Too early to settle the Aryan migration debate?

G.Chaubey

K. Thangaraj

With genetic data currently available, it is difficult to deduce the direction of migration either into India or out of India during the Bronze Age 


On June 17, The Hindu published an article by Tony Joseph (“How genetics is settling the Aryan migration debate”) on current genetic research in India and stated that “scientists are converging” on the Aryan migration to the Subcontinent around 2000-1500 BC. This conclusion was mainly based on the results obtained from the paternally inherited markers (Y chromosome), published on March 23, 2017 in a scientific journal, BMC Evolutionary Biology, by a team of 16 co-authors including Martin P. Richards of the University of Huddersfield, which compiled and analysed Y chromosome data mainly from the targeted South Asian populations living in the U.K. and U.S. However, anyone who understands the complexity of Indian population will appreciate that Indians living outside the Subcontinent do not reflect the full diversity of India, as the majority of them are from caste populations with limited subset of regions.

Under-representation

A recent paper by Dhriti Sengupta and colleagues (‘Genome Biology and Evolution 2016’; 8:3460-3470), showed that the South Asian populations included in the “1000 Genomes Project” under-represent the genomic diversity of the Subcontinent. Tribes are one of the founding populations of India, any conclusion drawn without studying them will fail to capture the complete genetic information of the Subcontinent.

Marina Silva/Richards et al. argued that the maternal ancestry (mtDNA) of the Subcontinent is largely indigenous, whereas 17.5% of the paternal ancestry (Y chromosome) is associated with the haplogroup R1a, an indication of the arrival of Bronze Age Indo-European speakers. However, India is a nation of close to 4,700 ethnic populations, including socially stratified communities, many of which have maintained endogamy (marrying within the community) for thousands of years, and these have been hardly sampled in the Y chromosome analysis led by Silva et al., and so do not provide an accurate characterisation of the R1a frequencies in India (several tribal populations carry substantial frequency of haplogroup R1a).

Equally important to understand is that the Y chromosome phylogeny suffered genetic drift (lineage loss), and thus there is a greater chance to lose less frequent R1a branches, if one concentrates only on specific populations, keeping in mind the high level of endogamy of the Subcontinent. These are extremely important factors one should consider before making any strong conclusions related to Indian populations. The statement made by Silva et al. that 17.5% of Indians carry R1a haplogroup actually means that 17.5% of the samples analysed by them (those who live in U.K. and U.S.) carry R1a, not that 17.5% of Indians carry R1a!

Genetic affinities

Indian genetic affinity with Europeans is not new information. In a study published in Nature (2009; 461:489-494), scientists from CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, and Harvard Medical School (HMS), U.S., using more than 5,00,000 autosomal genetic markers, showed that the Ancestral North Indians (ANI) share genetic affinities with Europeans, Caucasians and West Asians. However, there is a huge difference between this study and the study published by Silva et al., as the study by CSIR-CCMB and HMS included samples representing all the social and linguistic groups of India. It was evident from the same Nature paper that when the Gujarati Indians in Houston (GIH) were analysed for genetic affinities with different ethnic populations of India, it was found that the GIH have formed two clusters in Principal Component Analysis (PCA), one with Indian populations, another an independent cluster. Similarly, a recent study (‘Neurology Genetics’, 2017; 3:3, e149) by Robert D.S. Pitceathly and colleagues from University College of London and CSIR-CCMB has analysed 74 patients with neuromuscular diseases (of mitochondrial origin) living in the U.K. and found a mutation in RNASEH1 gene in three families of Indian origin. However, this mutation was absent in Indian patients with neuromuscular diseases (of mitochondrial origin). This mutation was earlier reported in Europeans, suggesting that these three families might have mixed with the local Europeans; highlighting the importance of the source of samples. Another study published in The American Journal of Human Genetics (2011; 89:731-744) by Mait Metspalu and colleagues, where CSIR-CCMB was also involved, analysed 142 samples from 30 ethnic groups and mentioned that “Modeling of the observed haplotype diversities suggests that both Indian ancestry components (ANI and ASI) are older than the purported Indo-Aryan invasion 3,500 YBP (years before present). As well as, consistent with the results of pairwise genetic distances among world regions, Indians share more ancestry signals with West than with East Eurasians”.

