A population genetics perspective of the Indus Valley

Annals of Human Biology, March–April 2005; 32(2): 154–162
A population genetics perspective of the Indus Valley
through uniparentally-inherited markers
K. MCELREAVEY1 & L. QUINTANA-MURCI2
1
Reproduction, Fertility and Populations and 2CNRS URA 1961, Institut Pasteur, Paris, France
Abstract
Analysis of mtDNA and Y-chromosome variation in the Indo-Gangetic plains shows that it was a
region where genetic components of different geographical origins (from west, east and south) met.
The genetic architecture of the populations now living in the area comprise genetic components
dating back to different time-periods during the Palaeolithic and the Neolithic. mtDNA data analysis
has demonstrated a number of deep-rooting lineages of Pleistocene origin that may be witness to the
arrival of the first settlers of South and Southwest Asia after humans left Africa around 60 000 YBP.
In addition, comparisons of Y-chromosome and mtDNA data have indicated a number of recent
and sexually asymmetrical demographic events, such as the migrations of the Parsis from Iran to
India, and the maternal traces of the East African slave trade.
Keywords: Y-chromosome, mtDNA, Indus Valley, population genetics
Introduction
The Indo-Gangetic plain of Pakistan and India contains a large number of ethnic groups
of diverse origins that speak several language families (such as Indo-European, Turkic, and
Sino-Tibetan as well as relict linguistic outliers) and endogamy is widely practised. Both
Pakistan and India lie on the postulated southern coastal route followed by anatomically
modern Homo sapiens out of Africa, and so this region may have been inhabited by modern
humans as early as 60 000–70 000 years ago (Quintana-Murci et al. 1999). Later agricultural
developments occurred in the eastern horn of the Fertile Crescent (8000 YBP), notably in
Elam (modern south-western Iran).
The Elamite peoples are considered to have spoken a language that belonged to
the Dravidian family (McAlpin 1981). The proto-Elamo-Dravidian language could
have spread eastwards with the movement of farmers from this region to the Indus
Valley and the Indian subcontinent (McAlpin 1981, Cavalli-Sforza 1996, Renfrew 1996).
Consistent with this hypothesis, Neolithic farming settlements, dating from around
6500 BC, have been uncovered in south-western Pakistan (Mehrgarh). These early settlements show evidence of cattle pastoralism and barley cultivation, rather than sheep and
goat domestication seen further to the west in the Fertile Crescent.
Correspondence: Dr K. McElreavey, Reproduction, Fertility and Populations, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris
Cedex 15, France. E-mail: [email protected]
ISSN 0301–4460 print/ISSN 1464–5033 online/00/000154–162 # 2005 Taylor & Francis Group Ltd
DOI: 10.1080/03014460500076223
Population genetics of the Indus Valley
155
In the 4th millennium BC the Indus Valley civilizations emerged and flourished during
the period 2600–1900 BC (Dales 1991), before declining dramatically from 1800 BC.
Domestication of the horse (5000 YBP) gave the inhabitants of the Central Asian steppes
the opportunity to expand geographically (Zvelebil 1980). Around 2000–1500 BC these
nomadic peoples, probably from the Andronovo and Srubnaya cultures, migrated through
Iran and Afghanistan to Pakistan and India, and their arrival was contemporaneous with
the decline of the Indus Valley civilizations. It seems likely that their arrival brought the
Indo-Iranian branch of the Indo-European language family and, eventually, caused the
replacement of Dravidian languages in Iran, Pakistan, and most of northern and central
India (Renfrew 1987, 1996, Cavalli-Sforza 1996). However, it is wrong to assume that
the rapid and dramatic collapse of the Indus Valley civilizations was a direct result of an
‘Aryan invasion’, with severe climatic and environmental changes a probable major factor.
The region also witnessed other major historical events, including invasion by the armies
of Alexander the Great, the Arab and Muslim conquests, and the rise of British Indian
Empire.
In the past decade, studies of mtDNA and Y-chromosome variation have provided
a substantial contribution to the understanding of human origins and migration patterns.
