Archaeology of the peacock hill of Karnataka

The Bellary District Archaeological Project (BDAP) 


The Bellary District Archaeological Project, undertaken in 2002, focused its efforts in particular on the Sanganakallu-Kupgal cluster of hills and sites. It also involved exploration and analysis of other sites in Bellary District, Karnataka and beyond.  The Sanganakallu-Kupgal cluster of archaeological sites has been known since at least the 19th century, and early reports refer to it as 'Peacock Hill'.  We refer to the cluster of sites as the 'Sanganakallu-Kupgal archaeological heritage area', due to the remarkable concentration of archaeological sites found in the area of these two villages (Sanganakallu and Kupgal).  The area appears to have been particularly important during the Neolithic period, when settlement was focused on the granitic hills themselves (see Intensive systematic survey).  The archaeological importance of the Sanganakallu-Kupgal heritage area is significant, and these sites deserve government protection (see Protection of sites and monuments)…


Exploring Neolithic and Megalithic south India: the Bellary District archaeological project


AntiquityDec, 2002 by Nicole BoivinRavi KorisettarP.C. VenkatasubbaiahHelen LewisDeepak HavanurKalyan MalagyannavarSubhas Chincholi

The southern part of the Indian peninsula is an area of outstanding archaeological interest. While its historic cities and temples have long attracted the interest of both scholars and tourists, however, south India's equally remarkable prehistoric period remains have only rarely received the attention they deserve. A new joint Cambridge-Karnatak University research project was thus initiated in 2002 to study the unique Neolithic and Iron Age remains of the southern Deccan. This 2-month pilot project focused its efforts on the Bellary District of Kamataka, where prehistoric megaliths and `ashmounds' (large mounds of burnt cattle dung) occupy a stunning landscape of naturally sculpted granitic rock formations (FIGURE 1). The aim of the project was to explore, survey and record visible archaeological and landscape features in order to acquire insights into the indigenous processes of neolithization and megalithism that lea to the formation of these unique and still enigmatic monuments of ash and stone….

Early village unearthed

One of the earliest village settlements in South India has been discovered at the Sanganakallu complex of hills near Bellary, write Santosh Martin and Sunil Kumar M

Bellary is changing the course of history. While the huge deposits of iron ore in Bellary are rewriting the political history and geography of the state, a chain of hills close to Bellary is adding to the interesting history and culture of human settlements in India.

About eight km from Bellary is the Sanganakallu complex of hills (also referred to as peacock hills) where archaeologists have discovered one of the earliest village settlements in South India. These settlements date from the Neolithic period (3000 BC – to the beginning of the Christian era). 

The first settlers here are said to be the ones who established the first villages in South India. These settlers traded stone tools among the Neolithic people in that region. The region is considered the largest stone tool producing centre anywhere in South India. 

Neolithic art on boulders

The Sanganakallu village settlement, spread over an area of 1,000 acres, is considered the largest village complex known so far.  The rock art that can be seen on the boulders of the hill chain is evidence of rituals and social ceremonies involving ringing rocks, still preserved by way of hand-percussion marks. 

Grinding grooves where stone axes were polished, shallow concave surfaces on boulders where grain was processed, and dykes where the dolerite was exploited to manufacture stone tools on a large scale bears testimony to the rich Neolithic culture and the skills of the people.

Earliest agriculturists

The people who settled at Sanganakallu were the earliest agriculturists who cultivated small millets and pulses. They kept cattle, and sheep and cattle domestication was prevalent in the area. They erected separate areas for dumping dung, including sheep and goat dung. These heaps have survived till today in the form of ash mounds. One can see them at Kupgal, Kudathini, etc. The people of Sanganakallu traded stone tools to the other Neolithic people in the wider Rayalaseema region. By about 2000 BC, this settlement was the largest stone tool producing centre anywhere in South India. The hill complex of Sanganakallu preserves the earliest houses of mud and stone, rock art evidence for rituals and social ceremonies. By 1500 BC, cemeteries were created to bury the dead. In fact different types of burial structures have been documented from these hills.

Archaeologist’s delight

Sanganakallu has been an archaeologist’s delight because of a high concentration of findings in a small area. In fact, archaelogists from the Karnatak University and Cambridge University have been working at this site since 1997. Over the years, they have carried out a series of multidisciplinary investigations. Many archaeologists from all over the country and abroad have worked in this area and the findings have been published in many leading journals devoted to archaeology.

Many publications are in progress including a 1,000 page scientific study. The entire area has been digitally mapped and every millimeter of the cultural landscape has been recorded on these maps.

Sanganakallu is not the only interesting archaeological site in Bellary. There are several more. But many of them are getting destroyed due to widespread quarrying and mining activities in Bellary. Luckily, for Sanganakallu and other sites, a museum similar to that in Hampi is coming up at the Kannada and Culture complex, adjacent to the Deputy Commissioner’s residence in Patel Nagar, Bellary. A fully built two-storied building (about 8000 sq ft) has been made available by the district administration for the museum. Many of the findings from the Sanganakallu site will be displayed at this museum.

The proposed museum complex aims to bring into focus the history and cultural heritage of Bellary and its environs. It aims to inculcate in the people a commitment to preserving their heritage with a deep sense of pride and concern. There are also plans  to create an audio-visual time capsule of landmark of the people of the region through the ages.

Seal with Indus script showing a zebu (Brahmi bull
Fig. 1 Geographic distribution compilation between mtDNA genetic patterns across Asia and the archaeological signs of spread of cattle pastoralism within the Indian subcontinent. (A) Median reduced networks constructed for zebu halplotypes across Asia; (B) A map of the Indian subcontinent showing median reduced networks for each potential domestication centre (Indus, Ganges and South India); (C) A map of the Indian subcontinent indicating the spread of cattle across time based on archaeological data. Circles represent sites containing domesticated zebu cattle faunal remains, and squares represent reports of Holocene wild-type cattle bones. For dates see Supplementary Table S3 (in the full text of the paper in Molecular Biology and Evolution -- Sept. 2009).

Indigenous Indians: genetic studies

Here are three genetic study reports. Two reports on Indian population genetics appeared in Nature of 24 Sept. 2009 and another on the origins of Zebu in South Asia in Molecular Biology and Evolution, Sept. 21, 2009. These studies throw light on the indigenous evolution of human population and zebu cattle in ancient India. David Reich et al., Reconstructing Indian population history (Nature, Vol. 461, 24 Sept. 2009)’s-invisible-threads Aravinda Chakravarti,Tracing India’s invisible threads (Nature, Vol. 46, 24 Sept. 2009) (Shanyuan Chen et al, Zebu cattle are an exclusive legacy of the South Asian Neolithic, Molecular Biology and Evolution, OUP, Sept. 21, 2009). Zebu is depicted on Indus script (Sarasvati hieroglyphs) and is often recognized as the signature-tune of Indian connections in Mesopotamian civilization finds of the 4th-5th millennium BCE.

Earlier genetic reports include the following, detailing ongoing genetic researches in many scientific institutions:


Dr. Petraglia (University of Oxford):  "Today, humans are concerned with the effects of burgeoning population size and climate change.  By pulling together an interdisciplinary and international group of scholars, we address the correspondence between environmental change, population size increase and technological innovations in prehistory.  Our research programme sets a new research agenda for those who wish to understand the prehistory of India, but also to those investigating similar issues worldwide. Our study, centering on archaeological sites across South Asia, and includingnew field research in the Kurnool District of Andhra Pradesh, finds that microlithic technologies are much earlier than assumed, and go back to at least 35,000 years ago. There are few better places to conduct this research than in India.  India is blessed with a rich archaeological record that can be used to test many theories of human adaptation and survival."

Dr. Gyaneshwer Chaubey (Institute of Molecular and Cell Biology, University of Tartu, Estonia): The extremely interesting outcome of this research is  finding the same result by genetics, palaeoenvironmental  as well as archaeological researches. The high genetic diversity in South Asian populations came from the large number of people who were already present in the subcontinent 35 thousand years ago. It is also notable that the South Asians have highest number of maternal lineages coming out directly from the root. We observed that the most of such lineages have an emergence time around 35 thousand years. The archaeological and palaeoenvironmental findings reached to the same conclusions suggesting a population expansion before LGM (last glacial maxima). It supports the indigenous South Asian in-situ development of maternal genepool in to the subcontinent rather than any major influx out of the subcontinent. This study stress the need of interdisciplinary approach for reconstruction of the complex population histories of South Asia, which needs to be resolved through the interaction of genetics, anthropology, archaeology and linguistic approaches.

Common genetic traits - Aryan theory demolished

An international team of genetic scientists has ruled out the theory of Aryan invasion of the Indian sub-continent.

“The age old argument that there was an Aryan invasion of the sub-continent is simply bunkum.

Scientific studies prove that there is no such thing as Aryan Indian or Dravidian Indian. Genetic high resolution studies carried out by us prove that all Indians are derived from same grandgrand parents who arrived here 60,000-70,000 years ago from Africa,” Dr Gyaneshwer Chaubey, a scientist of the team, told Deccan Chronicle.

Dr Chaubey, a member of the scientific community at the Instituteof Molecular an d Cell Biology, University of Tartu, Estonia, said the research also proved that all Indians had common genetic traits irrespective of the regions to which they belonged.

“It took us four years to complete the study and we analysed 12,200 samples to reach this conclusion,” said Dr Chaubey.

“Genetic studies help us to establish relations between populations. We focussed on the paternal (Y chromosomes) and maternal DNA genealogies. The data which we generated does not support any major influx to the subcontinent other than the earlier arrival of migrants from Africa,” he said.

“The present day caste/creed/religion is of indigenous origin,” said Dr Chaubey.

Additional comments:


We all are aware on social endogamy and caste division of India and this paper is a solid evidence that the sanatana dharma is deeply rooted. It can be also true that there are two roots of major civilizations.


But there are several shortcomings in the study reported in Nature of 24 Sept. 2009:

1) They have used population Santhal on the centre of "ancestral South India" which is not correct. ASI should be recalculated keeping real South Indian populations. Santhal is an East Indian population which has a East Asian genetic input.

2) The main problem of this paper is showing the upper caste closer to Central Asians and Europeans which is the same fault, which has been done by Bamshad and Stoneking in their older papers on India! The North Indian ancestry which they have misinterpreted as derived from central Asians and Europeans is actually is the genetic component of Indus people who have migrated from west to east after drying up the river Sarasvati. 

3) The dates of any founding lineage can't be calculated by the method used in this paper becase SNP's don't give any algorithm to calculate the time. Therefore, we think that south as well as north ancestry is quite old and needs further exploration.


It is clear that the genetic studies consistently point to 1) indigenous evolution of the present-day Bharatiya and 2) demolish the Aryan-invasion/migration as a myth. This myth was indeed a creation of indology, as Eurocentric academics sought to find their origins and ended up in India and could not stomach the possibility that India had an indigenously-founded and evolved civilization ca. 5th millennium BCE which ran counter to their wrongly perceived ‘white-man’s burden’ of civilizing forest-dwellers.

kalyanaraman, 25 Sept. 2009


The great Indian gene findings

 September 10, 2009


Who were the first Indians? Were they the chocolate-hued Dravidian southerners or the dark-skinned tribals that inhabit East India and the Andaman islands? Was the relatively fair Indo-European population of the North the original settler? Or did the Mongoloid-featured Tibetan-Burmans beat the rest to it? When and how did the pioneers reach India? What routes did they take?


The answers to these questions have always been the subject of contentious debate and till recently well nigh impossible to conclude. After all today there are more than a billion Indians consisting of 4,693 communities, 4,500 endogamous groups, 325 functioning languages and 25 scripts. Not to mention the four main castes and the hundreds of sub-castes that throw up even more controversial questions such as: Are the Brahmins from a different genetic pool than that of the Shudras?


Now an unprecedented surge in genetic research across the country is overturning long-held theories and coming out with some fascinating revelations of how Indians became, well, Indians. Equally significant and directly relevant to the quality of life, for the first time, major genetic studies are underway at a clutch of top national laboratories, which when complete will help us know if any of us run a higher risk of being afflicted with life-threatening diseases such as cancer, diabetes, malaria, cardio-vascular blocks, neurological disorders and asthma. And possibly help in ushering a revolution in healthcare.

 Blame gene

Recent studies show that some Indians exhibit genetic variations that make them susceptible to specific diseases.

Malaria: East and Central India populations were found to have a gene that makes them susceptible to 4,693 cerebral malaria.

Cancer: Initial studies have found certain populations in the extremes to have higher risk of cancer.

Immune response: Indians showed varying immune response to certain drugs holding the key for future treatment.

Heart diseases: North Indian vegetarians were more susceptible to heart diseases.

Among the more striking results is the finding that Indians are the global melting pot of human diversity containing every possible known genotype. That it is now clear that India was the first stop made by early settlers after the first known human populations migrated out of Africa. That the tremendous genetic diversity originated in the sub-continent itself rather than as a result of the so-called 'Aryan invasion' that historians have theorised about. That some regions in Northern India are more susceptible to heart diseases while some populations in Rajasthan and Jammu have a genetic immunity that puts them at lower risk of HIV infections.

The trigger for Indian researchers has been the most spectacular scientific achievement since man walked on the moon: deciphering the book of human life. In 2001, the international Human Genome Project (HGP) came out with a raw translation of the 3 billion strands of DNA-deoxyribonucleic acid-the basic building blocks of all life. To understand the complexity of the effort, if the genome sequence obtained for a single human being were to be published in typed form as books these would stack up as tall as Delhi's Qutab Minar.

What the HGP did show was that the human genetic code or genome is 99.9 per cent identical in all people. It was in line with the theory that we all had a common ancestry with the earliest humans who lived in Africa and possibly to a single woman, the "mitochrondial Eve." The 0.1 difference in DNA sequencing is responsible for our individual differences whether in hair or eye colour or our susceptibility to diseases.

The project revealed that humans have around 25,000 genes-the basic physical and functional units of heredity. Since then scientists have been able to decode the role played in 50 per cent of the known genes. The unravelling of the human genetic structure is helping researchers worldwide find the most fundamental answers to our origins and in enhancing healthcare.

In India, genetic research got a major boost in 2003 when the Council of Scientific and Industrial Research (CSIR), with funding from the government, launched the Indian Genome Variation (IGV) consortium consisting of seven major laboratories: the Institute of Genomics and Integrative Biology (IGIB), Delhi, Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Indian Statistical Institute (ISI), Kolkata, Central Drug Research Institute (CDRI), Lucknow, Institute of Microbial Technology (IMTECH), Chandigarh, Industrial Toxicological Research Centre (ITRC), Lucknow and Indian Institute of Chemical Biology (IICB), Kolkata.

The team first collected blood samples of 2,000 people from 55 populations representing the four major linguistic groups: Austro-Asiatic, Tibeto-Burman, Indo-European and Dravidian before splicing their genes and looking for tell-tale variations. In doing so the project established the first large-scale database of genomic diversity in the Indian population.

Samir Brahmachari, a geneticist of repute and CSIR's director-general says, "India is among the first country to do a diseases-specific, drug-response mapping on large populations which gives us risk analysis and benefits." Apart from reinforcing what Brahmachari calls the "genetic mosaic" of India, the study also showed that the risk of susceptibility to a disease was more specific to a geographical region rather than to caste, creed or linguistic affinities. Reviewing the consortium's work, Evelyne Heyer, geneticist at the French Natural History Museum, said, "This study forms a valuable first step in building our knowledge of the genetic diversity in India."

While the consortium released its preliminary findings last year, since then individual laboratories have come out with a host of important findings. At the CDRI, geneticist Saman Habib focused on the more lethal form of cerebral malaria caused by the Plasmodium falciparum. Studies were conducted on people who lived in the regions where malaria was endemic. Analysing the samples and also from control groups, Habib found a "clear indication of variety of genes affecting the susceptibility of the individual towards this deadly form of malaria including the severity of the attack". One pointer: Health officials would be well-advised to double their efforts in regions with such susceptibility.

At the IGIB, Shantanu Sengupta is coming out with surprising findings about cardiovascular diseases and genetic factors. Contrary to popular notions, vegetarians in India have a high susceptibility to heart diseases. That is now found to be due to a deficiency of Vitamin B12. But there was a significant variation of this phenomenon between North and South India.

ShompenShompen tribals of the Andaman And Nicobar Islands.

