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Genetic Evidence on the Origins of Indian Caste Populations
Page 1
Genetic Evidence on the Origins
of Indian Caste Populations
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. Jorde
3
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
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.
Shared Indo-European languages (i.e., Hindi and most
European languages) suggested to linguists of the nine-
teenth and twentieth centuries that contemporary
Hindu Indians are descendants of primarily West Eur-
asians who migrated from Europe, the Near East, Ana-
tolia, and the Caucasus 3000­8000 years ago (Poliakov
1974; Renfrew 1989a,b). These nomadic migrants may
Present addresses:
10
Eccles Institute of Human Genetics, 15
North 2030 East, Room 2100, Universityof Utah, Salt Lake City,
UT 84112-5330, USA.
11
Department of Biological Sciences, Bio-
logical Computation and Visualization Center, Louisiana State
University, 508 Life Sciences Building, Baton Rouge, LA 70803,
USA.
12
Corresponding author.
E-MAIL mike@genetics.utah.edu; FAX (801) 585-9148.
Article published on-line before print:
Genome Res.
, 10.1101/gr.173301.
Article and publication are at www.genome.org/cgi/doi/10.1101/
gr.173301.
Letter
994 Genome Research
11:994­1004 ©2001 by Cold Spring Harbor Laboratory Press ISSN 1088-9051/01 $5.00; www.genome.org
www.genome.org
Page 2
have consolidated their power by admixing with na-
tive Dravidic-speaking (e.g., Telugu) proto-Asian popu-
lations who controlled regional access to land, labor,
and resources (Cavalli-Sforza et al. 1994), and subse-
quently established the Hindu caste hierarchy to legiti-
mize and maintain this power (Poliakov 1974; Cavalli-
Sforza et al. 1994). It is plausible that these West Eur-
asian immigrants also appointed themselves to
predominantly castes of higher rank. However, ar-
chaeological evidence of the diffusion of material cul-
ture 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, Europe-
ans). These relationships are further confounded by
the wide geographic dispersal of caste populations. Ge-
netic affinities among caste populations are, in part,
inversely correlated with the geographic distance be-
tween 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 popu-
lations). 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 as-
sayed 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 selec-
tively 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 (hyper-
variable region 1 [HVR1] sequence and 14 restriction-
site polymorphisms [RSPs]), Y-chromosome (5 short-
tandem repeats [STRs] and 20 biallelic polymor-
phisms), 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). Com-
parisons 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 popula-
tions and Africans, Asians, and Europeans are signifi-
cantly different from zero (
p
< 0.001) and reveal that,
regardless of rank, each caste group is most closely re-
lated to Asians and is most dissimilar from Africans
(Table 1). The genetic distances from major continen-
tal populations (e.g., Europeans) differ among the
three caste groups, and the comparison reveals an in-
triguing 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 analy-
sis. 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 popu-
lations may have been proportionate to caste rank.
Conventional estimates of the standard errors of
genetic distances assume that polymorphic sites are in-
dependent of each other, that is, unlinked. Because
mtDNA polymorphisms are in complete linkage dis-
equilibrium (as are polymorphisms on the nonrecom-
Table 1. MtDNA (HVR1 Sequence) Genetic Distances
between Caste Groups from Andhra Pradesh and
Continental Populations
Caste group
Africans
Asians
Europeans
Upper
.179
.037
.100 (0.106)
a
Middle
.182
.025
.086 (0.084)
b
Lower
.163
.023
.113
All castes
.196
.026
.077
a
Genetic distance between upper castes and Europeans if the
Kshatriya and Vysya are excluded from the analysis.
b
Genetic distance between the middle castes and Europeans if
the Kshatriya and Vysya are grouped in the middle castes.
Genetic Evidence on Caste Origins
Genome Research 995
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Page 3
bining portions of the Y chromosome), this assump-
tion is violated. Alternatively, the mtDNA genome can
be treated as a single locus with multiple haplotypes.
However, even if this assumption is made, mtDNA dis-
tances do not differ significantly from one another
even at the level of the three major continental popu-
lations (Nei and Livshits 1989), the standard errors be-
ing greater than the genetic distances. Considering
that the distances between castes and continental
populations are less than those between different con-
tinental 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 contem-
porary Indian populations, we defined the identities of
specific mtDNA restriction-site haplotypes.