Detailed phylogenies can be readily constructed because both of these loci are haploid,
non-recombining and uniparentally inherited, and their small effective population size
makes mtDNA and the Y-chromosome more susceptible to drift than autosomal sequences.
mtDNA surveys in worldwide populations have shown a continent-specific distribution of
mtDNA lineages (Wallace et al. 1999, Ingman et al. 2000). African populations are characterized by the oldest superhaplogroups, L1, L2 and L3 (Bandelt et al. 1995, Watson et al.
1997, Salas et al. 2002), but it seems that only L3 radiated out of Africa, mainly in the form
of haplogroups M and N, 60 000 YBP, giving rise to the extant Eurasian variation (Watson
et al. 1997, Quintana-Murci et al. 1999, Wallace et al. 1999). Most western Eurasians are
characterized by clades within haplogroup N (Torroni et al. 1996, Macaulay et al. 1999,
Richards et al. 2000), whereas N and M contributed almost equally to the current eastern
Eurasian mtDNA pool (Stoneking et al. 1990, Redd and Stoneking 1999, Kivisild et al.
2002).
Y-chromosome variation has also been widely studied and a refined Y-chromosome phylogeny is now available (Underhill et al. 2000). Y-chromosome phylogenies show the most
divergent and deepest branches in sub-Saharan Africa and non-African lineages tend to be
a subset of African lineages, supporting the Out-of-Africa scenario (Underhill et al. 2000,
Hammer et al. 2001). Most Y-chromosome lineages, or haplogroups, show a strong
geographical structure and their variation is predominantly structured by geography, not
by language or ethnic affiliation (Rosser et al. 2000, Zerjal et al. 2002).
Maternal and paternal genetic components in the Indus Valley
Both mtDNA and Y-chromosome variation show a similar pattern in the Indus Valley, with
a mosaic composition of different components from West Eurasia, South Asia and East
Asia. However, patterns of population distribution are much more discernible for mtDNA
data than for the Y-chromosome. In general, mtDNA variation shows a simple west-to-east
divide and a sharp boundary underlying the mtDNA variation in this region (Figures 1
and 2).
Populations located west of the Indus basin exhibit a common mtDNA lineage composition, consisting mainly of western Eurasian lineages, with a very limited contribution from
South Asia and eastern Eurasia (Quintana-Murci et al. 2004, Figure 1). For example, there
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Figure 1. Map showing the different Pakistani and north-west Indian populations and their maternal
genetic components. Pie charts show the distribution of the main mtDNA lineage groups in the
populations studied; the sections reflect the frequency of different haplogroup clusters. Population
codes are: SH, Shugnan; KL, Kalash; HU, Hunza; HZ, Hazara; PT, Pathans; BA, Baluchi; SI,
Sindhi; GJ, Gujarati; PA, Parsi; KA, Karachi; MK, Makrani; BR, Brahui.
is a virtual absence of both common South Asian lineages (M*, U2a, U2b and U2c) and the
more autochthonous U9, R*, R2, R5, R6, N1d and HV2 lineages in the Anatolian/Caucasus
region and Iranian plateau, whereas these lineages make up > 50% of the haplogroup profile
in the adjacent Indus Valley (Quintana-Murci et al. 2004).
Some of these mtDNA lineages are ancient and are of probable Pleistocene origin. U7 is
the most widespread deep-rooting local lineage (38 000 YBP), and other lineages (HV2,
R2, R5, U2a, U2b, and U2c) in the Indus Valley and India show signals of in situ differentiation, which appears to be limited to this region. All these lineages have deep time-depths
(28 00 052 000 YBP), similar to haplogroup M* (32 000–53 000) in the region (Kivisild et al.
1999, Quintana-Murci et al. 1999, Roychoudhury et al. 2001). The distribution and ages
of these lineages suggest that they are the legacy of the first inhabitants of the south-western
Asian region who underwent important expansions during the Palaeolithic period.