The study found that Northern Indians who were also vegetarian had a much higher degree of susceptibility to heart problems than their southern brethren because of a genetic variation that made them vulnerable. The deficiency in Vitamin B12 and the genetic variation increased the level of an amino acids associated as a risk factor for cardiovascular disease.

In a laboratory not far from Sengupta, Balaram Ghosh, Head of the Genomics and Molecular Medicine Unit, IGIB is proving just how useful the emerging field known as pharmacogenomics could be. Researching on the cause of asthma in India, his team, after examining over 700 patients, found that many genetic variations that are known to make people susceptible to asthma among European populations were not seen among Indians. They were also able to identify a novel gene that is associated with asthma among Indian patients. These would help them identify high-risk individuals and also advise them on preventive steps.

Carrying the process forward, the team studied the absorptive ability of populations to the drug salbutamol used to treat asthma. In some people it was found to be not as effective as in others. Understanding the process would help in administering the right amount of doses of the drug and getting away from "the one-size-fits-all" approach.

Somewhat similar work is being done on Diabetes Type II by his colleague Dwaipayan Bharadwaj who is looking for genetic markers that could help doctors identify those susceptible to it long before they come in for treatment. Again here, after examining over 7,000 patients suffering from this type of diabetes, Bharadwaj's study shows that while Indians did have some main gene markers that Europeans had, large amount of them were absent too.


The hope is that if they could home in on genetic markers for Diabetes Type II they could warn those Indians at risk early to enable them to take preventive measures and improve their quality of life. Such is the promise of pharmacogenomics that Brahmachari says: "We should soon be able to do rapid tests to determine a patient's genotype and then guide treatment with the most effective drugs apart from reducing adverse reactions."

There is also the growing clamour to resort to gene therapy or the potential of using genes themselves to treat disease or enhance particular traits much like the research into stem cells. While genetics holds up the promise of revolutionising health care, there is need to be cautious about its use.

Genetic profiling would reveal some of the innermost secrets that could, for instance, be used by employers to weed out candidates found to be susceptible to certain ailments or diseases. "We deliberately didn't release details of the communities in our studies because of the social ramifications involved," says Mitali Mukerji, IGV consortium co-ordinator. So before you go out and get your genes sequenced-it costs around Rs 2.5 lakh abroad-know the benefits and the cost.

Experts speak 

GeneGene analysis at a Delhi laboratory

"India is the first country to do a disease-specific drug-response mapping on large populations. It will give us a risk analysis and also the benefits."
Samir Brahmachari
Director-General, CSIR

Samir"The tribals of India, especially those living in The Andamans, hold the clue to not just who were the earliest Indians but also the origin of man itself."
Lalji Singh
Former Director, CCMB

Lalji"South Asia played a pivotal role in the out-of-Africa colonisation and dispersal of modern humans."
Partha P. Majumder
Head of Human Genetics Unit, ISI


Partha"There is a clear indication of a variety of genes affecting the susceptibility of the individual towards lethal cerebral malaria."
Saman Habib
Scientist, CDRI


Saman"The best way to understand the Indian gene pool is to compare it to a large banyan tree which has a trunk with branches than twigs and leaves."
Ramaswamy Pitchappan
Professor Emeritus, Madurai Kamaraj University

Genetic diversity of Indian population studied


Ancient South Indians’ descendants have no genetic link to groups outside India Recessive gene disorder: Shared descent from a common ancestral population plays a bigger role than consanguinity for many recessive gene disorders

A paper published online today (September 24) in the journal Nature, shows that all diverse groups seen spread out in India today come from two major ancient populations that are genetically divergent.

The two ancient populations are the Ancestral North Indians (ANI) and the Ancestral South Indians (ASI). The study was based on genetic analysis.

While the Ancestral North Indians (ANI) group is genetically close to Middle Easterners, Central Asians, and Europeans, the Ancestral South Indians (ASI) are not related to any group outside India, notes the paper.

The study was undertaken by the Hyderabad-based Centre for Cellular and Molecular Biology (CCMB) and three other institutions in the U.S.

Samples from 132 people representing 25 groups from 15 States and speaking six language families (including two language families from the Andaman Islands) were studied.

The study also looked for genetic variations based on caste — upper and lower caste — from two the States of Uttar Pradesh and Andhra Pradesh.

The study found the groups (seen today) that emerged from the two ancient populations have distinct genetic affinity. “The populations (groups) that emerged from ANI show 40-80 per cent genetic affinity to European population.

“But the populations that emerged from ASI don’t show any affinity to any population outside India,” said Dr. Kumarasamy Thangaraj, Senior Scientist at CCMB, and one of the authors of the paper. “The Hyshi and Ao Nage population from north-east India show genetic affinity to the Chinese.”

The indigenous population seen in the Andamans have more affinity to the ASI. “Otherwise, they have no relationship with any other population anywhere in the world,” said Dr. Thangaraj.

Unlike the European and Chinese population, the Indian population are more scattered in a genetic sense.

Medical implications

While consanguinity is often implicated for many recessive gene disorders in a population, this study found that the “shared descent from a common ancestral population plays a bigger role. This is called as the ‘founder effect.’

Founder effect is nothing but the fact that many groups seen today have descended from a small group of founding individuals, and these founding individuals in turn have been isolated from other groups, genetically speaking.

It is based on this fact that the authors state that the founder effect plays a bigger role. “We propose that the founder effect is responsible for an even higher burden of recessive diseases in India than consanguinity,” the paper states.

Dr. Thangaraj explained the significance of this. A disease can occur due to the presence of a recessive gene due to mutation. In a small population with high endogamy [where people marry within the population], the mutation persists and spreads to more number of people.

After a point of time, a large number of people have the recessive gene and this increases the chance of a child receiving a recessive gene from both the parents and thus becoming diseased.

Existence of caste

Contrary to popular perception by historians that the caste system seen today is an invention of colonialism, the study found scientific evidence to show that “many current distinctions among groups are ancient.”

“The caste system is not recent,” said Dr. Thangaraj. “The social stratification existed right from early human divergence, some 50,000-60,000 years ago when initial settlement happened in India.”

The paper adds a word of caution: “Models in population genetics should be treated with caution. Although they provide an important framework for testing historical hypotheses, they are oversimplifications.”


Aryan-Dravidian divide a myth: Study
TNN 25 September 2009, 01:16am IST

HYDERABAD: The great Indian divide along north-south lines now stands blurred. A pathbreaking study by Harvard and indigenous researchers on ancestral Indian populations says there is a genetic relationship between all Indians and more importantly, the hitherto believed ``fact'' that Aryans and Dravidians signify the ancestry of north and south Indians might after all, be a myth.

``This paper rewrites history... there is no north-south divide,'' Lalji Singh, former director of the Centre for Cellular and Molecular Biology (CCMB) and a co-author of the study, said at a press conference here on Thursday.

Senior CCMB scientist Kumarasamy Thangarajan said there was no truth to the Aryan-Dravidian theory as they came hundreds or thousands of years after the ancestral north and south Indians had settled in India.

The study analysed 500,000 genetic markers across the genomes of 132 individuals from 25 diverse groups from 13 states. All the individuals were from six-language families and traditionally ``upper'' and ``lower'' castes and tribal groups. ``The genetics proves that castes grew directly out of tribe-like organizations during the formation of the Indian society,'' the study said. Thangarajan noted that it was impossible to distinguish between castes and tribes since their genetics proved they were not systematically different.

The study was conducted by CCMB scientists in collaboration with researchers at Harvard Medical School,
Harvard School of Public Health and the Broad Institute of Harvard and MIT. It reveals that the present-day Indian population is a mix of ancient north and south bearing the genomic contributions from two distinct ancestral populations - the Ancestral North Indian (ANI) and the Ancestral South Indian (ASI).

``The initial settlement took place 65,000 years ago in the Andamans and in ancient south India around the same time, which led to population growth in this part,'' said Thangarajan. He added, ``At a later stage, 40,000 years ago, the ancient north Indians emerged which in turn led to rise in numbers here. But at some point of time, the ancient north and the ancient south mixed, giving birth to a different set of population. And that is the population which exists now and there is a genetic relationship between the population within India.''

The study also helps understand why the incidence of genetic diseases among Indians is different from the rest of the world. Singh said that 70% of Indians were burdened with genetic disorders and the study could help answer why certain conditions restricted themselves to one population. For instance, breast cancer among Parsi women, motor neuron diseases among residents of Tirupati and Chittoor, or sickle cell anaemia among certain tribes in central India and the North-East can now be understood better, said researchers.

The researchers, who are now keen on exploring whether Eurasians descended from ANI, find in their study that ANIs are related to western Eurasians, while the ASIs do not share any similarity with any other population across the world. However, researchers said there was no scientific proof of whether Indians went to Europe first or the other way round.

Migratory route of Africans

Between 135,000 and 75,000 years ago, the East-African droughts shrunk the water volume of the lake Malawi by at least 95%, causing migration out of Africa. Which route did they take? Researchers say their study of the tribes of Andaman and Nicobar islands using complete mitochondrial DNA sequences and its comparison those of world populations has led to the theory of a ``southern coastal route'' of migration from East Africa through India.

This finding is against the prevailing view of a northern route of migration via Middle East, Europe, south-east Asia, Australia and then to India.,prtpage-1.cms

Reconstructing Indian-Australian phylogenetic link.

Satish Kumar email, Rajasekhara REDDY Ravuri email, Padmaja Koneru email, B P Urade email, B N Sarkar email, A Chandrasekar email and V R Rao email

BMC Evolutionary Biology 2009, 9:173doi:10.1186/1471-2148-9-173 Published: 22 July 2009

Abstract (provisional)


An early dispersal of biologically and behaviorally modern humans from their African origins to Australia, by at least 45 thousand years via southern Asia has been suggested by studies based on morphology, archaeology and genetics. However, mtDNA lineages sampled so far from south Asia, eastern Asia and Australasia show non-overlapping distributions of haplogroups within pan Eurasian M and N macrohaplogroups. Likewise, support from the archaeology is still ambiguous.


In our completely sequenced 966-mitochondrial genomes from 26 relic tribes of India, we have identified seven genomes, which share two synonymous polymorphisms with the M42 haplogroup, which is specific to Australian Aborigines.


Our results showing a shared mtDNA lineage between Indians and Australian Aborigines provides direct genetic evidence of an early colonization of Australia through south Asia, following the "southern route".

Full paper at

Vaclav Blazek, "Was there an Australian Substratum in Dravidian?", _Mother Tongue_ 11 (2006), pp. 275-294:  70 sets of Australian words (e.g., numerals, body parts, nature) are compared with reconstructed Proto-Dravidian, Nahali and Vedda words.

Inventions helped pre-historic people to survive

21 July 2009

A technological breakthrough 35,000 years ago allowed the hunter-gatherers of India to thrive despite the chall

Challenges of environmental change and an arid climate.

The findings, published yesterday in theProceedings of the National Academy of Sciences, show how a new, innovative type of small stone tool - called microliths - became the weapon of choice for Paleolithic hunters.

Dr Michael Petraglia, an archaeologist from the University of Oxford and lead author of the paper, uncovered thousands of stone blades and bladelets, no bigger than 4 cm long, from three locations in South Asia. The blades were probably inserted at the top of wooden shafts and used as spear-heads or arrow tips.

'This a pre-historic example of how humans adapted to environmental change.'
Dr Michael Petraglia, University of Oxford

The microliths were light and portable, and could easily be produced in large quantities. They were 'highly efficient weapons that made hunting easier and less risky,' he says.

But Petraglia and the team were also interested in the broader meaning of his tool findings. 'When you do archaeology, you have to put it in its proper environmental context,' he says. To get a better idea of what India looked like 35,000 years ago, the archaeologists joined forces with an international team of geneticists and earth scientists including researchers from Indian universities.

The team analysed available data on the environment and climate in South Asia to compile the first reconstructed vegetation map of the area about 30,000 years ago. At the time, global climate was turning colder at the onset of the Ice Age.

South Asia escaped the growing ice caps, but the summer monsoon became weaker and the amount of rainfall decreased across the region. As a result, the climate became drier and in some areas inhospitable.

This research, Petraglia says, 'is a pre-historic example of how humans adapted to environmental change.' Back then, South Asia was a mosaic of deserts, savannah and isolated patches of tropical woodlands. The region was not stable and the landscape changed frequently in hundred-year cycles.

Despite the challenging environment, the genetic findings of the study reveal that local populations actually increased during this period. 'It seems that the hunter-gatherers were doing very well,' says Petraglia.

This is particularly significant because up to now 'it was thought that the high population density of India started during the more recent period - the Holocene - as a consequence of domestication.'

'Our research suggests that the population was already increasing 35,000 years ago,' Petraglia adds.

The combination of archaeological, genetic and environmental data is 'unusual but powerful', argues Petraglia. 'We wouldn't be able to tell the whole story from a single viewpoint,' he says, adding that he hopes that this work will serve as an example for other research projects.

M. Petraglia, C. Clarkson, N. Boivin, M. Haslam, R. Korisettar, G. Chaubey, et al. Population increase and environmental deterioration correspond with microlithic innovations in South Asia ca. 35,000 years ago. PNAS, published online before print July 20, 2009, doi:10.1073/pnas.0900546106


Genetics substantiates autochthonous origin of castes in India

Full text of the article.

Journal of Human Genetics (2009) 54, 47–55; doi:10.1038/jhg.2008.2; published online 9 January 2009

The Indian origin of paternal haplogroup R1a1* substantiates the autochthonous origin of Brahmins and the caste system

Swarkar Sharma1,2,4, Ekta Rai1,2,4, Prithviraj Sharma1,3, Mamata Jena1, Shweta Singh1, Katayoon Darvishi1, Audesh K Bhat1, A J S Bhanwer2, Pramod Kumar Tiwari3 and Rameshwar N K Bamezai1

1.      1National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India

2.      2Department of Human Genetics, Guru Nanak Dev University, Amritsar, India

3.      3Centre for Genomics, School of Studies in Zoology, Jiwaji University, Gwalior, India

Correspondence: Professor RNK Bamezai, National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India. E-mail: and

4These authors contributed equally to this work.

Received 17 August 2008; Revised 30 October 2008; Accepted 6 November 2008; Published online 9 January 2009.


Many major rival models of the origin of the Hindu caste system co-exist despite extensive studies, each with associated genetic evidences. One of the major factors that has still kept the origin of the Indian caste system obscure is the unresolved question of the origin of Y-haplogroup R1a1*, at times associated with a male-mediated major genetic influx from Central Asia or Eurasia, which has contributed to the higher castes in India. Y-haplogroup R1a1* has a widespread distribution and high frequency across Eurasia, Central Asia and the Indian subcontinent, with scanty reports of its ancestral (R*, R1* and R1a*) and derived lineages (R1a1a, R1a1b and R1a1c). To resolve these issues, we screened 621 Y-chromosomes (of Brahmins occupying the upper-most caste position and schedule castes/tribals occupying the lower-most positions) with 55 Y-chromosomal binary markers and seven Y-microsatellite markers and compiled an extensive dataset of 2809 Y-chromosomes (681 Brahmins, and 2128 tribals and schedule castes) for conclusions. A peculiar observation of the highest frequency (up to 72.22%) of Y-haplogroup R1a1* in Brahmins hinted at its presence as a founder lineage for this caste group. Further, observation of R1a1* in different tribal population groups, existence of Y-haplogroup R1a* in ancestors and extended phylogenetic analyses of the pooled dataset of 530 Indians, 224 Pakistanis and 276 Central Asians and Eurasians bearing the R1a1* haplogroup supported the autochthonous origin of R1a1 lineage in India and a tribal link to Indian Brahmins. However, it is important to discover novel Y-chromosomal binary marker(s) for a higher resolution of R1a1* and confirm the present conclusions.   

Peopling of India: genetic studies

27 March 2009

A set of articles on genetics and peopling of India by Chaubey et al including a reply to  Clyde Winters.

Conclusion: autochthonous, indigenous nature of the peopling of India.

Evolutionary Biology Research article BioMed Central Phylogeography of mtDNA haplogroup R7 in the India...

Int J Hum Genet, 8(1-2): 41-50 (2008) Language Shift by Indigenous Population: A Model Genetic Study

Correspondence Did the Dravidian speakers originate in Africa?