The presence of the mtDNA restriction sites
Dde
I
10,394
and
Alu
I
10,397
defines a haplogroup (a group
of haplotypes that share some sequence variants), M,
that was originally identified in populations that mi-
grated from mainland Asia to Southeast Asia and Aus-
tralia (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 com-
mon 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 haplo-
types are inversely proportional to caste rank (Table 2).
Of the non-Asian mtDNA haplotypes found in In-
dian populations, most are of West Eurasian origin
(Table 2; Torroni et al. 1994; Richards et al. 1998).
However, most of these Indian West-Eurasian haplo-
types belong to an Indian-specific subset of hap-
logroup 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 haplo-
types increasing as one moves from lower to higher
castes. In addition, the frequency of mtDNA hap-
logroups 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 de-
rivatives of haplogroups found throughout Europe (Ri-
chards et al. 1998), the Middle East (Di Rienzo and
Wilson 1991), and to a lesser extent Central Asia (Co-
mas 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 haplo-
types.
Y-Chromosome Variation
Confirms
Indo-European Admixture
Genetic distances estimated
from Y-chromosome STR poly-
morphisms 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 ge-
netic distance between caste
populations and Africans is pro-
Table 2. MtDNA Haplogroup Frequencies in Dravidic and Hindi-Speaking Indians
Haplogroup
Dravidic (%)
Hindi (%)
upper
middle
lower
total
Asian
61 (5.5)
64.6 (3.8)
71.4 (5.3)
65.7 (2.7)
55.7 (2.9)
A
0
0
0
0
0.3 (.32)
B
0
0
0
0
0
F
0
0
0
0
2.7 (.94)
M
61 (5.5)
64.6 (3.8)
71.4 (5.3)
65.7 (2.7)
52.7 (2.9)
M3
18.6 (4.4)
3.5 (1.5)
1.4 (1.4)
6.6 (1.4)
6.0 (1.4)
M-C
0
0
0
0
0.7 (.48)
M-D
0
0
0
0
1.0 (.57)
M-G
0
0.9 (.74)
0
0.4 (.36)
0
M-E
0
1.8 (1.1)
0
0.8 (.51)
0
West Eurasian
23.7 (4.8)
14.2 (2.8)
7.1 (3.0)
14.5 (2.0)
27.4 (2.6)
U2i
b
16.9 (4.2)
9.7 (2.3)
5.7 (2.7)
10.3 (1.7)
15.3 (2.1)
W
1.7 (1.5)
0
0
0.4 (.36)
3.7 (.29)
H
3.4 (2.0
0
0
1.2 (.62)
2.3 (.87)
I
0
0
0
0
1.3 (.65)
J
0
0.9 (.75)
0
0.4 (.36)
0.7 (.48)
K
1.7 (1.5)
0
0
0.4 (.36)
0
T
0
2.7 (1.3)
1.4 (1.4)
1.7 (.73)
1.7 (.75)
X
0
0
0
0
0.7 (.48)
Others
15.3 (4.1)
21.2 (1.3)
21.4 (4.8)
19.8 (2.3)
16.7 (2.2)
standard errors are in parentheses.
a
These haplotypes belong to super-haplogroup R (ancestral to haplogroups B, F, H, T, J, V,
and U) but do not belong to any previously recognized haplogroup.
b
U2i is differentiated from haplogroup U by the presence of a transition at np 16051.
Bamshad et al.
996 Genome Research
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Page 4
gressively larger moving from lower to middle to upper
caste groups (Table 3).
Genetic distances estimated from Y-chromosome
biallelic polymorphisms differ significantly from zero
(
p
< 0.05), and the patterns differ from the mtDNA re-
sults 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, particu-
larly upper caste Y chromosomes, are more similar to
European than to Asian Y chromosomes. This under-
scores the close affinities between Hindu Indian and
Indo-European Y chromosomes based on a previously
reported analysis of three Y-chromosome polymor-
phisms (Quintana-Murci et al. 1999b).
Overall, these results indicate that the affinities of
Indians to continental populations varies according to
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.
Genetic Evidence on Caste Origins
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Page 5
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 autoso-
mal 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
ele-
ments 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 Ksha-
triya 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 sepa-
rate clusters. This is similar to the relationship between
genetic distances and caste rank estimated from
Table 3. Y Chromosome (STRs) Genetic Distances
between Caste Groups from Andhra Pradesh and
Continental Populations
Caste group
Africans
Asians
Europeans
Upper
.0166
.0104
.0092
Middle
.0156
.0110
.0108
Lower
.0131
.0088
.0108
All castes
.0151
.0101
.0102
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.
