadava, Kapu),
and lower castes (L; Mala, Madiga, Relli) are significantly correlated
with social rank.
Genotypic differentiation was significantly different from zero (p <
0.0001) between each pair of caste populations and between each caste
and continental population. Similar to the results of both the mtDNA and
Y-chromosome analyses, the distance between upper castes and European
populations is smaller than the distance between lower castes and
Europeans (Table 5). However, in contrast to the mtDNA results but
similar to the Y-chromosome results, the affinity between upper castes
and Europeans is higher than that of upper castes and Asians (Table 5).
If the Kshatriya and Vysya are excluded from the analysis or included in
the middle castes, the genetic distance between the upper caste
(Brahmins) and Europeans remains smaller than the distance between the
lower castes and Europeans and the distance between upper castes and
Asians (Table 5). Analysis of each caste separately reveals that the
genetic distance between the Brahmins and Europeans (0.013) is less than
the distance between Europeans and Kshatryia (0.030) or Vysya (0.020).
Nevertheless, each separate upper caste is more similar to Europeans
than to Asians.
Table 5. Autosomal Genetic Distancesa between Caste Groups from Andhra
Pradesh and Continental Populations
Because historical evidence suggests greater affinity between upper
castes and Europeans than between lower castes and Europeans
(Balakrishnan 1978, 1982; Cavalli-Sforza et al. 1994), it is appropriate
to use a one-tailed test of the difference between the corresponding
genetic distances. The 90% confidence limits of Nei’s standard distances
estimated between upper castes and Europeans (0.006-0.016) versus lower
castes and Europeans (0.017-0.037) do not overlap, indicating
statistical significance at the 0.05 level. Significance at 0.05 is not
achieved if the Kshatriya and Vysya are excluded. 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.
DISCUSSION
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. 1995; Mountain et al. 1995; Bamshad et al. 1996, 1997;
Majumder et al. 1999; Quintana-Murci et al. 1999a). 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.
The majority of Indian mtDNA restriction- site haplotypes belong to
Indian-specific subsets (e.g., M3) of a predominantly Asian haplogroup
M, although a substantial minority of mtDNA restriction site haplotypes
belong to West Eurasian haplogroups. 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.
Importantly, five different types of data (mtDNA HVR1 sequence, mtDNA
RSPs, Y-chromosome STRs, Y- chromosome biallelic polymorphisms, and
autosomal Alu polymorphisms) support the same general pattern:
relatively smaller genetic distances from European populations as one
moves from lower to middle to upper caste populations. 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.g., the distances
between different caste groups and Asians) may also reach statistical
significance.
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.
(1996), which was based on a comparison of mtDNA and blood group
results. 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. (1999)
determined the coalescence (~50,000 years before present) of the
Indian-specific subset of the West Eurasian haplotypes (i.e., U2i) and
suggested that West Eurasian admixture may have been much older than the
purported Dravidian and Indo-European incursions. Our analysis of Indian
mtDNA restriction- site haplotypes that do not belong to the U2i subset
of West Eurasian haplotypes (i.e., H, I, J, K, T) is consistent with
more recent West Eurasian admixture. 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.
This hypothesis can be tested by a more detailed comparison to West
Eurasian mtDNA haplotypes from Iran, Anatolia, and the Caucasus.
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. 1998). 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 32-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.K. 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. 1998; Bhattacharyya et al. 1999).
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. 1996; Torroni et al. 1996; de Knijff et al. 1997). 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. Analyses of recent caste history based on only mtDNA
or Y-chromosome polymorphisms clearly would suggest that castes are more
closely related to Asians or to Europeans, respectively. Furthermore, we
attempted to minimize the confounding effect of geographic differences
between populations by sampling from a highly restricted region of South
India. Because of the ubiquity of the caste system in India’s history,
it is reasonable to predict similar patterns in caste populations living
in other areas. Indeed, any genetic result becomes more compelling when
it is replicated in other populations. Therefore, comparable studies in
caste populations from other regions of India must be completed to test
the generality of these results.
The dispersal and subsequent growth of Indian populations since the
Neolithic Age is one of the most important events to shape the history
of South Asia. However, the origin and dispersal route of the aboriginal
inhabitants of the Indian subcontinent is unclear. Our findings suggest
a proto-Asian origin of the Indian-specific haplogroup-M haplotypes.
Haplogroup-M haplotypes are also found at appreciable frequencies in
some East African populations ~18% of Ethiopians (Quintana-Murci et al.
1999a) and 16% of Kenyans (M. Bamshad and L.B. Jonde, unpubl.). A
comparison of haplogroup-M haplotypes from East Africa and India has
suggested that this southern route may have been one of the original
dispersal pathways of anatomically modern humans out of Africa
(Quintana-Murci et al. 1999a). Together, these data support our previous
suggestion (Kivisild et al. 1999) that India may have been inhabited by
at least two successive late Pleistocene migrations, consistent with the
hypothesis of Lahr and Foley (1994). It also adds to the growing
evidence that the subcontinent of India has been a major corridor for
the migration of people between Africa, Western Asia, and Southeast Asia
(Cavalli-Sforza et al. 1994).
It should be emphasized that the DNA variation studied here is thought
to be selectively neutral and thus represents only the effects of
population history. These results permit no inferences about phenotypic
differences between populations. In addition, alleles and haplotypes are
shared by different caste populations, reflecting a shared history.
Indeed, these findings underscore the longstanding appreciation that the
distribution of genetic polymorphisms in India is highly complex.
Further investigation of the spread of anatomically modern humans
throughout South Asia will need to consider that such complex patterns
may be the norm rather than the exception.
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