Phylogenetics and systematics Peopling of South Asia: investigating the caste–tribe continuum in India

The Indian origin of paternal haplogroup R1a1* substantiates the autochthonous origin of Brahmins and the caste system by Swarkar Sharma et al., Journal of Human Genetics (2009) 54, 47-55

Genes, archaeology and language: resources compiled by M. Kelkar (March 2009)

Ethnography of ancient India by Robert Shafer (1954)

Peopling of India: Genetics markers speak out!

 The powerpoint presentation is on 14 slides. 

Gyaneshwer Chaubey (Presented on 24 October 2008, Conference on Vedic River Sarasvati and Hindu Civilization, India International Centre, New Delhi)

Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia

*Corresponding author:

Gyaneshwer Chaubey

Department of Evolutionary Biology,

Tartu University and Estonian Biocentre

Riia 23

Tartu, 51010


Tel.: (372) 7 375 052

Fax: (372) 7 420 194




Enormous amount of cultural and biological versatility is present in flora and fauna of Indian subcontinent, establishing its significance to study the diversity and population histories. Our results indicate that the tribal as well as caste populations of Indian subcontinent practicing a very high level of endogamy albeit they live in a close proximity and share the ritual customs. The present caste and tribal populations largely have a common stock of maternal as well as paternal Pleistocene heritage. They make a distinct cluster with other continental populations, advocating an in-situ demographic expansion just after the first arrival of modern humans from Africa. Genetic data doesn’t support any major influx to subcontinent in recent time and gainsay Aryan-invasion theory, nonetheless, it support Out-of-India theory. Indigenous origin of caste system is more plausible. Overall, our comprehensive study suggests that the several evolutionary forces (founder effects, gene flow and genetic drift) and factors (geographical, linguistic and cultural barriers) have produced the current phylogeography of present Indian gene pool.


By associating archaeological, linguistic and known historical events (such as the migrations of populations) with the variations in the presence of particular genetic sequences inside populations, researchers are often able to trace the ancestry of a particular group of people and find previously unknown genetic relations between populations. Major demographic events (population migrations, bottlenecks and expansions) leave imprints, in the form of altered gene frequencies, on the collective human genome. Because these imprints are transmitted to succeeding generations, the modern human genome contains an indelible record of our evolutionary past. The deeper we go into it, the more interesting and informative it becomes. As more genetic loci are examined in populations throughout the world, our evolutionary history should be largely decipherable. These mutations allow the tracing of both paternal (Y chromosome) and maternal (mtDNA) genealogies. Use of several markers of these genomes can establish a relation between different individuals and by using molecular approaches and statistical analyses one can draw several informative evolutionary trees. These uniparental markers were established as the best tools to infer prehistorical movement of any population(s). Another important question in population genetics is identifying the best predictors of genetic relationships among human populations. Several studies indicate strong correlations between genetic and linguistic relationships among globally distributed human populations. At the subcontinental scale, correlations between genetic variation and linguistic or geographic variation differ substantially.

Human social organization can deeply affect levels of genetic diversity. This fact implies that genetic information can be used to study social structures, which is the basis of ethnogenetics. India is a conglomeration of various ethnicities with 4693 communities, 325 languages, 25 scripts and numerous endogamous groups (Singh KS. 1997,2002). It is a home of several tribal and caste pockets which represent different genetic isolates and thus provides unique wealth to understand human evolution. These autochthonous populations reveal striking diversities in terms of language, marriage practices as well as in their genetic architecture. The social structure of the Indian population is governed by the hierarchical caste system. Most contemporary nontribal population of India belongs to Hindu religious fold and are arranged in the form of main caste classes viz. Brahmins, Kshatriya, Vyasa and Shudra. All the caste and tribes follow a strict endogamy (although, the permeability varies at different levels) and inside each and every castes there are many subclanes which are purely exogamous, for example ‘Gotra’ system.

The study of peopling of India is considered as ‘centroid’ to understand the early human prehistory, because it is proposed as a corridor of migration for Anatomically Modern Human (AMH) from Africa to Australia during late Pleistocene. Since, last ten years many genetic studies have given a large contribution to explore the incredible diversity of Indian subcontinent (Bamshad et al. 1998,2001; Kivisild et al. 1999, 2003; Cordaux et al. 2003,2004; Metspalu et al. 2004; Palanichamy et al. 2004; Sahoo et al. 2006; Sengupta et al. 2006; Sun et al. 2006; Chaubey et al. 2007,2008a,b). After the African exodus of humans there was an in-situ development of lineages as confirmed by numbers of deep-rooting mtDNA lineages emerging from the basal nodes of both superhaplogroups M and N (including R) (Metspalu et al. 2004; Thangaraj et al. 2006; Petraglia 2007). These deep-rooting mtDNA haplogroups are spread over the linguistic and other cultural borders confirming to the general autochthonous diversification of the Indian maternal gene pool and hence, the common Paleolithic origin for the people that today speak diverse languages and belong to different castes and tribes (Metspalu et al. 2004; Palanichamy et al. 2004; Sun et al. 2006; Thangaraj et al. 2006; Chaubey et al. 2008b). In recent years the increased resolution of genetic markers revealed new insights about the peopling of India and their dispersal. However, there are several issues such as origin of caste system, segregation of gotra and several historical issues which need to be testified.

Origin of social system and language groups

The reach of modern humans to Indian subcontinent through southern dispersal followed by in-situ differentiation led them to put their footsteps in different parts of India. The finding of several Mesolithic sites suggests the favorable climate and a rapid expansion of modern humans all over the subcontinent (Mishra. 2001). This process directed towards the settlement of humans in many unoccupied areas and the expansion was supported by wetter climate and abundance of diversity of plants and animals (Petragila and Allchin. 2007).  The increased food supply helped the hunterer and gatherer societies to stay at a place, resulting the advent of communal system. Agricultural system helped to amalgamate people in many small groups. One important aspect of the Indian social system, which makes substantial impact on the inferences one can make from the caste/tribal genetic variation, is that the definition of the scheduled caste has not been very clear. Specifically the scheduled tribes are gradually incorporated into the caste system as scheduled castes (Chaubey et al. 2007). The social uplifting process enhance gradual absorption of tribal populations in the caste system (for details see Chaubey et al. 2007,2008a). Above processes divided people in to several small pockets, initiating the formation of many castes and tribes and later sub-caste and sub-tribes. Consequently, the social behavior came in to the existence which has given rise a new system called endogamy. These clanes started practicing a marriage restriction within endogamous groups, having several exogamous sub-clanes. Such processes created a high level of strict endogamy in Indian populace in which the populations do not share genes even though they live at the same social level and exchange the rituals and other traditional occupations with one another and maintain their unique identity.

There are the four main language families spoken in India. Largest group, Indo-Europeans are prevalent in northern, central and western India. The second largest, the Dravidian family, covers the majority of the languages in the south. Austro-Asiatic speakers live mainly in east while Tibeto-Burmans resides in north eastern region. Most of the Indo-European speakers belong to castes, whereas the majority of the tribal populations speak languages from the other three families. Dravidian speaking populations also have the same type of caste hierarchy as in Indo-European. Indo-European and Dravidian largely share the same maternal and paternal genepool (Chaubey et al. 2008b). Additionally, the language shift phenomenon also shaped the present language phyla of Indian subcontinent (for detailed see Chaubey et al. 2008a). Thus, it is not wise to relate the initial Palaeolithic settlers of India on the basis of certain linguistic affiliations because language groups are much younger than deeply rooted genetic lineages. Origin of Austro-Asiatic groups is not very clear yet. There are two rival models about their origin, one suggest their origin in South east Asia and further migration to India (Diamond and Bellwood 2003; Sengupta et al. 2006; Sahoo et al. 2006), while other advocate their migration from Africa as a first settler (Basu et al. 2003; Kumar et al. 2007). Studies on mtDNA diversity have shown that the Austro-Asiatic speakers from Southeast Asia and the Indian subcontinent, carry mtDNAs of different stocks (Black et al. 2006; Chaubey et al. 2008a,b). Similarly, the Indian tribes speaking Austro-Asiatic language harbour the same autochthonous mtDNA haplogroup composition as the Indo European and Dravidic groups of India (Metspalu et al. 2004; Chaubey et al. 2008a,b). In contrast, the AA speaking populations of Indian and Southeast Asian’s Y chromosomes share a common marker, M95, which defines a single branch (O2a) of haplogroup O. Haplogroup O distribution and frequency put forward its origin further East to Indian subcontinent so, it is more likely that O2a originated in South east Asia and was brought by Austro-Asiatic speakers to India.


Origin of caste system and Indo-Aryan invasion

Although, there is a universal concurrence that Indian caste and tribal populations share a common late Pleistocene maternal as well as paternal ancestry in India (Kivisild et al. 2003), some studies on the Y-chromosome markers have suggested a recent, substantial invasion from Central or West Eurasia (Bamshad et al. 2001; Cordaux et al. 2004). The tribal and caste populations have been suggested to derive from different stocks (Cordaux 2004). A recent series of papers that claim to have traced the origins of the caste system to male-mediated, Indo-Aryan invasion that pushed indigenous Dravidian speaking populations southwards, and established Indo-Aryans at the top of the caste hierarchy (Bamshad et al. 2001; Quintana-Murci et al. 2001; Basu et al. 2003; Cordaux et al. 2004).  This is supported by analyses of maternally-inherited mitochondrial DNA that shows that Indian caste groups, regardless of rank, are more closely related to Asians and most dissimilar from Africans (Bamshad et al. 2001).  In contrast, the paternally-inherited Y-chromosome tells a different story while lower castes are still more similar to Asians, upper castes are more similar to Europeans. After these papers a trend started in population genetics studies. Most of the researches, either they have supporting datasets or not, started adding the Indo-Aryan invasion, assuming it as a universal solid fact (Quintana-Murci et al. 2004; Sharma et al. 2005; Thanseem et al. 2006; Zerjal et al. 2007).

The recent high resolution analyses on Y-chromosomal as well as mtDNA data (Fig.1,2) consistently suggest mainly a South Asian indigenous origin for Indian caste communities and hence disagree with any major influx, from regions north and west of India, of people associated either with the development of agriculture or the spread of the Indo-Aryan language family (Metspalu et al. 2004; Sahoo et al. 2006; Sengupta et al. 2006; Chaubey et al. 2007,2008a,b). The maternal Indian haplogroups shows an autochthonous origin (Thangaraj et al. 2006). All the haplogroups emerge from the basal node and they are deeply rooted (Fig.1). However, a West Eurasian and East Asian sharing of haplogroups are also observed in Indian subcontinent (Fig. 2), but most of them share their ancestry to India subcontinent well beyond the Last Glacial Maximum. In paternal genepool both Indo-European as well as Dravidian speakers show a high combined frequency of haplogroups C5, L, H, and R2 which are autochthonous to the subcontinent (Sahoo et al. 2006; Sengupta et al. 2006). The total frequency of these four haplogroups outside of India is marginally low and the dispersion of these haplogroups from India was due to several pre-historical/historial episodes which corroborate out of India theory (Fig.1). Furthermore, haplogroups E, I, G, J*, and R1* have high frequency in the Near East among the Turks and in Central Asians, but they are absent in India (Sahoo et al. 2006; Sengupta et al. 2006). Similarly, haplogroups C3, D, N, and O are specific to Central and Southeast Asia (Fig.1). Thus, only haplogroups J2 and R1a have interregional frequency patterns, but their associated high Y-STR diversity and variance attest their ancient split from Europeans and Central Asians, followed by a local expansion. Hence, the current data do not support a model that says a recent genetic input from Central Asia to explain the present genetic variation of India. It also suggests an autochthonous entrenched caste origin which goes back to pre-Vedic period. Based on occupation caste system was organized and that was meant to help in development of society by forming the division of labour. 


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Figure Legends:

Figure 1. The global maternal (mtDNA) (panel a) and paternal (Y-chromosome) (panel b), genepool allocation. Based on specific mutations a person assign for a precise haplogroup and phylogenetic tree drawn among different continental populations which illustrate their correlations. This tree is adapted from Chaubey et al. (2007) and redrawn. The uniqueness of Indian populations is highlighted.


Figure 2.  The deep rooting branching of autochthonous lineages, specific to India subcontinent and other lineages shared with West Eurasians and East Asias. 



The supereruption of Mt. Toba ca. 74k years ago did NOT wipe out the settlements in India. What began as a maritime civilization was a continuum – note Michael Petraglia et al..


Early maritime journey of mankind along IOC rim First exit out of Africa 150k-80k years ago, then Mt. Toba erupts

Mankind's continuing settlement in India ca. 80k years ago

Science 6 July 2007:
Vol. 317. no. 5834, pp. 114 - 116
DOI: 10.1126/science.1141564                                                                                             


Middle Paleolithic Assemblages from the Indian Subcontinent Before and After the Toba Super-Eruption

Michael Petraglia,1,2* Ravi Korisettar,3 Nicole Boivin,1 Christopher Clarkson,4 Peter Ditchfield,5 Sacha Jones,1 Jinu Koshy,3 Marta Mirazón Lahr,1 Clive Oppenheimer,6 David Pyle,7 Richard Roberts,8 Jean-Luc Schwenninger,5 Lee Arnold,8 Kevin White9

The Youngest Toba Tuff (YTT) eruption, which occurred in Indonesia 74,000 years ago, is one of Earth's largest known volcanic events. The effect of the YTT eruption on existing populations of humans, and accordingly on the course of human evolution, is debated. Here we associate the YTT with archaeological assemblages at Jwalapuram, in the Jurreru River valley of southern India. Broad continuity of Middle Paleolithic technology across the YTT event suggests that hominins persisted regionally across this major eruptive event.

1 Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge CB2 1QH, UK.
2 Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
3 Department of History and Archaeology, Karnatak University, Dharwad 580 003, India.
4 School of Social Science, University of Queensland, St. Lucia, Queensland 4072, Australia.
5 Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK.
6 Department of Geography, University of Cambridge, Downing Place, Cambridge CB2 3EN, UK.
7 Department of Earth Sciences, University of Oxford, Parks Road, Oxford OX1 3PR, UK.
8 GeoQuEST Research Centre, School of Earth and Environmental Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia.
9 Department of Geography, University of Reading, Whiteknights, Reading RG6 6AB, UK.

* To whom correspondence should be addressed. E-mail:

The Youngest Toba Tuff (YTT) eruption of 74,000 years ago (74 ka) was Earth's largest volcanic event in the past two million years (13). It was two orders of magnitude larger (in erupted mass) than the largest known historic eruption, that of Tambora, also in Indonesia (4). The YTT involved the eruption of a minimum of 2800 km3 (7 x 1015 kg) of magma, of which at least ~800 km3 was transported in atmospheric ash plumes that blanketed an area from the South China Sea to the Arabian Sea (2, 3). Its impact on Earth's atmosphere and climate (57) and on local animal and plant populations remains a matter of contention (5, 712).

The Indian subcontinent contains extensive YTT deposits (1315). Here we describe an archaeological sequence from south India that includes a substantial YTT layer and sheds light on the eruption's impact on climate, environments, and hominin populations. In the Kurnool District of Andhra Pradesh in southern India, stratified archaeological sites in the Jurreru River valley contain stone artifacts in association with faunal remains in caves, rockshelters, and open-air localities (16, 17) (Fig. 1). The archaeological record spans all periods of the Paleolithic. In addition, current mining activities have exposed tephra deposits over an area of 64 ha. Ash is, however, certainly buried over a wider area within the valley (fig. S1), and we estimate its total volume at 7 ± 0.7 x 105 m3, based on the interpolation of 225 depth observations made at mining exposures.

Fig. 1. Location of Jwalapuram, archaeological sites, and tephra deposits. (A) Location of the Jwalapuram study area. (B) Key archaeological localities in the Kurnool District include the Upper Paleolithic caves of Billasurgum (1) (17) and Muchchatla Chintamanu Gavi (2) (16). Jwalapuram localities include 17 (3, Middle Paleolithic), 9 (4, Microlithic), 3 (5, Middle Paleolithic), 20 (6, Middle Paleolithic), 21 (7, Middle Paleolithic), and Tank (8, Acheulean). [View Larger Version of this Image (21K GIF file)]


We conducted electron probe microanalysis (EPMA) of volcanic glass shards from the Jwalapuram tephra to compare their geochemical signatures with those of the Older Toba Tuff (OTT, dated to ~840 ka) and the Middle Toba Tuff (MTT, dated to ~500 ka) (4). The results show that the Jwalapuram ash is a distal deposit of the YTT (figs. S3 and S4), based on its close similarities with proximal deposits of YTT in Sumatra and with previously characterized distal occurrences in India (13, 14, 18).