The absence of these lineages west of Pakistan may be due either to limited gene flow from
the Indus basin or to important demographic expansions in the Fertile Crescent (including
its eastern lobe, represented by present-day Iran), associated with a substantial increase
in frequency and diversity of western Eurasian lineages (Quintana-Murci et al. 2001,
Wells et al. 2001, Qamar et al. 2002). The maternal genetic component of these populations
thus evinced a strong and significant genetic barrier that separates populations west of
Pakistan from those to the east and north of the Indus Valley (Figure 2). Gene flow from
the Fertile Crescent to India can, however, be detected and West Eurasian lineages are
Population genetics of the Indus Valley
157
Figure 2. Map showing the groupings and barrier, inferred from SAMOVA analyses when searching
for two groups. SAMOVA (spatial analysis of molecular variance) analysis defines groups of
populations that are geographically homogeneous and maximally differentiated from each other, and
the population symbols represent the groups of populations inferred from the SAMOVA analyses. A
strong genetic barrier separating populations west of the Indus Valley from Pakistani populations
emerged from the mtDNA data.
present at high frequencies (26–57%), with a gradient towards the Indian subcontinent
(Quintana-Murci et al. 2004). The eastern Eurasian contribution west of the Indus Valley
is virtually absent, despite the known historical population movements from the East
(e.g. Mongols, Altaic-speaking populations, etc.) to the west.
In striking contrast to the mtDNA data, there is no strong evidence in Pakistani populations of Y-chromosome signatures of the early inhabitants of the region following the African
exodus (Qamar et al. 2002, Zerjal et al. 2002), with their Y-chromosomes largely replaced
by subsequent migrations or gene flow. The Y-chromosome gene pool of Pakistani populations is mainly attributable to western Eurasian lineages, particularly from the Middle East
(Qamar et al. 2002). Conversely, few traces of East Asian haplogroups are observed in the
Indus Valley populations. One Y-chromosome haplogroup (L-M20) has a high mean frequency of 14% in Pakistan and so differs from all other haplogroups in its frequency distribution. L-M20 is also observed, although at lower frequencies, in neighbouring countries,
such as India, Tajikistan, Uzbekistan and Russia. Both the frequency distribution and estimated expansion time (7000 YBP) of this lineage suggest that its spread in the Indus
Valley may be associated with the expansion of local farming groups during the Neolithic
period (Qamar et al. 2002).
Genetic diversity and oral tradition
The origins of some populations located in the Indus Valley are strongly based on their oral
tradition. Two clear examples are the Hazaras and the Kalash Kafirs. The Hazaras claim
descent from Genghis Khan or his close male relatives, who established the largest land
empire in history. Although the Mongol empire soon disintegrated as a political unit,
male-line descendants ruled large areas of Asia for many generations. The presence and
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time-depth of the Y-chromosomal haplogroup C*(xC3c) in the Hazara, and its absence
from neighbouring populations, has been interpreted as the genetic legacy of Genghis Khan
and his male relatives (Qamar et al. 2002, Zerjal et al. 2003). The C*(xC3c) haplogroup is
rare in most Pakistani populations but is common in East Asia, including Mongolia.
Analysis of the mtDNA pool of the Hazara show that they are also characterized by very high
frequencies of eastern Eurasian mtDNAs (35%), which once again are virtually absent
from the surrounding populations, suggesting that the male descendants of Genghis Khan,
or other Mongols, were accompanied in their conquests by women of East Asian ancestry.
The Kalash claim origins from the armies of Alexander the Great. However, no support
for a Greek origin of their Y-chromosomes has been found, but this conclusion requires the
assumption that modern Greeks are genetically representative of Alexander’s armies (Qamar
et al. 2002). Western Eurasian mtDNAs have reached fixation in the Kalash with no detectable East or South Asian lineages. Moreover, although the population is composed of
western Eurasian lineages, the most prevalent (i.e. U4, pre-HV, U2e and J2) are rare or
absent in the surrounding populations and usually characterize populations from Eastern
Europe, the Middle East, and the Caucasus (Macaulay et al. 1999, Richards et al. 2000,
Tambets et al. 2000). Also, the internal HVS-I sequence diversity within each of these
haplogroups was surprisingly low, with specific sequence motifs almost entirely restricted
to the Kalash community, suggestive of considerable genetic drift. The strong effects of
drift and the small population size make genetic inferences on the geographical origin of
the Kalash difficult. However, in view of their maternal lineages which can ultimately be
traced back to the Middle East, a western Eurasian origin for this population seems likely.