Bamshad et al.
998 Genome Research
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Page 6
mtDNA (Bamshad et al. 1998). It is important to note,
however, that the autosomal genetic distances are es-
timated 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 autoso-
mal dataset, we next tested whether we could reconcile
the results of the analysis of mtDNA and Y-
chromosome markers in castes and continental popu-
lations.
Genotypic differentiation was significantly differ-
ent 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 up-
per castes and European popu-
lations is smaller than the dis-
tance between lower castes and
Europeans (Table 5). However,
in contrast to the mtDNA re-
sults but similar to the Y-
chromosome results, the affin-
ity 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 ge-
netic distance between the upper caste (Brahmins) and
Europeans remains smaller than the distance between
the lower castes and Europeans and the distance be-
tween 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.
Because historical evidence suggests greater affin-
ity 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 corre-
sponding genetic distances. The 90% confidence limits
of Nei's standard distances estimated between upper
castes and Europeans (0.006­0.016) versus lower castes
and Europeans (0.017­0.037) do not overlap, indicat-
ing statistical significance at the 0.05 level. Signifi-
cance 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 sup-
port either a European or an Asian origin of Indian
caste populations, with occasional indications of ad-
mixture 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 biparen-
tally inherited autosomal markers, genetic distances
between upper, middle, and lower castes are signifi-
cantly correlated with rank; upper castes are more simi-
lar 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 amalgam-
ation 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)
Table 4. Y Chromosome (Bi-Allelic Polymorphisms) Genetic Distances between
Caste Groups from Andhra Pradesh and Continental Populations
a
Caste group
Asians
Europeans
W. Europeans
S. Europeans
E. Europeans
Upper
.388
.135
.265
.168
.073
Middle
.291
.146
.249
.156
.133
Lower
.376
.173
.283
.189
.155
a
Includes comparisons to unpublished data of M.F.H.
Figure 3
Neighbor-joining network of genetic distances
among caste communities estimated from 40
Alu
polymor-
phisms. 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.
Genetic Evidence on Caste Origins
Genome Research 999
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Page 7
of a predominantly Asian haplogroup M, although a
substantial minority of mtDNA restriction site haplo-
types belong to West Eurasian haplogroups. A higher
proportion of proto-Asian mtDNA restriction-site hap-
lotypes 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 similar-
ity with Europeans, whereas the lower caste groups are
most similar to Asians. For Y biallelic polymorphism
variation, each caste group is more similar to Europe-
ans 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 up-
per caste populations. Genetic distances from Asian
populations become larger as one moves from lower to
middle to upper caste populations. It is especially note-
worthy that the analysis of Y biallelic polymorphisms,
which involved an independent set of comparative
Asian, European, and African populations, again indi-
cated the same pattern. Additional support is offered
by the fact that the autosomal polymorphisms yielded
a statistically significant difference between the upper-
caste­European and lower-caste­European genetic dis-
tances. 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, admix-
ture with West Eurasian males was greater than admix-
ture 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. Further-
more, the degree of West Eur-
asian admixture was propor-
tional to caste rank. This expla-
nation is consistent with either
the hypothesis that proportion-
ately more West Eurasians be-
came 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) deter-
mined the coalescence (
50,000 years before present)
of the Indian-specific subset of the West Eurasian hap-
lotypes (i.e., U2i) and suggested that West Eurasian ad-
mixture may have been much older than the pur-
ported 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 hypoth-
esis 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 Eur-
asians populations into India. Regardless of their ori-
gin, West Eurasian admixture resulted in rank-related
differences in the genetic affinities of castes to Europe-
ans 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
Table 5. Autosomal Genetic Distances
a
between Caste Groups from Andhra
Pradesh and Continental Populations
Caste group
Africans
Asians
Europeans
Upper
.140 (0.074 .018)
.058 (0.024 .009)
.032
b
(.011 .003)
Middle
.149 (0.082 .018)
.032 (0.013 .005)
.057
c
(.020 .006)
Lower
.147 (0.083 .017)
.044 (0.017 .005)
.073 (.027 .006)
All castes
.147
.039
.045
a
Nei standard distances standard errors are in parentheses.
b
If the Kshatriya and Vysya are excluded, the genetic distance between the upper castes and
Europeans is 0.038.
c
If the Kshatriya and Vysya are grouped in the middle castes, the genetic distance between
the middle castes and Europeans is 0.050.