Jwalapuram locality 3 preserves more than 7.5 m of sedimentary deposits, including a 2.55-m-thick deposit of ash, and a sequence of lithic artifacts that straddle the ash layer (fig. S2). Soft sediment deformation structures suggest that the tephra initially accumulated on a wet clay substrate, probably in a lacustrine environment. The abrupt transition from light gray ash to an orange (but still ash-rich) silt horizon immediately above the ash sequence represents a major change in depositional regime. We interpret this as evidence that the lake dried up soon after the ash fall, possibly during the onset of glacial conditions in oxygen isotope stage 4.

The stone tool assemblages were found in trenches placed across the landscape (that is, at Jwalapuram localities 3, 17, and 21). At Jwalapuram locality 3, we used optical dating to obtain burial ages for sediment samples from archaeological layers above (JLP-380) and below (JLP3A-200) the ash. Ages of 77 ± 6 and 74 ± 7 ka were obtained for the pre- and post-Toba samples, respectively (tables S2 and S3). These indicate that the dated quartz grains were last exposed to sunlight shortly before and after the Toba eruption, with no substantial hiatus in sediment deposition.

The pre-Toba archaeological layer at locality 3, chronologically bracketed by the ~74,000-year-old YTT and the underlying sediments dated to 77 ± 6 ka, contained 215 artifacts as well as a piece of red ochre that shows striations due to use. This stone tool assemblage consists of faceted unidirectional cores made from limestone (60%), quartzite (22%), and chert (11%), with elongate parallel flake scars indicating the production of blades. Frequent preparation of flake platforms is seen, suggesting that these flakes were struck from prepared cores similar to those found at the site. A small proportion of flakes were retouched into notches, informal scrapers, retouched blades, and a burin (Fig. 2). This pre-Toba assemblage falls within the Indian Middle Paleolithic (19, 20).

Fig. 2. Selected Jwalapuram artifacts that pre-date (locality 3) and post-date (localities 3, 17, and 21) the YTT. Above the ash: 1, bladelet core with faceted platform; 2 and 3, flake cores with faceted platforms; 4, side scraper; 5, utilized flake; 6, atypical end scraper on blade; 7, side and end scraper; 8, utilized flake; 9, broken blade; 10, broken blade. Below the ash: 11, notch and burin; 12, ventrally retouched side scraper; 13, side scraper on broken blade; 14, side scraper on ridge straightening flake; 15, ventrally retouched side and end scraper; 16, ventrally retouched scraper; 17, notch; 18, ground ochre. Scale bar, 1 cm. [View Larger Version of this Image (58K GIF file)]


The post-Toba layer at locality 3, optically dated to 74 ± 7 ka, contains an assemblage of 108 stone artifacts that occur throughout the orange sandy stratum; a further 37 and 131 artifacts were recovered from the same matrix above the ash at localities 17 and 21, respectively. The technology and tool types at these three post-ash localities are similar to those found in the pre-ash assemblage, involving faceted unidirectional cores with some blade scars (Fig. 2). However, raw materials were used in different frequencies (limestone 31%, chert 28%, chalcedony 23%, and quartzite 12%). Most flakes are short and squat, although a few blades and bladelets (<2 cm in length) are also present (<5%), along with a bladelike core and a small bidirectional blade core with a faceted platform (Fig. 2). Retouched flakes above the ash include notches and side and end scrapers. Burins and bipolar reduction are also present, but rare. This combination of tool types is common in Late Pleistocene assemblages of India, usually identified as Middle Paleolithic (19, 20).

We provide here firm chronological evidence that hominins were present in the Jurreru River valley, south India, immediately before and after the YTT eruption. Analyses of the archaeological industries recovered from the site indicate a strong element of technological continuity between the pre- and post-Toba assemblages. Together with the presence of faceted unidirectional and bidirectional bladelike core technology, these pre- and post-Toba industries suggest closer affinities to African Middle Stone Age traditions (such as Howieson's Poort) than to contemporaneous Eurasian Middle Paleolithic ones that are typically based on discoidal and Levallois techniques (Fig. 3). The coincidence of (i) evidence of hominins flexible enough to exhibit continuity through a major eruptive event, (ii) technology more similar to the Middle Stone Age than the Middle Paleolithic, and (iii) overlap of the Jwalapuram artifact ages with the earlier end of the most commonly cited genetic coalescence dates (2123) may suggest the presence of modern humans in India at the time of the YTT event. This interpretation would be consistent with a southern route of dispersal of modern humans from the Horn of Africa (24); the latter, however, will remain speculative until other Middle Paleolithic sites in the Indian subcontinent and Arabian Peninsula (25) are excavated and dated.

Fig. 3. Discriminant analysis of 670 cores from Middle Stone Age (MSA), Middle Paleolithic (MP), and early Upper Paleolithic (UP) contexts in Africa, the Levant, and India. Functions 1 and 2 account for 70.1% of the variation. Functions 1 to 3 are all significant at the P = < 0.0005 level. JWP, Jwalapuram; KRM, Klasies River Mouth. [View Larger Version of this Image (30K GIF file)]


References and Notes

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  • 26. This project was funded by the Natural Environment Research Council (NERC) (Environmental Factors in the Chronology of Human Evolution and Dispersal program), the Leakey Foundation, the NERC Arts and Humanities Research Council Oxford Radiocarbon Accelerator Dating Service, the McDonald Institute for Archaeological Research, the Australian Research Council, and Queens' College (Cambridge). We thank the Archaeological Survey of India for permission to conduct the field work and the other participants in the project for their contributions to the excavations and artifact cataloguing. We thank C. Chesner for providing tephra samples; C. Hayward for technical support on the electron microprobe; and R. Foley, Z. Jacobs, T. Kivisild, and P. Mellars for useful discussions.


Modern humans reached India early

N. Gopal Raj (The Hindu, Date:09/07/2007 )

Evidence found in excavations by international team of scientists at Jwalapuram in Kurnool district of Andhra Pradesh

THIRUVANANTHAPURAM: In the course of archaeological excavations at Jwalapuram in Kurnool district of Andhra Pradesh, an international team of scientists has found evidence that anatomically modern humans are likely to have reached India before a massive volcanic eruption in what is today Indonesia occurred tens of thousands of years ago.


The “super-eruption” of the Toba volcano in Sumatra some 74,000 years ago was the largest volcanic event to have occurred in the last two million years and the ash thrown up high into the atmosphere by that cataclysmic explosion reached India too, said Ravi Korisettar of the Department of History and Archaeology at Karnatak University in Dharwad, Karnataka.

During five years of excavations at Jwalapuram, Indian, British, and Australians scientists unearthed fine stone flakes that had been turned into tools for various purposes.

The stone tools were to be found in layers of earth above as well as below the fine ash from the Toba super-eruption, the scientists noted in a paper published in the latest issue of the journal Science.

“Volcanic winter”

It had been thought that the vast amounts of volcanic ash flung into the atmosphere by the eruption could have blocked sunlight and produced a “volcanic winter” that decimated the humans living then. But the evidence from the Jwalapuram excavations, however, suggests that the volcanic eruption did not have such a catastrophic impact on the early human population there.

Stone tools

The stone tools also pointed to a more exciting possibility. The stone tool assemblages found in Jwalapuram were “very similar to ones that we see produced in Africa at the same time,” said Michael Petraglia of the Leverhulme Centre for Human Evolutionary Studies at the University of Cambridge in the U.K, the first author of the paper.

Those stone tools in Africa had been produced by modern humans.

“Closer affinities”

In the Science paper, the researchers noted that the techniques used for making the stone tools at Jwalapuram suggested “closer affinities” to African Middle Stone Ages traditions than to contemporaneous Eurasian ones. T his finding is significant because genetic studies of tell-tale patterns in the DNA of people living in various parts of the world have supported the view that all modern humans arose in Africa.

It is believed that these modern humans then migrated out of Africa and settled all across the globe.

“So what we are saying is that modern humans probably dispersed from Africa into India at a very early date, earlier than anyone has suggested before,” Dr. Petraglia told this correspondent.

There is a hypothesis that modern humans could have taken the “southern route of dispersal,” utilising the coastlines to travel from Africa, through Arabia, across the Indian subcontinent and then into South-East Asia and finally into Australia, he said. The presence of modern humans in India at the time of the Toba super-eruption would be consistent with humans having used the southern route, but would remain speculative till further excavations were carried out in the Indian subcontinent and Arabian peninsula, remarked the scientists in their journal paper.

Key role

India has a played a key role in the migration of modern humans out of Africa, says K. Thangaraj of the Centre for Cellular and Molecular Biology at Hyderabad. In a paper published in Science two years ago, Dr. Thangaraj and others held that genetic lineages to be found among Andaman islanders supported an out-of-Africa migration by modern humans some 50,0000 to 70,000 years ago.

Archaeological data

Dr. Korisettar is, however, sceptical about modern humans opting for a coastal route for their migration.

There was currently no archaeological evidence of such ancient human migrations along India’s west coast and into southern Tamil Nadu. Rather, the available archaeological data favoured a continental route whereby early humans came through the Bolan and Khyber passes to the north-western parts of the Indian subcontinent and then into Rajasthan before dispersing to other parts of the country, he added.

Peopling of India: Abstracts of genetic studies


The grand narrative which emerges from these studies is clear and emphatic. Peopling of India was an indigenous and autochthonous evolution. There are markers of gene flows OUT of India. All so-called jaati or vanavaasi groups are of the same gene pool of India. This is consistent with the work, Indus script encodes mleccha speech which demonstrates the essential semantic unity of all bharatiya or Indian languages in a linguistic area of Sarasvati civilization from ca. 7500 BCE.


I shall be grateful for information on any specific, additional studies should be added to this compendium. Also, comments, suggestions and conclusions which can be drawn  -- and presented in simple terms for incorporation in school/college text books – excerpted or deduced from the intensely technical nature of the genetic study results.




Ann Hum Biol. 2005 Mar-Apr;32(2):154-62

A population genetics perspective of the Indus Valley through uniparentally-inherited markers.

McElreavey K, Quintana-Murci L.

Reproduction, Fertility and Populations, Institut Pasteur, Paris, France.

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.

PMID: 16096211 [PubMed - indexed for MEDLINE]

Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of central asian pastoralists.

Sengupta S, Zhivotovsky LA, King R, Mehdi SQ, Edmonds CA, Chow CE, Lin AA, Mitra M, Sil SK, Ramesh A, Usha Rani MV, Thakur CM, Cavalli-Sforza LL, Majumder PP, Underhill PA

Although considerable cultural impact on social hierarchy and language in South Asia is attributable to the arrival of nomadic Central Asian pastoralists, genetic data (mitochondrial and Y chromosomal) have yielded dramatically conflicting inferences on the genetic origins of tribes and castes of South Asia. We sought to resolve this conflict, using high-resolution data on 69 informative Y-chromosome binary markers and 10 microsatellite markers from a large set of geographically, socially, and linguistically representative ethnic groups of South Asia. We found that the influence of Central Asia on the pre-existing gene pool was minor. The ages of accumulated microsatellite variation in the majority of Indian haplogroups exceed 10,000-15,000 years, which attests to the antiquity of regional differentiation. Therefore, our data do not support models that invoke a pronounced recent genetic input from Central Asia to explain the observed genetic variation in South Asia. R1a1 and R2 haplogroups indicate demographic complexity that is inconsistent with a recent single history. Associated microsatellite analyses of the high-frequency R1a1 haplogroup chromosomes indicate independent recent histories of the Indus Valley and the peninsular Indian region. Our data are also more consistent with a peninsular origin of Dravidian speakers than a source with proximity to the Indus and with significant genetic input resulting from demic diffusion associated with agriculture. Our results underscore the importance of marker ascertainment for distinguishing phylogenetic terminal branches from basal nodes when attributing ancestral composition and temporality to either indigenous or exogenous sources. Our reappraisal indicates that pre-Holocene and Holocene-era--not Indo-European--expansions have shaped the distinctive South Asian Y-chromosome landscape.


Proc Natl Acad Sci U S A. 2006 Jan 24;103(4):843-8. Epub 2006 Jan 13

A prehistory of Indian Y chromosomes: evaluating demic diffusion scenarios.

Sahoo S, Singh A, Himabindu G, Banerjee J, Sitalaximi T, Gaikwad S, Trivedi R, Endicott P, Kivisild T, Metspalu M, Villems R, Kashyap VK.

National DNA Analysis Centre, Central Forensic Science Laboratory, Kolkata 700014, India.

Understanding the genetic origins and demographic history of Indian populations is important both for questions concerning the early settlement of Eurasia and more recent events, including the appearance of Indo-Aryan languages and settled agriculture in the subcontinent. Although there is general agreement that Indian caste and tribal populations share a common late Pleistocene maternal ancestry in India, some studies of the Y-chromosome markers have suggested a recent, substantial incursion from Central or West Eurasia. To investigate the origin of paternal lineages of Indian populations, 936 Y chromosomes, representing 32 tribal and 45 caste groups from all four major linguistic groups of India, were analyzed for 38 single-nucleotide polymorphic markers. Phylogeography of the major Y-chromosomal haplogroups in India, genetic distance, and admixture analyses all indicate that the recent external contribution to Dravidian- and Hindi-speaking caste groups has been low. The sharing of some Y-chromosomal haplogroups between Indian and Central Asian populations is most parsimoniously explained by a deep, common ancestry between the two regions, with diffusion of some Indian-specific lineages northward. The Y-chromosomal data consistently suggest a largely South Asian origin for Indian caste communities and therefore argue against any major influx, from regions north and west of India, of people associated either with the development of agriculture or the spread of the Indo-Aryan language family. The dyadic Y-chromosome composition of Tibeto-Burman speakers of India, however, can be attributed to a recent demographic process, which appears to have absorbed and overlain populations who previously spoke Austro-Asiatic languages.

PMID: 16415161 [PubMed - indexed for MEDLINE]

PMCID: PMC1347984


BMC Genet. 2006 Aug 7;7:42

Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA.

Thanseem I, Thangaraj K, Chaubey G, Singh VK, Bhaskar LV, Reddy BM, Reddy AG, Singh L.

Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad- 500 007, India.

BACKGROUND: India is a country with enormous social and cultural diversity due to its positioning on the crossroads of many historic and pre-historic human migrations. The hierarchical caste system in the Hindu society dominates the social structure of the Indian populations. The origin of the caste system in India is a matter of debate with many linguists and anthropologists suggesting that it began with the arrival of Indo-European speakers from Central Asia about 3500 years ago. Previous genetic studies based on Indian populations failed to achieve a consensus in this regard. We analysed the Y-chromosome and mitochondrial DNA of three tribal populations of southern India, compared the results with available data from the Indian subcontinent and tried to reconstruct the evolutionary history of Indian caste and tribal populations. RESULTS: No significant difference was observed in the mitochondrial DNA between Indian tribal and caste populations, except for the presence of a higher frequency of west Eurasian-specific haplogroups in the higher castes, mostly in the north western part of India. On the other hand, the study of the Indian Y lineages revealed distinct distribution patterns among caste and tribal populations. The paternal lineages of Indian lower castes showed significantly closer affinity to the tribal populations than to the upper castes. The frequencies of deep-rooted Y haplogroups such as M89, M52, and M95 were higher in the lower castes and tribes, compared to the upper castes. CONCLUSION: The present study suggests that the vast majority (> 98%) of the Indian maternal gene pool, consisting of Indio-European and Dravidian speakers, is genetically more or less uniform. Invasions after the late Pleistocene settlement might have been mostly male-mediated. However, Y-SNP data provides compelling genetic evidence for a tribal origin of the lower caste populations in the subcontinent. Lower caste groups might have originated with the hierarchical divisions that arose within the tribal groups with the spread of Neolithic agriculturalists, much earlier than the arrival of Aryan speakers. The Indo-Europeans established themselves as upper castes among this already developed caste-like class structure within the tribes.

PMID: 16893451 [PubMed - indexed for MEDLINE]

PMCID: PMC1569435



Curr Biol. 2004 Feb 3;14(3):231-5.


Independent origins of Indian caste and tribal paternal lineages.

Cordaux R, Aunger R, Bentley G, Nasidze I, Sirajuddin SM, Stoneking M.

Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

The origins of the nearly one billion people inhabiting the Indian subcontinent and following the customs of the Hindu caste system are controversial: are they largely derived from Indian local populations (i.e. tribal groups) or from recent immigrants to India? Archaeological and linguistic evidence support the latter hypothesis, whereas recent genetic data seem to favor the former hypothesis. Here, we analyze the most extensive dataset of Indian caste and tribal Y chromosomes to date. We find that caste and tribal groups differ significantly in their haplogroup frequency distributions; caste groups are homogeneous for Y chromosome variation and more closely related to each other and to central Asian groups than to Indian tribal or any other Eurasian groups. We conclude that paternal lineages of Indian caste groups are primarily descended from Indo-European speakers who migrated from central Asia approximately 3,500 years ago. Conversely, paternal lineages of tribal groups are predominantly derived from the original Indian gene pool. We also provide evidence for bidirectional male gene flow between caste and tribal groups. In comparison, caste and tribal groups are homogeneous with respect to mitochondrial DNA variation, which may reflect the sociocultural characteristics of the Indian caste society.

PMID: 14761656 [PubMed - indexed for MEDLINE]


Ann Hum Genet. 2004 Sep;68(Pt 5):453-60


Mitochondrial DNA diversity in tribal and caste groups of Maharashtra (India) and its implication on their genetic origins.

Baig MM, Khan AA, Kulkarni KM.

Population Biology Laboratory, Department of Zoology, Government Vidarbha Institute of Science and Humanities, Amravati, MS, India.

Genetic relationships among caste-groups are not uniform across the geographical regions of India. Many anthropologists have speculated on the tribal origin of some caste groups in Maharashtra and other states of India. To test this hypothesis, we used neutral mtDNA markers to study genetic relatedness among tribal and caste groups from Maharashtra. Descriptive statistics such as nucleotide diversity, gene diversity and average mismatches were found to be of the same magnitude. Phylogenetic network analysis exhibited a star-like expansion that may date back to the peopling of Eurasia, approximately 50,000 year ago. The reconstruction of mtDNA haplogroups showed that both the caste and tribal populations share similar branches of the tree. Also, the coalescence age estimation of caste and tribal populations suggests the persistence of maternal lineages with their root in early late Pleistocene. Our mtDNA analyses show some preliminary and significant evidence for the origin of prehistoric tribal and hierarchical caste societies of Maharashtra.

PMID: 15469422 [PubMed - indexed for MEDLINE]


Am J Phys Anthropol. 2006 Sep;131(1):84-97


Phylogeography of mitochondrial DNA and Y-chromosome haplogroups reveal asymmetric gene flow in populations of Eastern India.

Sahoo S, Kashyap VK.

National DNA Analysis Centre, Central Forensic Science Laboratory, Kolkata 700 014, India.

Polymorphisms in mitochondrial (mt) DNA and Y-chromosomes of seven socially and linguistically diverse castes and tribes of Eastern India were examined to determine their genetic relationships, their origin, and the influence of demographic factors on population structure. Samples from the Orissa Brahmin, Karan, Khandayat, Gope, Juang, Saora, and Paroja were analyzed for mtDNA hypervariable sequence (HVS) I and II, eight Y-chromosome short tandem repeats (Y-STRs), and lineage-defining mutations diagnostic for Indian- and Eurasian-specific haplogroups. Our results reveal that haplotype diversity and mean pairwise differences (MPD) was higher in caste groups of the region (>0.998, for both systems) compared to tribes (0.917-0.996 for Y-STRs, and 0.958-0.988 for mtDNA haplotypes). The majority of paternal lineages belong to the R1a1, O2a, and H haplogroups (62.7%), while 73.2% of maternal lineages comprise the Indian-specific M*, M5, M30, and R* mtDNA haplogroups, with a sporadic occurrence of West Eurasian lineages. Our study reveals that Orissa Brahmins (a higher caste population) have a genetic affinity with Indo-European speakers of Eastern Europe, although the Y-chromosome data show that the genetic distances of populations are not correlated to their position in the caste hierarchy. The high frequency of the O2a haplogroup and absence of East Asian-specific mtDNA lineages in the Juang and Saora suggest that a migration of Austro-Asiatic tribes to mainland India was exclusively male-mediated which occurred during the demographic expansion of Neolithic farmers in southern China. The phylogeographic analysis of mtDNA and Y-chromosomes revealed varied ancestral sources for the diverse genetic components of the populations of Eastern India. 2006 Wiley-Liss, Inc.

PMID: 16485297 [PubMed - indexed for MEDLINE]


Genome Res. 2001 Jun;11(6):994-1004


Genetic evidence on the origins of Indian caste populations.

Bamshad M, Kivisild T, Watkins WS, Dixon ME, Ricker CE, Rao BB, Naidu JM, Prasad BV, Reddy PG, Rasanayagam A, Papiha SS, Villems R, Redd AJ, Hammer MF, Nguyen SV, Carroll ML, Batzer MA, Jorde LB.

Department of Pediatrics, University of Utah, Salt Lake City, Utah 84112, USA.

The origins and affinities of the approximately 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 approximately 265 males from eight castes of different rank to approximately 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 (approximately 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.

PMID: 11381027 [PubMed - indexed for MEDLINE]

PMCID: PMC311057


Am J Hum Genet. 2003 Feb;72(2):313-32. Epub 2003 Jan 20


The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations.

Kivisild T, Rootsi S, Metspalu M, Mastana S, Kaldma K, Parik J, Metspalu E, Adojaan M, Tolk HV, Stepanov V, Gölge M, Usanga E, Papiha SS, Cinnioğlu C, King R, Cavalli-Sforza L, Underhill PA, Villems R.

Institute of Molecular and Cell Biology, Tartu University, Tartu, Estonia.

Two tribal groups from southern India--the Chenchus and Koyas--were analyzed for variation in mitochondrial DNA (mtDNA), the Y chromosome, and one autosomal locus and were compared with six caste groups from different parts of India, as well as with western and central Asians. In mtDNA phylogenetic analyses, the Chenchus and Koyas coalesce at Indian-specific branches of haplogroups M and N that cover populations of different social rank from all over the subcontinent. Coalescence times suggest early late Pleistocene settlement of southern Asia and suggest that there has not been total replacement of these settlers by later migrations. H, L, and R2 are the major Indian Y-chromosomal haplogroups that occur both in castes and in tribal populations and are rarely found outside the subcontinent. Haplogroup R1a, previously associated with the putative Indo-Aryan invasion, was found at its highest frequency in Punjab but also at a relatively high frequency (26%) in the Chenchu tribe. This finding, together with the higher R1a-associated short tandem repeat diversity in India and Iran compared with Europe and central Asia, suggests that southern and western Asia might be the source of this haplogroup. Haplotype frequencies of the MX1 locus of chromosome 21 distinguish Koyas and Chenchus, along with Indian caste groups, from European and eastern Asian populations. Taken together, these results show that Indian tribal and caste populations derive largely from the same genetic heritage of Pleistocene southern and western Asians and have received limited gene flow from external regions since the Holocene. The phylogeography of the primal mtDNA and Y-chromosome founders suggests that these southern Asian Pleistocene coastal settlers from Africa would have provided the inocula for the subsequent differentiation of the distinctive eastern and western Eurasian gene pools.

PMID: 12536373 [PubMed - indexed for MEDLINE]

PMCID: PMC379225


Ann Hum Genet. 2005 Nov;69(Pt 6):680-92


Diversity and divergence among the tribal populations of India.

Watkins WS, Prasad BV, Naidu JM, Rao BB, Bhanu BA, Ramachandran B, Das PK, Gai PB, Reddy PC, Reddy PG, Sethuraman M, Bamshad MJ, Jorde LB.

Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.

Tribal populations of the Indian subcontinent have been of longstanding interest to anthropologists and human geneticists. To investigate the relationship of Indian tribes to Indian castes and continental populations, we analyzed 45 unlinked autosomal STR loci in 9 tribal groups, 8 castes, and 18 populations from Africa, Europe and East Asia. South Indian tribal populations demonstrate low within-population heterozygosity (range: 0.54 - 0.69), while tribal populations sampled further north and east have higher heterozygosity (range: 0.69 - 0.74). Genetic distance estimates show that tribal Indians are more closely related to caste Indians than to other major groups. Between-tribe differentiation is high and exceeds that for eight sub-Saharan African populations (4.8% vs. 3.7%). Telugu-speaking populations are less differentiated than non-Telugu speakers (F(ST): 0.029 vs. 0.079), but geographic distance was not predictive of genetic affinity between tribes. South Indian tribes show significant population structure, and individuals can be clustered statistically into groups that correspond with their tribal affiliation. These results are consistent with high levels of genetic drift and isolation in Indian tribal populations, particularly those of South India, and they imply that these populations may be potential candidates for linkage disequilibrium and association mapping.

PMID: 16266407 [PubMed - indexed for MEDLINE]


Hum Genet. 2004 Aug;115(3):221-9. Epub 2004 Jul 1


Directional migration in the Hindu castes: inferences from mitochondrial, autosomal and Y-chromosomal data.

Wooding S, Ostler C, Prasad BV, Watkins WS, Sung S, Bamshad M, Jorde LB.

Department of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT 84112-5330, USA.

Genetic, ethnographic, and historical evidence suggests that the Hindu castes have been highly endogamous for several thousand years and that, when movement between castes does occur, it typically consists of females joining castes of higher social status. However, little is known about migration rates in these populations or the extent to which migration occurs between caste groups of low, middle, and high social status. To investigate these aspects of migration, we analyzed the largest collection of genetic markers collected to date in Hindu caste populations. These data included 45 newly typed autosomal short tandem repeat polymorphisms (STRPs), 411 bp of mitochondrial DNA sequence, and 43 Y-chromosomal single-nucleotide polymorphisms that were assayed in more than 200 individuals of known caste status sampled in Andrah Pradesh, in South India. Application of recently developed likelihood-based analyses to this dataset enabled us to obtain genetically derived estimates of intercaste migration rates. STRPs indicated migration rates of 1-2% per generation between high-, middle-, and low-status caste groups. We also found support for the hypothesis that rates of gene flow differ between maternally and paternally inherited genes. Migration rates were substantially higher in maternally than in paternally inherited markers. In addition, while prevailing patterns of migration involved movement between castes of similar rank, paternally inherited markers in the low-status castes were most likely to move into high-status castes. Our findings support earlier evidence that the caste system has been a significant, long-term source of population structuring in South Indian Hindu populations, and that patterns of migration differ between males and females. Copyright 2004 Springer-Verlag

PMID: 15232732 [PubMed - indexed for MEDLINE]


Eur J Hum Genet. 2001 Sep;9(9):695-700


Y-chromosome SNP haplotypes suggest evidence of gene flow among caste, tribe, and the migrant Siddi populations of Andhra Pradesh, South India.

Ramana GV, Su B, Jin L, Singh L, Wang N, Underhill P, Chakraborty R.

Human Genetics Center, University of Texas, School of Public Health, Houston, Texas, TX 77030, USA.

From observations of lack of haplotype sharing based on Y-chromosome specific short tandem repeat (STR) loci, previous reports suggested negligible gene flow among different geographic populations of India. Using Single Nucleotide Polymorphism (SNP) sites in combination with STRs, we observed evidence of haplotype sharing across caste-tribe boundaries in South India. We examined 27 SNPs in the non-recombining region of the Y chromosome to investigate gene flow in 204 individuals belonging to three caste groups (Vizag Brahmins, Peruru Brahmins, Kammas), three tribes (Bagata, Poroja, Valmiki) and an additional group (the Siddis) of African ancestry. Principal component and AMOVA analyses show that the between group component of variation is non-significant (P>0.05), while that among populations within the caste and tribal groups is significant (P<0.001). In particular, the Valmikis and Siddis are close to the caste groups. Of a total of 11 distinct SNP-haplotypes observed, the two tribal groups (Bagata and Poroja) lack the haplotypes H4, H4A, H5A and H16, which are seen in the caste groups. In contrast, all three tribal groups exhibit the Southeast Asian haplotype H11 that is absent in the caste populations. The presence of haplotypes H4, H5, H14, and H16 in the Siddis indicate that they have assimilated considerable non-African admixture. The evidence of haplotype sharing between castes and tribes is also found when the H14 lineage was further subdivided by five STR loci. We conclude that even though these SNP-based Y-haplotypes are able to distinguish the populations, gene flow in these South Indian populations is not as negligible as that inferred from other studies based on Y-specific short tandem repeat markers.

PMID: 11571559 [PubMed - indexed for MEDLINE]


Hum Biol. 1996 Feb;68(1):1-28.


mtDNA variation in caste populations of Andhra Pradesh, India.

Bamshad M, Fraley AE, Crawford MH, Cann RL, Busi BR, Naidu JM, Jorde LB.

Department of Pediatrics, Health Sciences Center, University of Utah, Salt Lake City 84132, USA.

Various anthropological analyses have documented extensive regional variation among populations on the subcontinent of India using morphological, protein, blood group, and nuclear DNA polymorphisms. These patterns are the product of complex population structure (genetic drift, gene flow) and a population history noted for numerous branching events. As a result, the interpretation of relationships among caste populations of South India and between Indians and continental populations remains controversial. The Hindu caste system is a general model of genetic differentiation among endogamous populations stratified by social forces (e.g., religion and occupation). The mitochondrial DNA (mtDNA) molecule has unique properties that facilitate the exploration of population structure. We analyzed 36 Hindu men born in Andhra Pradesh who were unrelated matrilineally through at least 3 generations and who represent 4 caste populations: Brahmin (9), Yadava (10), Kapu (7), and Relli (10). Individuals from Africa (36), Asia (36), and Europe (36) were sampled for comparison. A 200-base-pair segment of hypervariable segment 2 (HVS2) of the mtDNA control region was sequenced in all individuals. In the Indian castes 25 distinct haplotypes are identified. Aside from the Cambridge reference sequence, only two haplotypes are shared between caste populations. Middle castes form a highly supported cluster in a neighbor-joining network. Mean nucleotide diversity within each caste is 0.015, 0.012, 0.011, and 0.012 for the Brahmin, Yadava, Kapu, and Relli, respectively. mtDNA variation is highly structured between castes (GST = 0.17; p < 0.002). The effects of social structure on mtDNA variation are much greater than those on variation measured by traditional markers. Explanations for this discordance include (1) the higher resolving power of mtDNA, (2) sex-dependent gene flow, (3) differences in male and female effective population sizes, and (4) elements of the kinship structure. Thirty distinct haplotypes are found in Africans, 17 in Asians, and 13 in Europeans. Mean nucleotide diversity is 0.019, 0.014, 0.009, and 0.007 for Africans, Indians, Asians, and Europeans, respectively. These populations are highly structured geographically (GST = 0.15; p < 0.001). The caste populations of Andhra Pradesh cluster more often with Africans than with Asians or Europeans. This is suggestive of admixture with African populations.

PMID: 8907753 [PubMed - indexed for MEDLINE]


Genome Res. 2003 Oct;13(10):2277-90.

Ethnic India: a genomic view, with special reference to peopling and structure.

Basu A, Mukherjee N, Roy S, Sengupta S, Banerjee S, Chakraborty M, Dey B, Roy M, Roy B, Bhattacharyya NP, Roychoudhury S, Majumder PP.

Anthropology & Human Genetics Unit, Indian Statistical Institute, Calcutta 700 108, India.

We report a comprehensive statistical analysis of data on 58 DNA markers (mitochondrial [mt], Y-chromosomal, and autosomal) and sequence data of the mtHVS1 from a large number of ethnically diverse populations of India. Our results provide genomic evidence that (1) there is an underlying unity of female lineages in India, indicating that the initial number of female settlers may have been small; (2) the tribal and the caste populations are highly differentiated; (3) the Austro-Asiatic tribals are the earliest settlers in India, providing support to one anthropological hypothesis while refuting some others; (4) a major wave of humans entered India through the northeast; (5) the Tibeto-Burman tribals share considerable genetic commonalities with the Austro-Asiatic tribals, supporting the hypothesis that they may have shared a common habitat in southern China, but the two groups of tribals can be differentiated on the basis of Y-chromosomal haplotypes; (6) the Dravidian tribals were possibly widespread throughout India before the arrival of the Indo-European-speaking nomads, but retreated to southern India to avoid dominance; (7) formation of populations by fission that resulted in founder and drift effects have left their imprints on the genetic structures of contemporary populations; (8) the upper castes show closer genetic affinities with Central Asian populations, although those of southern India are more distant than those of northern India; (9) historical gene flow into India has contributed to a considerable obliteration of genetic histories of contemporary populations so that there is at present no clear congruence of genetic and geographical or sociocultural affinities.