We agree that the major Indian R1a1 branch, i.e. L657, is not more than 5,000 years old. However, the phylogenetic structure of this branch cannot be considered as a derivative of either Europeans or Central Asians. The split with the European is around 6,000 years and thereafter the Asian branch (Z93) gave rise to the South Asian L657, which is a brother branch of lineages present in West Asia, Europe and Central Asia. Such kind of expansion, universally associated with most of the Y chromosome lineages of the world, as shown in 2015 by Monika Karmin et al., was most likely due to dramatic decline in genetic diversity in male lineages four to eight thousand years ago (Genome Research, 2015; 4:459-66). Moreover, there is evidence which is consistent with the early presence of several R1a branches in India (our unpublished data).

The Aryan invasion/migration has been an intense topic of discussion for long periods. However, one has to understand the complexity of the Indian populations and to select samples carefully for analysis. Otherwise, the findings could be biased and confusing.

With the information currently available, it is difficult to deduce the direction of haplogroup R1a migration either into India or out of India, although the genetic data certainly show that there was migration between the regions. Currently, CSIR-CCMB and Harvard Medical School are investigating a larger number of samples, which will hopefully throw more light on this debate.

Tony Joseph responds:

There is a technical point in suggesting that the South Asian populations included in the “1000 Genomes Project” under-represent the complete genomic diversity of the Subcontinent and, therefore, the 17.5 % R1a frequency the ‘BMC Evolutionary Biology’ study arrived at may not be precise.
That a sample under-represents the complete genomic diversity of India could be said of virtually any study whatsoever, including the studies that the authors of the rejoinder have done. The point about the Marina Silva/Martin P. Richards et al. study is that its conclusions about the chronology of multiple migrations into South Asia are not dependent upon the precise percentage of R1a population — they remain robust whether the R1a percentage is 12.5 % or 17.5% or 22.5 %. The precision of the percentage or the impugned under-representation would have been an issue if the study were to make detailed conclusions about, say, how the Bronze Age migrations spread across different regions in India. Since it is not doing that, under-representation ceases to be a material issue.
In an email to me on May 29, weeks before my article was published, this is what Prof. Richards said about the sample: “It’s true that some of the 1000 Genomes Project (1KGP) sequences that we analysed for genome-wide and Y-chromosome data were sampled from Indians in the U.K. and U.S., and lack tribal groups, which might well be an issue for a detailed regional study of the subcontinent (our mtDNA database was much larger). But we are simply looking at the big picture across the region (what was the role of Palaeolithic, Neolithic and Bronze Age settlement, primarily) and the signals we describe across the five 1KGP sample sets are clear and consistent and also fit well with the lower-resolution data that has been collected in the past (e.g. for R1a distributions). By putting everything together, we feel the sketch of the big picture that we propose is very well supported, even though there will certainly be a huge amount of further analysis needed to work through the regional details.”
The second argument that the rejoinder makes, as summed up in its last paragraph, is that ‘Out of India’ is a possible explanation for the genetic spread that we observe. This is helpful insofar as it accepts that the genetic spread that we observe does need an explanation. But the problem with proposing ‘Out of India’ as that explanation is the following: it is not as if the ‘Out of India’ hypothesis is new; it has been around for decades. But the rejoinder makes no reference to a single peer-reviewed genetic study that makes a serious case for ‘Out of India’.
If the hypothesis were tenable at all, shouldn’t there have been many peer-reviewed papers by now making the case and fleshing out the details?

 K. Thangaraj is with the CSIR-Centre for Cellular and Molecular Biology, Hyderabad, and G. Chaubey is with the Estonian Biocentre in Tartu, Estonia

Tony Joseph is a writer and former editor of ‘BusinessWorld’. Twitter: @tjoseph0010

Yog.