Bamshad et al.
1000 Genome Research
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Page 8
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 Ksha-
triya (an upper caste), whose members served as war-
riors, are closer to Europeans than any other caste (data
not shown). Furthermore, the 32-bp deletion polymor-
phism 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 dis-
tances 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 polymor-
phisms than Y-chromosome STRs. This could be attrib-
uted 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 cluster-
ing at the continental level has been observed in sev-
eral studies of Y-chromosome STRs (Deka et al. 1996;
Torroni et al. 1996; de Knijff et al. 1997). The autoso-
mal
Alu
and biallelic Y-chromosome polymorphisms,
in contrast, have a slower rate of drift than Y-
chromosome STRs because of a higher effective popu-
lation size, and their mutation rate is very low. Thus,
the Y-chromosome biallelic polymorphisms and auto-
somal
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. Analy-
ses 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 Eu-
ropeans, respectively. Furthermore, we attempted to
minimize the confounding effect of geographic differ-
ences between populations by sampling from a highly
restricted region of South India. Because of the ubiq-
uity of the caste system in India's history, it is reason-
able to predict similar patterns in caste populations
living in other areas. Indeed, any genetic result be-
comes more compelling when it is replicated in other
populations. Therefore, comparable studies in caste
populations from other regions of India must be com-
pleted 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 aborigi-
nal inhabitants of the Indian subcontinent is unclear.
Our findings suggest a proto-Asian origin of the In-
dian-specific haplogroup-M haplotypes. Hap-
logroup-M haplotypes are also found at appreciable fre-
quencies 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 Af-
rica and India has suggested that this southern route
may have been one of the original dispersal pathways
of anatomically modern humans out of Africa (Quin-
tana-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 popula-
tions, reflecting a shared history. Indeed, these find-
ings 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.
METHODS
Sample Collection
All studies of South Indian populations were performed with
the approval of the Institutional Review Board of the Univer-
sity of Utah, Andhra University, and the government of India.
Adult males living in the district of Visakhapatnam, Andhra
Pradesh, were questioned about their caste affiliations and
surnames and the birthplaces of their parents. Those who
were unrelated to any other subject by at least three genera-
tions were considered eligible to participate.
We classified caste populations based upon the tradi-
tional ranking of these castes by
varna
(defined below), occu-
pation, and socioeconomic status. According to various San-
skrit texts, Hindu populations were partitioned originally into
four categories or
varna
: Brahmin, Kshatriya, Vysya, and Sudra
(Tambia 1973; Elder 1996). Those in each
varna
performed
occupations assigned to their category. Brahmins were priests;
Kshatriya were warriors; Vysya were traders; and Sudra were to
serve the three other
varna
(Tambia 1973; Elder 1996). Each
varna
was assigned a status; Brahmin, Kshatriya, and Vysya
were considered of higher status than the Sudra because the
Brahmin, Kshatriya, and Vysya are considered the twice-born
Genetic Evidence on Caste Origins
Genome Research 1001
www.genome.org
Page 9
castes and are differentiated from all other castes in the caste
hierarchy. This is the rationale behind classifying them as the
upper group of castes (Tambia 1973).
The Kapu and the Yadava are called once-born castes that
have traditionally been classified in the Sudra, the lowest of
the original four
varna
. However, the status of the Sudra was
actually higher than that of a fifth
varna
, the Panchama. This
fifth
varna
was added at a later date to include the so-called
untouchables, who were excluded from the other four
varna
(Elder 1996). The untouchable
varna
includes the Mala and
Madiga. The position of the Relli in the caste hierarchy is
somewhat ambiguous, but they have usually been classified in
the lower caste group. Therefore, prior to the collection of any
data, males from eight different Telugu-speaking castes
(
n
= 265) were ranked into upper (Niyogi and Vydiki Brah-
min, Kshatriya, Vysya [
n
= 80]), middle (Telega and Turpu
Kapu, Yadava [
n
= 111]), and lower (Relli, Madiga, Mala
[
n
= 74]) groups (Bamshad et al. 1998). This ranking has been
used by previous investigators (Krishnan and Reddy 1994).
After obtaining informed consent,
8 mL of whole blood
or 5 plucked scalp hairs were collected from each participant.
Extractions were performed at Andhra University using estab-
lished methods (Bell et al. 1981).