PMID: 14525929 [PubMed - indexed for MEDLINE]

PMCID: PMC403703


Hum Biol. 2005 Feb;77(1):93-114


Balinese Y-chromosome perspective on the peopling of Indonesia: genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders.

Karafet TM, Lansing JS, Redd AJ, Reznikova S, Watkins JC, Surata SP, Arthawiguna WA, Mayer L, Bamshad M, Jorde LB, Hammer MF.

Division of Biotechnology, Biosciences West, University of Arizona, Tucson, AZ 85721, USA.

The island of Bali lies near the center of the southern chain of islands in the Indonesian archipelago, which served as a stepping-stone for early migrations of hunter-gatherers to Melanesia and Australia and for more recent migrations of Austronesian farmers from mainland Southeast Asia to the Pacific. Bali is the only Indonesian island with a population that currently practices the Hindu religion and preserves various other Indian cultural, linguistic, and artistic traditions (Lansing 1983). Here, we examine genetic variation on the Y chromosomes of 551 Balinese men to investigate the relative contributions of Austronesian farmers and pre-Neolithic hunter-gatherers to the contemporary Balinese paternal gene pool and to test the hypothesis of recent paternal gene flow from the Indian subcontinent. Seventy-one Y-chromosome binary polymorphisms (single nucleotide polymorphisms, SNPs) and 10 Y-chromosome-linked short tandem repeats (STRs) were genotyped on a sample of 1,989 Y chromosomes from 20 populations representing Indonesia (including Bali), southern China, Southeast Asia, South Asia, the Near East, and Oceania. SNP genotyping revealed 22 Balinese lineages, 3 of which (O-M95, O-M119, and O-M122) account for nearly 83.7% of Balinese Y chromosomes. Phylogeographic analyses suggest that all three major Y-chromosome haplogroups migrated to Bali with the arrival of Austronesian speakers; however, STR diversity patterns associated with these haplogroups are complex and may be explained by multiple waves of Austronesian expansion to Indonesia by different routes. Approximately 2.2% of contemporary Balinese Y chromosomes (i.e., K-M9*, K-M230, and M lineages) may represent the pre-Neolithic component of the Indonesian paternal gene pool. In contrast, eight other haplogroups (e.g., within H, J, L, and R), making up approximately 12% of the Balinese paternal gene pool, appear to have migrated to Bali from India. These results indicate that the Austronesian expansion had a profound effect on the composition of the Balinese paternal gene pool and that cultural transmission from India to Bali was accompanied by substantial levels of gene flow.

PMID: 16114819 [PubMed - indexed for MEDLINE]


Hum Genet. 2007 Mar;121(1):137-44. Epub 2006 Oct 31

Y-chromosomal insights into the genetic impact of the caste system in India.

Zerjal T, Pandya A, Thangaraj K, Ling EY, Kearley J, Bertoneri S, Paracchini S, Singh L, Tyler-Smith C.

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, CB10 1SA, UK.

The caste system has persisted in Indian Hindu society for around 3,500 years. Like the Y chromosome, caste is defined at birth, and males cannot change their caste. In order to investigate the genetic consequences of this system, we have analysed male-lineage variation in a sample of 227 Indian men of known caste, 141 from the Jaunpur district of Uttar Pradesh and 86 from the rest of India. We typed 131 Y-chromosomal binary markers and 16 microsatellites. We find striking evidence for male substructure: in particular, Brahmins and Kshatriyas (but not other castes) from Jaunpur each show low diversity and the predominance of a single distinct cluster of haplotypes. These findings confirm the genetic isolation and drift within the Jaunpur upper castes, which are likely to result from founder effects and social factors. In the other castes, there may be either larger effective population sizes, or less strict isolation, or both.

PMID: 17075717 [PubMed - indexed for MEDLINE]


Bioessays. 2007 Jan;29(1):91-100

Peopling of South Asia: investigating the caste-tribe continuum in India.

Chaubey G, Metspalu M, Kivisild T, Villems R.

Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia.

In recent years, mtDNA and Y chromosome studies involving human populations from South Asia and the rest of the world have revealed new insights about the peopling of the world by anatomically modern humans during the late Pleistocene, some 40,000-60,000 years ago, over the southern coastal route from Africa. Molecular studies and archaeological record are both largely consistent with autochthonous differentiation of the genetic structure of the caste and tribal populations in South Asia. High level of endogamy created by numerous social boundaries within and between castes and tribes, along with the influence of several evolutionary forces such as genetic drift, fragmentation and long-term isolation, has kept the Indian populations diverse and distant from each other as well as from other continental populations. This review attempts to summarize recent genetic studies on Indian caste and tribal populations with the focus on the information embedded in the socially defined structure of Indian populations.

PMID: 17187379 [PubMed - indexed for MEDLINE]


Eur J Hum Genet. 2003 Mar;11(3):253-64


Mitochondrial DNA analysis reveals diverse histories of tribal populations from India.

Cordaux R, Saha N, Bentley GR, Aunger R, Sirajuddin SM, Stoneking M.

Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

We analyzed 370 bp of the first hypervariable region of the mitochondrial DNA (mtDNA) control region in 752 individuals from 17 tribal and four nontribal groups from the Indian subcontinent, to address questions concerning the origins, genetic structure and relationships of these groups. Southern Indian tribes showed reduced diversity and large genetic distances, both among themselves and when compared with other groups, and no signal of prehistoric demographic expansions. These results probably reflect enhanced genetic drift because of small population sizes and/or bottlenecks in these groups. By contrast, northern groups exhibited more diversity and signals of prehistoric demographic expansions. Phylogenetic analyses revealed that southern and northern groups (except northeastern ones) have related mtDNA sequences albeit at different frequencies, further supporting the larger impact of drift on the genetic structure of southern groups. The Indian mtDNA gene pool appears to be more closely related to the east Eurasian gene pool (including central, east and southeast Asian populations) than the west Eurasian one (including European and Caucasian populations). Within India, northeastern tribes are quite distinct from other groups; they are more closely related to east Asians than to other Indians. This is consistent with linguistic evidence in that these populations speak Tibeto-Burman languages of east Asian origin. Otherwise, analyses of molecular variance suggested that caste and tribal groups are genetically similar with respect to mtDNA variation.

PMID: 12678055 [PubMed - indexed for MEDLINE]



Am J Phys Anthropol. 2006 Feb;129(2):260-7


Microsatellite diversity reveals the interplay of language and geography in shaping genetic differentiation of diverse Proto-Australoid populations of west-central India.

Gaikwad S, Vasulu TS, Kashyap VK.

DNA Typing Unit, Central Forensic Science Laboratory, Kolkata 700014, India.

Microsatellite diversity was analyzed in four Proto-Australoid tribes, including Indo-European (Marathi)-speaking Katkari, Pawara, Mahadeo-Koli, and Dravidian (Gondi)-speaking groups of Maharashtra, west-central India, to understand their genetic structure and to identify the congruence between language and gene pool. Allele frequency data at 15 short tandem repeat (STR) loci in studied tribes was compared with data of 22 Indo-European- and Dravidian-speaking caste and tribal populations using heterozygosity, allele size variance, analysis of molecular variance (AMOVA), G(ST) estimate, PC plot, and Mantel correlation test. Our results demonstrate that "Gondi" tribes comprising the Madia-Gond, a hunter-gatherer population, and the agriculturist Dheria-Gond harbor lower diversity than "Marathi" tribal groups, which are culturally and genetically distinct. Katkari, a hunter-gatherer tribe, showed greater diversity and the presence of a large number of unique alleles, genetically distinct from all others except the Pawara, supporting their old cultural links. The agriculturist Pawara tribe represents a splinter subgroup of the Bhil tribe and has experienced gene flow. The Mahadeo-Koli, an agriculturally oriented tribe, displayed significant heterozygote deficiency, attributable to the practice of high endogamy. The Proto-Australoid tribal populations were genetically differentiated from castes of similar morphology, suggesting different evolutionary mechanisms operating upon the populations. The populations showed genetic and linguistic similarity, barring a few groups with varied migratory histories. The microsatellite variation clearly demonstrates the interplay of sociocultural factors including linguistic, geographical contiguity, and microevolutionary processes in shaping the genetic diversity of populations in contemporary India. This study supports the ethno-historical relationships of Indian populations.

PMID: 16323197 [PubMed - indexed for MEDLINE]


BMC Genet. 2005 Feb 5;6(1):4


Influence of language and ancestry on genetic structure of contiguous populations: a microsatellite based study on populations of Orissa.

Sahoo S, Kashyap VK.

National DNA Analysis Centre, Central Forensic Science Laboratory, 30, Gorachand Road, Kolkata-700 014 India.

BACKGROUND: We have examined genetic diversity at fifteen autosomal microsatellite loci in seven predominant populations of Orissa to decipher whether populations inhabiting the same geographic region can be differentiated on the basis of language or ancestry. The studied populations have diverse historical accounts of their origin, belong to two major ethnic groups and different linguistic families. Caucasoid caste populations are speakers of Indo-European language and comprise Brahmins, Khandayat, Karan and Gope, while the three Australoid tribal populations include two Austric speakers: Juang and Saora and a Dravidian speaking population, Paroja. These divergent groups provide a varied substratum for understanding variation of genetic patterns in a geographical area resulting from differential admixture between migrants groups and aboriginals, and the influence of this admixture on population stratification. RESULTS: The allele distribution pattern showed uniformity in the studied groups with approximately 81% genetic variability within populations. The coefficient of gene differentiation was found to be significantly higher in tribes (0.014) than caste groups (0.004). Genetic variance between the groups was 0.34% in both ethnic and linguistic clusters and statistically significant only in the ethnic apportionment. Although the populations were genetically close (FST = 0.010), the contemporary caste and tribal groups formed distinct clusters in both Principal-Component plot and Neighbor-Joining tree. In the phylogenetic tree, the Orissa Brahmins showed close affinity to populations of North India, while Khandayat and Gope clustered with the tribal groups, suggesting a possibility of their origin from indigenous people. CONCLUSIONS: The extent of genetic differentiation in the contemporary caste and tribal groups of Orissa is highly significant and constitutes two distinct genetic clusters. Based on our observations, we suggest that since genetic distances and coefficient of gene differentiation were fairly small, the studied populations are indeed genetically similar and that the genetic structure of populations in a geographical region is primarily influenced by their ancestry and not by socio-cultural hierarchy or language. The scenario of genetic structure, however, might be different for other regions of the subcontinent where populations have more similar ethnic and linguistic backgrounds and there might be variations in the patterns of genomic and socio-cultural affinities in different geographical regions.

PMID: 15694006 [PubMed - indexed for MEDLINE]

PMCID: PMC549189


Curr Biol. 1999 Nov 18;9(22):1331-4

Deep common ancestry of indian and western-Eurasian mitochondrial DNA lineages.

Kivisild T, Bamshad MJ, Kaldma K, Metspalu M, Metspalu E, Reidla M, Laos S, Parik J, Watkins WS, Dixon ME, Papiha SS, Mastana SS, Mir MR, Ferak V, Villems R.

Department of Evolutionary Biology, Tartu University, Tartu, 51010, Estonia.

About a fifth of the human gene pool belongs largely either to Indo-European or Dravidic speaking people inhabiting the Indian peninsula. The 'Caucasoid share' in their gene pool is thought to be related predominantly to the Indo-European speakers. A commonly held hypothesis, albeit not the only one, suggests a massive Indo-Aryan invasion to India some 4,000 years ago [1]. Recent limited analysis of maternally inherited mitochondrial DNA (mtDNA) of Indian populations has been interpreted as supporting this concept [2] [3]. Here, this interpretation is questioned. We found an extensive deep late Pleistocene genetic link between contemporary Europeans and Indians, provided by the mtDNA haplogroup U, which encompasses roughly a fifth of mtDNA lineages of both populations. Our estimate for this split is close to the suggested time for the peopling of Asia and the first expansion of anatomically modern humans in Eurasia [4] [5] [6] [7] [8] and likely pre-dates their spread to Europe. Only a small fraction of the 'Caucasoid-specific' mtDNA lineages found in Indian populations can be ascribed to a relatively recent admixture.

PMID: 10574762 [PubMed - indexed for MEDLINE]


Am J Phys Anthropol. 2007 Jul;133(3):1004-12


North Indian Muslims: enclaves of foreign DNA or Hindu converts?

Terreros MC, Rowold D, Luis JR, Khan F, Agrawal S, Herrera RJ.

Department of Biological Sciences, Florida International University, University Park, Miami, FL 33199, USA.

The mtDNA composition of two Muslim sects from the northern Indian province of Uttar Pradesh, the Sunni and Shia, have been delineated using sequence information from hypervariable regions 1 and 2 (HVI and HVII, respectively) as well as coding region polymorphisms. A comparison of this data to that from Middle Eastern, Central Asian, North East African, and other Indian groups reveals that, at the mtDNA haplogroup level, both of these Indo-Sunni and Indo-Shia populations are more similar to each other and other Indian groups than to those from the other regions. In addition, these two Muslim sects exhibit a conspicuous absence of West Asian mtDNA haplogroups suggesting that their maternal lineages are of Indian origin. Furthermore, it is noteworthy that the maternal lineage data indicates differences between the Sunni and Shia collections of Uttar Pradesh with respect to the relative distributions of Indian-specific M sub-haplogroups (Indo Shia > Indo Sunni) and the R haplogroup (Indo Sunni > Indo Shia), a disparity that does not appear to be related to social status or geographic regions within India. Finally, the mtDNA data integrated with the Y-chromosome results from an earlier study, which indicated a major Indian genetic (Y-chromosomal) contribution as well, suggests a scenario of Hindu to Islamic conversion in these two populations. However, given the substantial level of the African/Middle Eastern YAP lineage in the Indo-Shia versus its absence in the Indo-Sunni, it is likely that this conversion was somewhat gender biased in favor of females in the Indo-Shia. (c) 2007 Wiley-Liss, Inc.

PMID: 17427927 [PubMed - indexed for MEDLINE]


Ann Hum Genet. 2006 Jan;70(Pt 1):42-58.


High-resolution mtDNA studies of the Indian population: implications for palaeolithic settlement of the Indian subcontinent.

Barnabas S, Shouche Y, Suresh CG.

Division of Biochemical Sciences, National Chemical Laboratory, Pune 411008, India.

The population of the Indian subcontinent represents a very complex social and cultural structure. Occupying a geographically central position for the early modern human migrations, indications are that the founder group that migrated out of East Africa also reached India. In the present study we used the twin strategy of mapping the whole mitochondrial DNA (mtDNA) using the standard 14 restriction enzymes, and sequencing the non-transcribed HVSI region, to derive maximum maternal lineages from a sample of non-tribal Indians. The essential features of the reduced median network of the two datasets were the same. Both showed two demographic expansions of two major haplogroups, 'M' and 'N'. The reduced median network was drawn with inputs from other studies on the Indian population, and correlated with data from other ethnic populations. The coalescence time of expansions and genetic diversity were estimated. A reduced median network was also drawn combining data from studies on Africans, Southeast Asians and West-Eurasians, tracing the migration of 'M' from East Africa to India. A time estimate of the migration of major mtDNA haplogroups from Africa was attempted. The comparison of a set of Indian maternal lineages belonging to different geographical regions of the country, with other populations revealed the in-situ differentiation and antiquity of the Indian population. Our analysis places the 'southern route' migration as the source of haplogroup 'M'. Multiple migrations might have brought the other major haplogroups, 'N' and 'R', found in our sample to India. Archaeological evidence of modern humans in the subcontinent supports this mtDNA study.

PMID: 16441256 [PubMed - indexed for MEDLINE]


BMC Genet. 2004 Aug 31;5:26


Most of the extant mtDNA boundaries in south and southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans.

Metspalu M, Kivisild T, Metspalu E, Parik J, Hudjashov G, Kaldma K, Serk P, Karmin M, Behar DM, Gilbert MT, Endicott P, Mastana S, Papiha SS, Skorecki K, Torroni A, Villems R.

Institute of Molecular and Cell Biology, Tartu University, Tartu, Estonia.