See also :
Genetics and the Aryan invasion debate 

Biomolecular Prehistory of South Asia Project

This project applies a novel, multi-proxy approach, incorporating stable isotope analysis, dental calculus, proteomics and aDNA, to elucidate changes in diet, demography, and ecology across major cultural transitions in South Asia.
Yog. 

There is also the upcoming presentation on some aDNA data : 

Title: E-P18.02 - Reconstructing the human population history of the Indian subcontinent using ancient population genomics.

Keywords: Ancient DNA; population Genetics

Authors: N. Rai1, K. Thangaraj1, V. Shinde2; 

1Centre for Cellular and Molecular Biology, Hyderabad, India, 2 Deccan College Post-Graduate and Research Institute, Pune, India.

Abstract: The more than 1.3 billion people who live in Indian subcontinent correspond to several large ethnic groups who are highly diverse and complex. Importantly, India’s genetic past remains a subject a great debate due to numerous hypotheses surrounding population origins and migrations within and from outside India. In order to reconstruct and explain the patterns of genetic diversity evident in modern humans, an understanding of both past and present population dynamics is crucial. Several studies have shown that genetic data from ancient individuals are indispensable when reconstructing past population histories. We for the first time use the ancient genomics approach in South Asia to reconstruct the complex human population history of Indian Sub continent. We are exploring the recent technological advancement to directly test these hypotheses using ancient and modern human DNA in India. We have collected several ancient skeletal remains from different time scale of human civilization ranging from early Mesolithic, Neolithic, Harappan (Indus Valley civilization) and Megalithic culture. With the whole/partial genome NGS data, we are reconstructing the prehistoric peopling and migration of modern human in the Indian subcontinent. We are also testing the pervasive founder events and gradient of recessive genes accumulation by comparing the ancient genome with the modern human population of India.

Presentation Time: Sunday, May 28, 2017, 9:00 AM - 5:45 PM 

See here and also here . 

This is something that we are all waiting for a long time . We can be confident, that the data will be very important regarding the Aryan controversy . Although without the clear cut decipherment of the SSVC/IVC script , a decisive knowledge is still a bit far . 

THE GENOME-WIDE ANALYSIS OF THE BHILS: THE SECOND LARGEST TRIBAL POPULATION OF INDIA

Gyaneshwer Chaubey, Periyasamy Govindaraj, Niraj Rai, George van Driem and
Kumarasamy Thangaraj


Abstract :

The name of the Bhil population was mentioned in early literature of the Subcontinent, which suggests their presence in India since prehistoric times. Studies based on classical and genetic markers suggest a unique identity of the Bhil, who currently live in western and central Indian states. Our previous studies on two Bhil groups living in central and western Indian regions drew different conclusions on their origin. However, the first study on the Bhil of central India was based on haploid DNA and a few autosomal markers, whereas the second study on the western Bhil explored large number of autosomal SNPs. Therefore, in this study we have reconnoitered the inter-population and intra-population relationships of Bhil groups at four different geographical locations by using >95,000 autosomal SNPs. A combination of statistical analysis revealed that all Bhil populations are likely to have had a common source sharing a pan-Bhil ancestry. This common ancestry is clearly seen amongst the Bhil of Gujarat who turned out to show the lowest degree of admixture with their neighbours, whereas the Bhil of Rajasthan showed the highest diversity with extensive admixture with the surrounding populations. Both inter-population and intra-population comparison suggest a shared Bhil genome followed by chunks sharing with the Nihali population, a language community speaking a so-called language isolate.

Yog .

Its practically a flawless paper . But the suggestion that Bhils are mentioned in  Mahabharata and Ramayana , is a bit dubious .

J.P. Mallory's Current assessment on Proto-Indo-Europeans

He still favors the Steppe Model , which is natural , he is after all , regarded as one of the most celebrated proponents of the theory. But in recent publications , a clear change is visible . He has now accepted the importance of Agriculture, in the Proto-Indo-European culture . He correctly admits that, this importance of agriculture , is a serious flaw for the steppe argument . But just not for The Kurgan Model, actually, he shows no hesitation when he remarks :

If there are any lessons to be learned, it is that every model of Indo-European origins can be found to reveal serious deficiencies as we increase our scrutiny.