Of genes and languages in the Indus Valley region
An additional interest of the Indus Valley region is that populations living in the area speak
languages from diverse language families, including Indo-European and Altaic, and also
language isolates, such as the Dravidian Brahui and the Hunza Burusho. Despite this
linguistic diversity, study of the mtDNA and Y-chromosome pools of present-day
populations living in the south-west Asian corridor shows that the linguistic differences
are not reflected in patterns of genetic diversity (Qamar et al. 2002, Quintana-Murci et al.
2004).
However, the two previously mentioned outliers, the Hunza Burusho and the Brahui,
merit further consideration. The Hunzas live mainly in the remote Hunza Valley of northern
Pakistan and speak Burushaski, a language isolate of uncertain origin that has been subject
of many linguistic studies. mtDNA, Y-chromosome and autosomal microsatellite data indicate that the Hunza gene pool is shared with neighbouring populations, particularly with
southern Pakistanis. This genetic pattern could have been established before linguistic differentiation took place, or there could have been substantial gene flow from neighbouring
populations. In any case, no distinctive genetic signature accompanies the linguistic and
geographical isolation of the Hunza Burusho population (Qamar et al. 2002, QuintanaMurci et al. 2004).
The second linguistic outlier is the Brahui population, who are one of the few Dravidianspeaking populations resident outside India. Dravidian languages are now mainly restricted
to southern India and Sri Lanka, but the proto-Elamo-Dravidian hypothesis (McAlpin 1981)
proposed that they originated in Iran and were once spoken across the entire region.
The Brahui population is characterized by high prevalences of western Eurasian mtDNAs
(55%) accompanied by the highest frequency of the Y-chromosome haplogroup J (28%)
in Pakistan, which otherwise has been associated with the expansion of Dravidian-speaking
Population genetics of the Indus Valley
159
farmers from the Fertile Crescent (Quintana-Murci et al. 2001). Thus mtDNA and
Y-chromosome analyses both indicate that the Brahui gene pool comprises lineages from
western Eurasia, particularly from the Middle East, excluding the possibility that this
Dravidian-speaking population in Pakistan is the result of recent incursions from India.
Traces of a recent and sexually asymmetrical event: The migration
of the Zoroastrian Parsi from Iran
Historical records indicate that the Parsis, who are followers of the prophet Zoroaster,
originated in Iran and started their eastward migrations in the 7th century AD, settling in
the north-western Indian province of Gujarat around 900 AD and eventually moving to
Mumbai in India and Karachi in Pakistan. Y-chromosome data show that their gene pool is
essentially of Iranian origin, leading to an admixture estimate from Iran of 100% (Qamar
et al. 2002), and supporting the historical records. In strong contrast, about 60% of the Parsi
maternal mtDNA gene pool belongs to South Asian haplogroups, which make up only 7%
of the combined Iranian sample. The very high frequency of haplogroup M among Parsis
(55%), similar to those of Indian populations and much higher than that of a combined
Iranian sample (1.7%), highlights their close affinities with India and the mtDNA data led
to an admixture estimate of 100% from India. The combined Y-chromosome and mtDNA
results therefore suggest male-mediated migration of the ancestors of the present-day
Parsi population from Iran to India, where they married local females, or directional mating
in Gujarat between Iranian males and local women, through time leading to the loss of
mtDNAs of Iranian origin.
Genetic traces of the East African slave trade
Another example of an unequal sex-specific contribution is seen in the ‘Negroid’ Makrani of
coastal Baluchistan who show distinct African physical traits (Sultana 1995). The mtDNA
pool of the Makrani population indicate that 39% of their maternal lineages are of subSaharan African origin. However, the presence of African mtDNAs among the Makrani
seems to be of recent origin, since their haplotypes are identical to those observed in modern
sub-Saharan African populations (Pereira et al. 2001, Salas et al. 2002), particularly Bantuspeaking populations from Mozambique. These data contrast with the Makrani
Y-chromosome profile, which is similar to that of other Pakistani populations and is
dominated by western Eurasian lineages (Qamar et al. 2002). The maternal and paternal
contributions of sub-Saharan Africans to the current Makrani gene pool have been
estimated at 12% for the Y-chromosome and 40% for the mtDNA (Quintana-Murci et al.