MtDNA Polymorphisms
The mtDNA data consisted of 68, 116, and 73 HVR1 se-
quences and 79, 159, and 72 restriction-site haplotypes from
largely the same individuals in upper, middle, and lower
castes, respectively. These data were compared to data from
143 Africans (15 Sotho-Tswana, 7 Tsonga, 14 Nguni, 24 San, 5
Biaka Pygmies, 33 Mbuti Pygmies, 9 Alur, 18 Hema, and 18
Nande), 78 Asians (12 Cambodians, 17 Chinese, 19 Japanese,
6 Malay, 9 Vietnamese, 2 Koreans, and 13 Asians of mixed
ancestry), and 99 Europeans (20 unrelated males of the French
CEPH kindreds, 69 unrelated Utah males of Northern Euro-
pean descent, and 10 Poles) (Jorde et al. 1995, 1997). Mito-
chondrial sequence data from these 597 individuals are avail-
able at: http://www.genome.org/supplemental/.
In addition to our samples, the phylogenetic analyses
also included data from 98 published HVR1 sequences from
two castes (48 Havlik and 43 Mukri), and a tribal population
(7 Kadar) living in south-western India (Mountain et al. 1995)
and restriction-site haplotypes from one caste (62 Lobana)
from Northern India, three tribal populations from Northern
(12 Tharu and 18 Bhoksa) and Southern (86 Lambadi) India,
and 122 individuals from various caste populations in Uttar
Pradesh (Kivisild et al. 1999). Phylogenetic relationships of
HVR1 sequences assigned to haplogroup M were estimated for
Indians (this study), Turks (this study), Central Asian popula-
tions (Comas et al. 1998), Mongolians (Kolman et al. 1996),
Chinese (Horai et al. 1996), and Japanese (Horai et al. 1996;
Seo et al. 1998).
The mtDNA HVR1 sequence was determined by fluores-
cent Sanger sequencing using a Dye terminator cycle sequenc-
ing kit (Applied Biosystems) according to the manufacturer's
specifications (Bamshad et al. 1998). Sequencing reactions
were resolved on an ABI 377 automated DNA sequencer, and
sequence data were analyzed using ABI DNA analysis software
and
SEQUENCHER
software (Genecodes). To identify mtDNA
haplotypes and haplogroups (a group of haplotypes that share
some sequence variants), major continent-specific genotypes
(Torroni et al. 1994, 1996; Wallace 1995) for the following
polymorphic mtDNA restriction sites were determined:
Hpa
I
3592
,
Dde
I
10394
,
Alu
I
10397
,
Alu
I
13262
,
Bam
HI
13366
,
Alu
I
5176
,
Hae
III
4830
,
Alu
I
7025
,
Hinf
I
12308
,
Acc
I
14465
,
Ava
II
8249
,
Alu
I
10032
,
Bst
OI
13704
, and
Hae
II
9052
.
Y-Chromosome and Autosomal Polymorphisms
Y-chromosome-specific STRs (DYS19, DYS288, DYS388,
DYS389A, DYS390) were amplified using published condi-
tions (Hammer et al. 1998). PCR products were separated
on an ABI 377 automated sequencer and scored using ABI
Genotyper
software. Y-chromosome STR data were collected
from 622 males including 280 South Indians,
200 Africans
(Seielstad et al. 1999; this study), 40 Asians, and 102 Europe-
ans. Autosomal data were collected from 608 individuals in-
cluding 265 South Indians, 155 Africans, 70 Asians, and 118
Europeans.
The Y-chromosome-specific biallelic polymorphisms
tested included: DYS188
792
, DYS194
469
, DYS211
105
,
DYS221
136
, DYS257
108
, DYS287, M3, M4, M9, M12, M15,
SRY
4064
, SRY
10831.1
, SRY
10831.2
, p12f2, PN1, PN2, PN3,
RPS4Y
711
, and Tat (Hammer and Horai 1995; Hammer et al.
1997, 1998, 2000; Underhill et al. 1997; Zerjal et al. 1997;
Karafet et al. 1999). All individuals tested negative for the Y
Alu
insert (DYS287). A complete description of the Y-
chromosome STR loci can be found in Kayser et al. (1997). A
table of the biallelic Y-chromosome haplotype frequencies in
the upper, middle, and lower castes is available at http://
www.genome.org/supplemental/.