Talk about honesty . That is certainly as best as it can get!.Indeed, time has come when we start forgetting about the theories and start following actual data . There will be of course difficulties, there must be , but at least , we will be under no illusion . Yes, illusion, which is generated by creationism .

Here are the two latest articles by him :

Twenty-first century clouds over Indo-European homelands

The Problem of Tocharian Origins: An Archaeological Perspective 

BTW, recently, I have also found a nice attempt , concerning the Indo-European History of India. I think , that this attempt has the spirit, which is scientific and necessary !.

Today i came across a very handy website filled with some very interesting articles from genetics.
Genetic Links in the Indus Valley
 

  This month’s feature article explores genetic links in the Indus Valley, the location of the Bronze Age Harappan Civilization. The historical background section includes a discussion of emerging new models of South Asian prehistory. This new research challenges the traditional academic theory of a "Vedic invasion"  from outside of India, and suggests instead local continuity in South Asia dating to the expansion of Neolithic cultures from West Asia.

 The Old Theory (Vedic Invasion): Despite this vivid archaeological record of Harappan life, the
ancient Harappan language (or languages) is unknown, because the Indus Script remains undeciphered.
When the ancient cities of Harappa were excavated, Western archaeologists generally assumed that the
ancient Harappan culture had been replaced by invaders from the Eurasian Steppe and Central Asia at the
end of the Harappan period around 1700-1300 BCE. The new Central Asian invaders were thought to be
the composers of the Rigveda and other Vedic literature written in the Sanskrit language, ancestral to
Hindi and other languages spoken throughout South Asia to the present day.
This “invasion theory” remains the traditional academic model for Indian prehistory, in part
because it explains the similarity of Sanskrit to ancient Greek and Latin. However, archaeologists have
not found clear evidence for a culture from the Eurasian Steppe or Central Asia that influenced South
Asia in the relevant period. The best effort to address this lack of archaeological evidence is currently the
“Kulturkugel” model, in which invaders spread a new Indo-European language without noticeably
impacting the material culture of South Asia. Similarly, linguistic evidence for any pre-Vedic “substrate”
language of the Indus Valley is somewhat limited.

 A New Model (Vedic Harappans): To address this lack of evidence for Vedic invaders from
Central Asia, some scholars are beginning to explore evidence for greater antiquity of the Vedic culture
(dating to the Harappan period) and a South Asian geographical setting for the Rigveda and other texts.
Proposed evidence for the antiquity of Vedic cultures has included astronomical references in
Vedic texts that date to 2,500 BCE and possibly older based on changed star positions (due to the
precession of the equinoxes). Geographical terms in the Rigveda suggest a South Asian setting, including
areas near the Indus Valley and as far east as the lower Ganges. Similarly, river names in the Punjab
suggest the local antiquity of Sanskrit speaking cultures in northern India.2
Most importantly, the Rigveda itself does not mention any migration to northern India. In
contrast, related Zoroastrian texts from Central and West Asia do mention a migration from an earlier
homeland (possibly near the Hindu Kush Mountains). Early evidence from outside of India also includes
West Asian Mitannian and Kassite cultures (contemporary with the Harappan Civilization), which used
Rigvedic like deity names and the peacock (a South Asian animal) as an artistic motif. Taken together,
this suggests the possibility that Vedic cultures were indigenous South Asians (possibly one of several
Harappan cultures), appearing in West Asia through the trade links known to archaeologists.