2004).
These findings strongly support the historical hypothesis that the East African slave trade,
in contrast to the Atlantic slave trade, favoured women over men (Lovejoy 2000). Slave
women were mainly domestics and/or concubines, and children fathered by the master
were freed. Strong cultural barriers also hindered male slaves from fathering children,
a situation that was exacerbated by the proportion of slaves imported as eunuchs (Lovejoy
2000). As a consequence of these practices, the contribution of paternal African genes to
the current Makrani population is low, and a similar sex-contrast has been observed in
the Yemeni Hadramawt population (Richards et al. 2003). Both the Makrani and the
Hadramawt data thus support a female-biased slave trade from East African to the Indian
Ocean and show that this sexually asymmetrical pattern extended to the eastern limits of
the East African slave trade.
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Résumé. L’analyse de la variation de l’ADN-mitochondrial et du chromosome Y dans les
plaines Indo-Gangétique, montre qu’il s’agissait d’une région où se rencontraient des
composants génétiques de différentes origines géographiques (de l’ouest, du sud et de l’est).
L’architecture génétique des populations qui vivent maintenant dans cette zone, comprend
des composants génétiques qui remontent à diverses périodes du Paléolithique et du
Néolithique. L’analyse de l’ADNmt a indiqué de nombreux lignages profonds remontant au
Pleistocène, qui pourraient être des témoins des premiers arrivants de l’Asie du Sud et du
Sud-ouest, après que les humains aient quitté l’Afrique aux environs de 60 000 ans BP. Par
ailleurs, la comparaison des données du chromosome Y et de l’ADNmt indiquent des
événements démographiques récents et sexuellement asymétriques, tels que les migrations
des Parsis de l’Iran vers l’Inde et des traces maternelles du trafic des esclaves de l’Afrique de
l’Est.
Zusaammenfassung. Die Analyse von mtDNA und Y-Chromosom-Variation in den
Ebenen von Indus und Ganges zeigt, dass es sich um ein Gebiet handelt, wo sich genetische
Komponenten verschiedenen geographischen Ursprungs (aus dem Westen, dem Osten und
dem Süden) treffen. Die genetische Architektur der zur Zeit in dieser Gegend lebenden
Bevölkerung besteht aus genetischen Bestandteilen, die sich auf verschiedene Zeitepochen
während des Paläolithikums und des Neolithikums zurückdatieren lassen. Die Analyse von
mtDNA-Daten hat eine Anzahl sehr alter Stammbäume aus dem Pleistozän gezeigt, die
möglicherweise die Ankunft der ersten Siedler aus Süd- und Südwestafrika bezeugen,
nachdem Menschen vor etwa 60 000 Jahren Afrika verlassen hatten. Zusätzlich verweisen
Vergleiche der Y-Chromosomen- und der mtDNA-Daten auf eine Reihe von erst kürzlich
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stattgehabten sexuell asymmetrischen demographischen Ereignissen, wie die Wanderung
der Parsen aus dem Iran nach Indien und die mütterlichen Spuren des ostafrikanischen
Sklavenhandels.
Resumen. El análisis la variación del ADNmt y del cromosoma Y en las llanuras del IndoGanges muestra que hay una región donde confluyen componentes genéticos de diferentes
orı́genes geográficos (del oeste, este y sur). La arquitectura genética de las poblaciones que
viven actualmente en este área incluye componentes genéticos que datan de diferentes
periodos del Paleolı́tico y el Neolı́tico. El análisis de datos del ADNmt ha demostrado la
existencia de una serie de linajes profundamente arraigados de origen Pleistoceno, que
pueden ser testimonio de la llegada de los primeros pobladores del sur y sudoeste asiáticos
tras la salida de los humanos de África hace unos 60 000 años D.C. Además, las
comparaciones de los datos del cromosoma Y y del ADNmt han indicado la existencia de
varios sucesos demográficos sexualmente asimétricos y recientes, como las migraciones de
los Parsis desde Irán a la India y las huellas maternas del comercio de esclavos del este
africano.