BACKGROUND: Recent advances in the understanding of the maternal and paternal heritage of south and southwest Asian populations have highlighted their role in the colonization of Eurasia by anatomically modern humans. Further understanding requires a deeper insight into the topology of the branches of the Indian mtDNA phylogenetic tree, which should be contextualized within the phylogeography of the neighboring regional mtDNA variation. Accordingly, we have analyzed mtDNA control and coding region variation in 796 Indian (including both tribal and caste populations from different parts of India) and 436 Iranian mtDNAs. The results were integrated and analyzed together with published data from South, Southeast Asia and West Eurasia. RESULTS: Four new Indian-specific haplogroup M sub-clades were defined. These, in combination with two previously described haplogroups, encompass approximately one third of the haplogroup M mtDNAs in India. Their phylogeography and spread among different linguistic phyla and social strata was investigated in detail. Furthermore, the analysis of the Iranian mtDNA pool revealed patterns of limited reciprocal gene flow between Iran and the Indian sub-continent and allowed the identification of different assemblies of shared mtDNA sub-clades. CONCLUSIONS: Since the initial peopling of South and West Asia by anatomically modern humans, when this region may well have provided the initial settlers who colonized much of the rest of Eurasia, the gene flow in and out of India of the maternally transmitted mtDNA has been surprisingly limited. Specifically, our analysis of the mtDNA haplogroups, which are shared between Indian and Iranian populations and exhibit coalescence ages corresponding to around the early Upper Paleolithic, indicates that they are present in India largely as Indian-specific sub-lineages. In contrast, other ancient Indian-specific variants of M and R are very rare outside the sub-continent.

PMID: 15339343 [PubMed - indexed for MEDLINE]

PMCID: PMC516768


Hum Genet. 2001 Sep;109(3):339-50.


Genomic structures and population histories of linguistically distinct tribal groups of India.

Roychoudhury S, Roy S, Basu A, Banerjee R, Vishwanathan H, Usha Rani MV, Sil SK, Mitra M, Majumder PP.

Human Genetics and Genomics Department, Indian Institute of Chemical Biology, Calcutta, India.

There are various conflicting hypotheses regarding the origins of the tribal groups of India, who belong to three major language groups--Austro-Asiatic, Dravidian and Tibeto-Burman. To test some of the major hypotheses we designed a genetic study in which we sampled tribal populations belonging to all the three language groups. We used a set of autosomal DNA markers, mtDNA restriction-site polymorphisms (RSPs) and mtDNA hypervariable segment-1 (HVS-1) sequence polymorphisms in this study. Using the unlinked autosomal markers we found that there is a fair correspondence between linguistic and genomic affinities among the Indian tribal groups. We reconstructed mtDNA RSP haplotypes and found that there is extensive haplotype sharing among all tribal populations. However, there is very little sharing of mtDNA HVS-1 sequences across populations, and none across language groups. Haplogroup M is ubiquitous, and the subcluster U2i of haplogroup U occurs in a high frequency. Our analyses of haplogroup and HVS-1 sequence data provides evidence in support of the hypothesis that the Austro-Asiatic speakers are the most ancient inhabitants of India. Our data also support the earlier finding that some of the western Eurasian haplogroups found in India may have been present in India prior to the entry of Aryan speakers. However, we do not find compelling evidence to support the theory that haplogroup M was brought into India on an "out of Africa" wave of migration through a southern exit route from Ethiopia. On the contrary, our data raise the possibility that this haplogroup arose in India and was later carried to East Africa from India.

PMID: 11702215 [PubMed - indexed for MEDLINE]


Am J Hum Genet. 2001 Dec;69(6):1314-31. Epub 2001 Nov 9.


Origins and divergence of the Roma (gypsies).

Gresham D, Morar B, Underhill PA, Passarino G, Lin AA, Wise C, Angelicheva D, Calafell F, Oefner PJ, Shen P, Tournev I, de Pablo R, Kuĉinskas V, Perez-Lezaun A, Marushiakova E, Popov V, Kalaydjieva L.

Centre for Human Genetics, Edith Cowan University, Perth, WA, Australia.

The identification of a growing number of novel Mendelian disorders and private mutations in the Roma (Gypsies) points to their unique genetic heritage. Linguistic evidence suggests that they are of diverse Indian origins. Their social structure within Europe resembles that of the jatis of India, where the endogamous group, often defined by profession, is the primary unit. Genetic studies have reported dramatic differences in the frequencies of mutations and neutral polymorphisms in different Romani populations. However, these studies have not resolved ambiguities regarding the origins and relatedness of Romani populations. In this study, we examine the genetic structure of 14 well-defined Romani populations. Y-chromosome and mtDNA markers of different mutability were analyzed in a total of 275 individuals. Asian Y-chromosome haplogroup VI-68, defined by a mutation at the M82 locus, was present in all 14 populations and accounted for 44.8% of Romani Y chromosomes. Asian mtDNA-haplogroup M was also identified in all Romani populations and accounted for 26.5% of female lineages in the sample. Limited diversity within these two haplogroups, measured by the variation at eight short-tandem-repeat loci for the Y chromosome, and sequencing of the HVS1 for the mtDNA are consistent with a small group of founders splitting from a single ethnic population in the Indian subcontinent. Principal-components analysis and analysis of molecular variance indicate that genetic structure in extant endogamous Romani populations has been shaped by genetic drift and differential admixture and correlates with the migrational history of the Roma in Europe. By contrast, social organization and professional group divisions appear to be the product of a more recent restitution of the caste system of India.

PMID: 11704928 [PubMed - indexed for MEDLINE]

PMCID: PMC1235543


DNA Cell Biol. 2003 Nov;22(11):707-19


Analysis of Indian population based on Y-STRs reveals existence of male gene flow across different language groups.

Saha A, Udhayasuriyan PT, Bhat KV, Bamezai R.

National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India.

A study of three different Y-specific microsatellites (Y-STRs) in the populations from Uttar Pradesh (UP), Bihar (BI), Punjab (PUNJ), and Bengal (WB), speaking modern indic dialects with its roots in Indo-Aryan language, and from South of India (SI), speaking the South Indian languages with their root in Dravidian language, has shown that the predominant alleles observed represent the whole range of allelic variation reported in different population groups globally. These results indicate that the Indian population is most diverse. The similarity between the allelic variants between the populations studied by others in Africa and Asia and in this study between WB, PUNJ, UP, BI, and SI are of interest. It demonstrates that these population groups, housed in eight states of the country in different geographic locations, broadly correspond with Indo-Aryan and Dravidian language families. Further, our analyses based on haplotype frequency of different marker loci and gene diversity reveals that none of the population groups have remained isolated from others. High levels of haplotype diversity exist in all the clusters of population. Nonsignificant results based on Markov chain steps and Slatkin's linearized genetic distances indicate that there has been migration to and from in these population groups. However, some of the marginally significant interpopulation differences could be attributed to one or more of the castes with high diversity embedded within the population groups studied. Haplotype sharing between populations, F(ST) statistics, and phylogenetic analysis identifies genetic relatedness to be more between individuals belonging to two different states of India, WB and PUNJ, followed by UP and BI, whereas SI branched out separately.

PMID: 14659043 [PubMed - indexed for MEDLINE]


Hum Biol. 2000 Jun;72(3):499-510


Molecular genetic diversity in 5 populations of Madhya Pradesh, India.

Mastana SS, Reddy PH, Das MK, Reddy P, Das K.

Department of Human Sciences, Loughborough University, United Kingdom.

This paper presents data on the distribution of 3 amplified fragment length polymorphisms (D1S80, APOB, and YNZ22) in 5 populations of Central India. Using the polymerase chain reaction technique, 3 caste (Brahmin, Khatri, and Dhimer) and 2 tribal (Gond and Baiga) populations were studied for the 3 loci. The allelic variations observed in the caste populations are compatible with those of many Caucasian populations, but the caste populations showed significant overall and interpopulation variability within the region. D1S80 allele *24 varied from 32% (Dhimers) to 42% (Brahmins). Allele *18 was not observed in Baiga tribal populations, but in caste populations it varied from 11% (Dhimers) to 24% (Brahmins). Both tribal populations showed higher frequencies of allele *31 (17%-18%). For APOB, caste populations again showed bimodal distribution of alleles *35 and *37, but in tribal populations higher allele numbers (*47, *49) were also frequent. For YNZ22, extensive variation was observed for all populations studied. Allele *4 was the most common in caste populations, while alleles *2, *7, and *10 were prominent in tribal populations. The level of gene differentiation is not very high for the 3 systems studied in the 5 populations. Overall, allele frequency distribution, heterozygosity, and genetic diversity analysis show that the genetic diversity observed is socially and geographically structured.

PMID: 10885195 [PubMed - indexed for MEDLINE]


BMC Evol Biol. 2007 Mar 28;7:47

Y-chromosome evidence suggests a common paternal heritage of Austro-Asiatic populations.

Kumar V, Reddy AN, Babu JP, Rao TN, Langstieh BT, Thangaraj K, Reddy AG, Singh L, Reddy BM.

Molecular Anthropology Group, Biological Anthropology Unit, Indian Statistical Institute, Hubsiguda, Hyderabad, India. <>

BACKGROUND: The Austro-Asiatic linguistic family, which is considered to be the oldest of all the families in India, has a substantial presence in Southeast Asia. However, the possibility of any genetic link among the linguistic sub-families of the Indian Austro-Asiatics on the one hand and between the Indian and the Southeast Asian Austro-Asiatics on the other has not been explored till now. Therefore, to trace the origin and historic expansion of Austro-Asiatic groups of India, we analysed Y-chromosome SNP and STR data of the 1222 individuals from 25 Indian populations, covering all the three branches of Austro-Asiatic tribes, viz. Mundari, Khasi-Khmuic and Mon-Khmer, along with the previously published data on 214 relevant populations from Asia and Oceania. RESULTS: Our results suggest a strong paternal genetic link, not only among the subgroups of Indian Austro-Asiatic populations but also with those of Southeast Asia. However, maternal link based on mtDNA is not evident. The results also indicate that the haplogroup O-M95 had originated in the Indian Austro-Asiatic populations ~65,000 yrs BP (95% C.I. 25,442-132,230) and their ancestors carried it further to Southeast Asia via the Northeast Indian corridor. Subsequently, in the process of expansion, the Mon-Khmer populations from Southeast Asia seem to have migrated and colonized Andaman and Nicobar Islands at a much later point of time. CONCLUSION: Our findings are consistent with the linguistic evidence, which suggests that the linguistic ancestors of the Austro-Asiatic populations have originated in India and then migrated to Southeast Asia.

PMID: 17389048 [PubMed - indexed for MEDLINE]

PMCID: PMC1851701


Mol Biol Evol. 2004 Aug;21(8):1525-33. Epub 2004 May 5


The northeast Indian passageway: a barrier or corridor for human migrations?

Cordaux R, Weiss G, Saha N, Stoneking M.

Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

The northeast Indian passageway connecting the Indian subcontinent to East/Southeast Asia is thought to have been a major corridor for human migrations. Because it is also an important linguistic contact zone, it is predicted that northeast India has witnessed extensive population interactions, thus, leading to high genetic diversity within groups and heterogeneity among groups. To test this prediction, we analyzed 14 biallelic and five short tandem-repeat Y-chromosome markers and hypervariable region 1 mtDNA sequence variation in 192 northeast Indians. We find that both northeast Indian Y chromosomes and mtDNAs consistently show strikingly high homogeneity among groups and strong affinities to East Asian groups. We detect virtually no Y-chromosome and mtDNA admixture between northeast and other Indian groups. Northeast Indian groups are also characterized by a greatly reduced Y-chromosome diversity, which contrasts with extensive mtDNA diversity. This is best explained by a male founder effect during the colonization of northeast India that is estimated to have occurred within the past 4,000 years. Thus, contrary to the prediction, these results provide strong evidence for a genetic discontinuity between northeast Indian groups and other Indian groups. We, therefore, conclude that the northeast Indian passage way acted as a geographic barrier rather than as a corridor for human migrations between the Indian subcontinent and East/Southeast Asia, at least within the past millennia and possibly for several tens of thousand years, as suggested by the overall distinctiveness of the Indian and East Asian Y chromosome and mtDNA gene pools.

PMID: 15128876 [PubMed - indexed for MEDLINE]


Am J Hum Genet. 2004 May;74(5):827-45. Epub 2004 Apr 7


Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridor.

Quintana-Murci L, Chaix R, Wells RS, Behar DM, Sayar H, Scozzari R, Rengo C, Al-Zahery N, Semino O, Santachiara-Benerecetti AS, Coppa A, Ayub Q, Mohyuddin A, Tyler-Smith C, Qasim Mehdi S, Torroni A, McElreavey K.

Centre National de la Recherche Scientifique (CNRS) URA 1961, Institut Pasteur, 75724 Paris Cedex 15, France.

The southwestern and Central Asian corridor has played a pivotal role in the history of humankind, witnessing numerous waves of migration of different peoples at different times. To evaluate the effects of these population movements on the current genetic landscape of the Iranian plateau, the Indus Valley, and Central Asia, we have analyzed 910 mitochondrial DNAs (mtDNAs) from 23 populations of the region. This study has allowed a refinement of the phylogenetic relationships of some lineages and the identification of new haplogroups in the southwestern and Central Asian mtDNA tree. Both lineage geographical distribution and spatial analysis of molecular variance showed that populations located west of the Indus Valley mainly harbor mtDNAs of western Eurasian origin, whereas those inhabiting the Indo-Gangetic region and Central Asia present substantial proportions of lineages that can be allocated to three different genetic components of western Eurasian, eastern Eurasian, and south Asian origin. In addition to the overall composite picture of lineage clusters of different origin, we observed a number of deep-rooting lineages, whose relative clustering and coalescent ages suggest an autochthonous origin in the southwestern Asian corridor during the Pleistocene. The comparison with Y-chromosome data revealed a highly complex genetic and demographic history of the region, which includes sexually asymmetrical mating patterns, founder effects, and female-specific traces of the East African slave trade.

PMID: 15077202 [PubMed - indexed for MEDLINE]

PMCID: PMC1181978


Am J Phys Anthropol. 1999 Jun;109(2):147-58.

Multiple origins of the mtDNA 9-bp deletion in populations of South India.

Watkins WS, Bamshad M, Dixon ME, Bhaskara Rao B, Naidu JM, Reddy PG, Prasad BV, Das PK, Reddy PC, Gai PB, Bhanu A, Kusuma YS, Lum JK, Fischer P, Jorde LB.

Department of Human Genetics, University of Utah, Salt Lake City 84112-0533, USA.

The origins and genetic affinities of the more than 500 tribal populations living in South Asia are widely disputed. This may reflect differential contributions that continental populations have made to tribal groups in South Asia. We assayed for the presence of the intergenic COII/tRNALys 9-bp deletion in human mtDNA in 646 individuals from 12 caste and 14 tribal populations of South India and compared them to individuals from Africa, Europe, and Asia. The 9-bp deletion is observed in four South Indian tribal populations, the Irula, Yanadi, Siddi, and Maria Gond, and in the Nicobarese. Length polymorphisms of the 9-bp motif are present in the Santal, Khonda Dora, and Jalari, all of whom live in a circumscribed region on the eastern Indian coast. Phylogenetic analyses of mtDNA control region sequence from individuals with the 9-bp deletion indicate that it has arisen independently in some Indian tribal populations. Other 9-bp deletion haplotypes are likely to be of Asian and African origin, implying multiple origins of the 9-bp deletion in South India. These results demonstrate varying genetic affinities of different South Indian tribes to continental populations and underscore the complex histories of the tribal populations living in South Asia.

PMID: 10378454 [PubMed - indexed for MEDLINE]


Eur J Hum Genet. 2004 Jun;12(6):495-504.


Admixture, migrations, and dispersals in Central Asia: evidence from maternal DNA lineages.

Comas D, Plaza S, Wells RS, Yuldaseva N, Lao O, Calafell F, Bertranpetit J.

Unitat de Biologia Evolutiva, Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona 08003, Spain.