For the Y-chromosome biallelic dataset, comparisons
were made to a different set of worldwide populations includ-
ing: East Asians from Japan, Korea, China, and Vietnam
(
n
= 460); Western Europeans from Britain and Germany
(
n
= 77); Southern Europeans from Italy and Greece (
n
= 148);
and Eastern Europeans from Russia and Romania (
n
= 102)
(M.F. Hammer, unpubl.). The complete dataset of Indians
consisted of 55 Brahmin, 111 Yadava and Kapu, and 74 Relli,
Mala, and Madiga.
Autosomal polymorphisms were amplified using condi-
tions specifically optimized for each system. Further informa-
tion on these conditions is available at the Web site: http://
www.genetics.utah.edu/
swatkins/pub/Alu_data.htm or
http://www.genome.org/supplemental. With minor excep-
tions caused by typing failures or other causes, the same in-
dividuals from each population were used to create each
dataset (i.e., mtDNA, Y chromosome, and autosomal). The
complete dataset of genotypes from all 40 autosomal loci is
available at: http://www.genome.org/supplemental/.
Statistical Analyses
Genetic distances for Y-chromosome STRs were estimated us-
ing the method of Shriver et al. (1995), which assumes a step-
wise mutation model. Genetic distances for mitochondrial
and autosomal markers were calculated as pairwise
F
ST
dis-
tances, using the
ARLEQUIN
package (Schneider et al. 1997).
For autosomal polymorphisms, Nei's standard distances and
their standard errors were estimated using
DISPAN
(http://
www.bio.psu.edu/IMEG); and 90% confidence intervals were
estimated by multiplying the standard error by 1.65. The sig-
nificance of the
F
ST
distances between populations was esti-
mated by generating a null distribution of pairwise
F
ST
dis-
tances by permuting haplotypes between populations. The
p
-value of the test is the proportion of permutations leading
to an
F
ST
value larger than or equal to the observed one. Ge-
notypic differentiation was estimated using
GENEPOP
(Ray-
mond and Rousset 1995) vers. 3.2 (http://www.cefe.cnrs-
mop.fr/). The null hypothesis tested is that there is a random
Bamshad et al.
1002 Genome Research
www.genome.org
Page 10
distribution of
K
different haplotypes among
r
populations
(the contingency table). All potential states of the contin-
gency table are explored with a Markov chain, and the prob-
ability of observing a table less than or equally likely to the
observed sample configuration is estimated.
Estimates of significance for the correlation between in-
terindividual caste rank differences and interindividual auto-
somal genetic distances were made by forming two
n
n
ma-
trices, where
n
is the number of individuals. For the first ma-
trix, interindividual genetic distances were based on the
proportion of
Alu
insertions/deletions shared by each pair of
individuals. To form the second matrix, each individual was
assigned a score according to his rank in the caste hierarchy
for caste groups (i.e., upper caste = 1, middle caste = 2, lower
caste = 3) and also for separate castes (i.e., Brahmin = 1, Ksha-
triya = 2, Vysya = 3, Kapu = 4, Yadava = 5, Relli = 6, Mala = 7,
and Madiga = 8). An interindividual matrix of score distances
was formed by comparing the absolute value of the difference
between the scores of each pair of individuals. The matrix of
genetic distances was compared to 10,000 permuted matrices
of score distances using a Mantel matrix comparison test
(Mantel 1967).
To illustrate phylogenetic relationships we constructed
reduced median (Bandelt et al. 1995) and neighbor-joining
networks (Felsenstein 1989). Coalescence times were calcu-
lated as in Forster et al. (1996), using the estimator , which is
the average transitional distance from the founder haplotype.
ACKNOWLEDGMENTS
We thank all participants, the faculty and staff of Andhra
University for their discussion and technical assistance, as
well as Henry Harpending for comments and criticisms. We
acknowledge the contributions of an anonymous reviewer
who suggested that the Kshatriya and Vysya be analyzed sepa-
rately from the other upper castes. Genetic distances between
STRs were estimated by the program
DISTNEW
, kindly pro-
vided by L. Jin. This work was supported by NSF SBR-9514733,
SBR-9700729, SBR-9818215, NIH grants GM-59290 and PHS
MO1­00064, the Estonian Science Fund (1669 and 2887), and
the Newcastle University small grants committee.
The publication costs of this article were defrayed in part
by payment of page charges. This article must therefore be
hereby marked "advertisement" in accordance with 18 USC
section 1734 solely to indicate this fact.
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