 The Language Puzzle and Evidence for Early Migrations: A new model of “Vedic
Harappans” would however, create a new puzzle: if there was no Vedic invasion, how did Indo-European
languages find their way to both Europe and South Asia? Archaeological evidence supports two major
expansions into South Asia: (1) a Neolithic expansion (possibly from West Asia) between 6,000-4,500
BCE; and (2) an Iron Age expansion (possibly from Central Asia) between 800-200 BCE.
Neolithic (Pre-Harappan) Expansion: One possibility is that food producing cultures of West
Asia brought Indo-European languages to South Asia during the Neolithic expansion (6,000-4,500 BCE).

 This early date for the languages ancestral to Sanskrit would not contradict the Neolithic date for the
Proto-Indo-European language that has been proposed by some linguists

 It was going nice unill got struck by this funny and idiotic assumption-

 Iron Age (Shakya) Expansion: The second expansion dating to 800-200 BCE has been
associated with Shakya or Saka (Scythian related) cultures from Central Asia that influenced early
Buddhist culture in India. For instance, the Sanskrit scholar Michael Witzel has suggested Central Asian
links for some Shakya customs, such as the use of burial mounds (stupas) and Zoroastrian concepts in
Buddhist literature.
First emerging in Śākyamuni’s native kingdom of Lumbini (in present day Nepal), Buddhism
eventually spread outward from the Indian Subcontinent and flourished in the mercantile Silk Road oasis
settlements of Central Asia. In the context of a “Vedic Harappans” model, these Shakyas might have been
peripheral Harappan or Vedic influenced cultures from Central Asia that returned to the core Vedic
location of India during the Iron Age.

This shakya-saka connection theory is an old one with recently regenerated by Indologists like Michael Witzel but has no real base at all. Now just see the vital conclusion-

 Both STR and SNP based analyses indicated substantial genetic links between the Indus Valley
and both the interior of the Indian Subcontinent and West Asia. Archaeological evidence for a population
expansion (possibly from West Asia) between 6,000 and 4,500 BCE might relate to genetic links with the
Mesopotamian region (STR) and Caucasus-Anatolian region (SNP). Expansions of food producing
cultures during this period might have provided an opportunity for the Indo-European languages
(ancestral to Vedic Sanskrit) to reach the Indian Subcontinent.
In contrast, genetic links with Siberian populations were smaller. These included relatively small
Altaian (STR), Baltic-Urals (SNP), and Mongolian (SNP) genetic components. These genetic links might
express later and less extensive population expansions from the Eurasian Steppe and Central Asia, such as
possible Shakya migrations during the Iron Age.
In addition, results also suggested genetic expansions from India to Central Asia. This included
South India components identified in Kalash, Tajik, and Turkmen populations near the periphery of the
Indus Valley region. These genetic links might express population expansions from South Asia, such as
during the period of the Bronze Age Harappan Civilization. Future research might explore South Asian
genetic links in more distant locations (such as the BMAC and Urals), where evidence for Vedic
influences in material culture have been suggested by archaeologists.
In summary, results are consistent with emerging alternative models of South Asian prehistory, in
which the Vedic cultures were descended from indigenous Harappans already resident in South Asia.
Rather than a putative “Indo-European invasion” from Central Asia in the late Bronze Age, results
suggest the possibility of an earlier and more peaceful “Indo-European diffusion” of food producing
cultures from West Asia during the Copper Age.

yog

 My conclusion:

Atleast the age of Indo-European language here is getting older which i think is correct and yes Rikved should be pushed 6-5 centuries deeper than its current date of around 1700-1100 B.C.

  About the 800 B.C. intrusion( should be close to 600b.c. instead of 800b.c. See the BMAC post link) i think they were related to the Parthians or to the  Dasa-Dasyu people mentioned frequently in the Rikved  rather than the saka people.

As we should know the scythian related people started to venture here only from the middle 2nd century b.c.

We should also remember that Chandragupta  with the help of his teacher Chanakya  aka Vishnu Gupta aka kautilya  estabilished an unified Indian empire the legacy of which lasted  untill 185 B.C. starting from 322B.C. so i don't see  much of intrusional admixtures happening during that period!

so the 800-200 b.c. idea is not that promising at all.

And at the last the age of the components is more vital than the proportion on certain populations.