Mitochondrial DNA (mtDNA) lineages of 232 individuals from 12 Central Asian populations were sequenced for both control region hypervariable segments, and additional informative sites in the coding region were also determined. Most of the mtDNA lineages belong to branches of the haplogroups with an eastern Eurasian (A, B, C, D, F, G, Y, and M haplogroups) or a western Eurasian (HV, JT, UK, I, W, and N haplogroups) origin, with a small fraction of Indian M lineages. This suggests that the extant genetic variation found in Central Asia is the result of admixture of already differentiated populations from eastern and western Eurasia. Nonetheless, two groups of lineages, D4c and G2a, seem to have expanded from Central Asia and might have their Y-chromosome counterpart in lineages belonging to haplotype P(xR1a). The present results suggest that the mtDNA found out of Africa might be the result of a maturation phase, presumably in the Middle East or eastern Africa, that led to haplogroups M and N, and subsequently expanded into Eurasia, yielding a geographically structured group of external branches of these two haplogroups in western and eastern Eurasia, Central Asia being a contact zone between two differentiated groups of peoples.

PMID: 14872198 [PubMed - indexed for MEDLINE]


Tissue Antigens. 2004 Jul;64(1):58-65.


HLA-B and HLA-C alleles and haplotypes in the Dravidian tribal populations of southern India.

Thomas R, Nair SB, Banerjee M.

Human Molecular Genetics Laboratory, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, India.

The Dravidians are believed to be the earliest inhabitants of India. Their subsequent migration and admixture with invading racial groups has been of scientific interest for population geneticists. In the present study, seven highly endogamous and extremely isolated colonies of Dravidian tribal populations (n = 105) from Kerala in South India were analysed and compared with random non-tribal Dravidian (RND) samples (n = 78) of southern India using the polymerase chain reaction with sequence-specific primer method for HLA-B and HLA-C typing. The tribal group comprises Adiya, Kanikkar, Kattunaikka, Kuruma, Kurichiya, Malapandaram and Paniya, while the RND group includes Malayalam-speaking individuals from various non-tribal castes of Kerala selected randomly. Some of the most frequent HLA-B alleles in the RND population were similar to the North Indian population and included B*07, B*61 (B*40), B*44, B*51, B*35 and B*52. Although B*61 was the most frequent allele in our total study population, the frequency fluctuated in individual populations. HLA-Cw*14 was one of the most frequent alleles while HLA-Cw*17 was totally absent in all populations studied. The haplotype B*61-Cw*14 was present in all the study groups except in Kurichiya, and the haplotype B*51-Cw*14 was only absent in Kattunaikka. Phylogenetic tree and correspondence analysis indicate that all the Dravidian tribal communities group together as a separate cluster, while the RND group of individuals from South India lie close to the North Indian population. This suggests that the RND population of South India might have a crypto-Dravidian origin, while the smaller Dravidian tribal communities have a distinct Dravidian origin.

PMID: 15191523 [PubMed - indexed for MEDLINE]


Hum Biol. 1996 Oct;68(5):607-28.


Genetic variation in India.

Papiha SS.

Department of Human Genetics, University of Newcastle upon Tyne, England.

In the last 25 years a number of genetic studies on the populations of the Indian subcontinent have been conducted. Unfortunately, most of the studies covered a limited number of genetic systems, and only a few provide information on the genetic differentiation and population structure of some regional caste, tribal, religious, and urban groups. Despite a recent report suggesting that in eastern India genetic affinity does not show any large degree of congruence with sociocultural hierarchy, three distinct surveys reported here indicate that geographic proximity, ethnohistory, and biosocial and cultural affiliation are important determinants of genetic affinity. Gene differentiation studies are few, but from the information of some previous papers and results presented in this special issue of Human Biology, the pattern of differentiation is becoming clear. In general, genetic differentiation in populations of India is low (0.26-1.7%), but overall genetic differentiation in 18 mixed populations of India is higher (2.23%), similar to the largest single study on 16 tribal groups from central India (2.18%). The tribal population of South India shows the highest FST value (4.1%), and this value is similar to a study of the Dhangar caste group. The reason for this high FST value is not clear. One possibility may be (semi-) isolation associated with such factors as random inbreeding and drift, which can cause high levels of genetic differentiation among the tribal groups of India and among the castes such as Dhangar. However, further studies are needed to explore the causes of such high values of genetic differentiation, especially in these populations.

PMID: 8908794 [PubMed - indexed for MEDLINE]


Hum Biol. 1993 Jun;65(3):413-23


PGM1 subtypes in populations of the Indian subcontinent.

Papiha SS.

Department of Human Genetics, University of Newcastle upon Tyne, United Kingdom.

Isoelectric focusing was performed to analyze PGM1 polymorphism in six tribal, five caste, and five Muslim populations from the Indian subcontinent. Although a considerable range of allele frequencies was observed in certain caste and Muslim groups, the phenotypic distribution showed significant genetic heterogeneity only among the tribal groups. Discriminant analysis suggests that the PGM1 locus provides useful anthropogenetic information to differentiate the populations of the subcontinent in terms of their social structure. In the three population groups studied the variation in the heterozygosity levels suggests that the genetic diversity at the PGM1 locus may be the result of the structure of various population groups.

PMID: 8319941 [PubMed - indexed for MEDLINE]


Hum Biol. 1996 Oct;68(5):679-705


Population structure and genetic differentiation among 16 tribal populations of central India.

Das K, Malhotra KC, Mukherjee BN, Walter H, Majumder PP, Papiha SS.

Anthropometry and Human Genetics Unit, Indian Statistical Institute, Calcutta, India.

Genetic polymorphisms for six blood groups, three red cell enzymes, three serum proteins, and hemoglobin were examined in sixteen central Indian tribal populations. Nine of the tribes belonged to Orissa, five to Madhya Pradesh, and two to Maharashtra. Eleven tribes spoke the Dravidian language, three Indo-Ayran, and two the language of the Austro-Asiatic families. The population structure of these tribal populations was analyzed at the inter- and intrastate and linguistic levels, using data for 13 genetic systems (38 alleles or haplotypes). Nine of the 13 loci showed significant heterogeneity in the 16 tribes, and the pattern of heterogeneity was also discernible in the different states and in the Dravidian-speaking tribes. As expected, the extent of genetic differentiation or gene diversity was the highest so far reported from central India. The mean FIS and HS for each locus in the different state, linguistic, and total tribal groups were consistently higher than the FST and GST values, respectively, showing that the genetic structure of each tribe is highly influenced by inbreeding. In a genetic affinity analysis by genetic distance the Indo-Aryan and Austro-Asiatic language groups showed little affinity with each other, although there was some tendency toward geographic affinity. The present analysis indicates that, in addition to genetic drift, gene flow, and selection, the genetic structure of the populations of central India is also highly influenced by sociocultural adaptation and inbreeding.

PMID: 8908797 [PubMed - indexed for MEDLINE]


Acta Anthropogenet. 1984;8(3-4):159-79


Population genetic studies of PI, Tf, Gc and PGM1 subtypes among various caste groups in North India.

Kamboh MI.

Approximately 500 blood samples from various endogamous groups in north India have been subjected to isoelectric focusing to reveal genetic variation at the PI, Tf, Gc and PGM1 loci. The average heterozygosity per locus varies from 40% to 60% and the gene frequency data reflects considerable variation among the caste groups studied. The Nei genetic distances calculated from the 4 loci demonstrate that Khatri, Arora and Rajput are strongly clustered together and genetically they are closer to Brahmin than to Vaish and Scheduled Castes. Vaish emerge as a unique group showing maximum genetic distances with all other caste groups. The comparison of the present populations with our own data from two south Indian populations indicates that the tribal population of Soliga is distinct from the non-tribal populations, but the non-tribal south Indian series clusters closely with the main caste populations in north India.

PMID: 6242530 [PubMed - indexed for MEDLINE]


J Hum Genet. 2005;50(1):49-51. Epub 2004 Dec 21


Genetic affinity among five different population groups in India reflecting a Y-chromosome gene flow.

Saha A, Sharma S, Bhat A, Pandit A, Bamezai R.

National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.

Four binary polymorphisms and four multiallelic short tandem repeat (STR) loci from the nonrecombining region of the human Y-chromosome were typed in different Indian population groups from Uttar Pradeh (UP), Bihar (BI), Punjab (PUNJ), and Bengal (WB) speaking the Indo-Aryan dialects and from South India (SI) with the root in the Dravidian language. We identified four major haplogroups [(P) 1+, (C and F) 2+, (R1a) 3, (K) 26+] and 114 combinations of Y-STR haplotypes. Analyses of the haplogroups indicated no single origin from any lineage but a result of a conglomeration of different lineages from time to time. The phylogenetic analyses indicate a high degree of population admixture and a greater genetic proximity for the studied population groups when compared with other world populations.

PMID: 15611834 [PubMed - indexed for MEDLINE]


Curr Biol. 2002 Apr 16;12(8):673-7


Gene flow from the Indian subcontinent to Australia: evidence from the Y chromosome.

Redd AJ, Roberts-Thomson J, Karafet T, Bamshad M, Jorde LB, Naidu JM, Walsh B, Hammer MF.

Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA.

Phenotypic similarities between Australian Aboriginal People and some tribes of India were noted by T.H. Huxley during the voyage of the Rattlesnake (1846-1850). Anthropometric studies by Birdsell led to his suggestion that a migratory wave into Australia included populations with affinities to tribal Indians. Genetic evidence for an Indian contribution to the Australian gene pool is contradictory; most studies of autosomal markers have not supported this hypothesis (; and references therein). On the other hand, affinities between Australian Aboriginal People and southern Indians were suggested based on maternally inherited mitochondrial DNA. Here, we show additional DNA evidence in support of Huxley's hypothesis of an Indian-Australian connection using single-nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) on the nonrecombining portion of the Y chromosome (NRY). Phylogenetic analyses of STR variation associated with a major Australian SNP lineage indicated tight clustering with southern Indian/Sri Lankan Y chromosomes. Estimates of the divergence time for these Indian and Australian chromosomes overlap with important changes in the archaeological and linguistic records in Australia. These results provide strong evidence for an influx of Y chromosomes from the Indian subcontinent to Australia that may have occurred during the Holocene.

PMID: 11967156 [PubMed - indexed for MEDLINE]


BMC Genet. 2004 Aug 19;5:23


Genetic structure of four socio-culturally diversified caste populations of southwest India and their affinity with related Indian and global groups.

Rajkumar R, Kashyap VK.

DNA Typing Unit, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata, India-700014.

BACKGROUND: A large number of microsatellites have been extensively used to comprehend the genetic diversity of different global groups. This paper entails polymorphism at 15 STR in four predominant and endogamous populations representing Karnataka, located on the southwest coast of India. The populations residing in this region are believed to have received gene flow from south Indian populations and world migrants, hence, we carried out a detailed study on populations inhabiting this region to understand their genetic structure, diversity related to geography and linguistic affiliation and relatedness to other Indian and global migrant populations. RESULTS: Various statistical analyses were performed on the microsatellite data to accomplish the objectives of the paper. The heretozygosity was moderately high and similar across the loci, with low average GST value. Iyengar and Lyngayat were placed above the regression line in the R-matrix analysis as opposed to the Gowda and Muslim. AMOVA indicated that majority of variation was confined to individuals within a population, with geographic grouping demonstrating lesser genetic differentiation as compared to linguistic clustering. DA distances show the genetic affinity among the southern populations, with Iyengar, Lyngayat and Vanniyar displaying some affinity with northern Brahmins and global migrant groups from East Asia and Europe. CONCLUSION: The microsatellite study divulges a common ancestry for the four diverse populations of Karnataka, with the overall genetic differentiation among them being largely confined to intra-population variation. The practice of consanguineous marriages might have attributed to the relatively lower gene flow displayed by Gowda and Muslim as compared to Iyengar and Lyngayat. The various statistical analyses strongly suggest that the studied populations could not be differentiated on the basis of caste or spatial location, although, linguistic affinity was reflected among the southern populations, distinguishing them from the northern groups. Our study also indicates a heterogeneous origin for Lyngayat and Iyengar owing to their genetic proximity with southern populations and northern Brahmins. The high-ranking communities, in particular, Iyengar, Lyngayat, Vanniyar and northern Brahmins might have experienced genetic admixture from East Asian and European ethnic groups.

PMID: 15317657 [PubMed - indexed for MEDLINE]

PMCID: PMC515297


J Biosci. 2003 Jun;28(4):507-22


Status of Austro-Asiatic groups in the peopling of India: An exploratory study based on the available prehistoric, linguistic and biological evidences.

Kumar V, Reddy BM.

Anthropology and Human Genetics Unit, Indian Statistical Institute, Kolkata 700 108, India.

Among the most contentious currently debated issues is about the people who had settled first in the Indian subcontinent. It has been suggested that the communities affiliated to the Austro-Asiatic linguistic family are perhaps the first to settle in India and the palaeoanthropological evidences suggest the earliest settlement probably around 60,000 years BP. Recent speculations, based on both traditional genetic markers and DNA markers, seem to corroborate the aforesaid view. However, these studies are inadequate both in terms of the representation of the constituent groups within this broad linguistic category as well as the number of samples that represent each of them. We strongly feel that, before making any formidable conclusions on the peopling of India and/or the history of settlement, it is necessary to ascertain that the Austro-Asiatic speakers, represented by over 30 different tribal groups, either genetically constitute a homogenous single entity or are a heterogeneous conglomeration, derived from different sources. As a first step towards this we tried to collate and analyse the existing information geographic, ethno-historic, cultural and biological. The results of the analyses of anthropometric and genetic marker data indicate that the Austro-Asiatic groups, particularly the Mundari speakers, with certain exceptions, show greater homogeneity among them when compared to the other linguistic groups, although certain groups show as outliers. However, traditional genetic markers show lower within population heterozygosity compared to Dravidian and other Indian populations. This is contrary to what has been claimed in case of certain DNA markers. Given that relatively greater heterozygosity among the Austro-Asiatic populations has been taken as one of the important evidences supporting greater antiquity of these populations one should await results of detailed DNA studies being currently undertaken by us, involving a number of Austro-Asiatic and other ethnic populations of India to resolve the issue unequivocally.

PMID: 12799497 [PubMed - indexed for MEDLINE]



11 Jan. 2009

See: Genetics and the Aryan debate by Michel Danino (2005)

Ancient African Exodus Mostly Involved Men, Geneticists Find

ScienceDaily (Jan. 2, 2009) — Modern humans left Africa over 60,000 years ago in a migration that many believe was responsible for nearly all of the human population that exist outside Africa today.

Now, researchers have revealed that men and women weren't equal partners in that exodus. By tracing variations in the X chromosome and in the non-sex chromosomes, the researchers found evidence that men probably outnumbered women in that migration.

The scientists expect that their method of comparing X chromosomes with the other non-gender specific chromosomes will be a powerful tool for future historical and anthropological studies, since it can illuminate differences in female and male populations that were inaccessible to previous methods.

While the researchers cannot say for sure why more men than women participated in the dispersion from Africa—or how natural selection might also contribute to these genetic patterns—the study's lead author, Alon Keinan, notes that these findings are "in line with what anthropologists have taught us about hunter-gatherer populations, in which short distance migration is primarily by women and long distance migration primarily by men."

Journal reference:

1.                     Alon Keinan, James C Mullikin, Nick Patterson, David Reich. Accelerated genetic drift on chromosome X during the human dispersal out of Africa. Nature Genetics, 2008; DOI: 10.1038/ng.303

Adapted from materials provided by Harvard Medical School, via EurekAlert!, a service of AAAS.


Letter abstract

Nature Genetics 41, 66 - 70 (2008)
Published online: 21 December 2008 | doi:10.1038/ng.303

Accelerated genetic drift on chromosome X during the human dispersal out of Africa

Alon Keinan1,2, James C Mullikin3, Nick Patterson2 & David Reich1,2

Comparisons of chromosome X and the autosomes can illuminate differences in the histories of males and females as well as shed light on the forces of natural selection. We compared the patterns of variation in these parts of the genome using two datasets that we assembled for this study that are both genomic in scale. Three independent analyses show that around the time of the dispersal of modern humans out of Africa, chromosome X experienced much more genetic drift than is expected from the pattern on the autosomes. This is not predicted by known episodes of demographic history, and we found no similar patterns associated with the dispersals into East Asia and Europe. We conclude that a sex-biased process that reduced the female effective population size, or an episode of natural selection unusually affecting chromosome X, was associated with the founding of non-African populations.

1.      Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

2.      Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.

3.      Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

Correspondence to: Alon Keinan1,2 e-mail:

Correspondence to: David Reich1,2 e-mail: