Some sneak previews of The Genographic Project

By Razib Khan | November 7, 2011 10:59 pm

The Genographic Project has been going on for 6 years now, and it seems like some interesting results are going to come out soon. CeCe Moore was at the FTDNA conference, and relayed the following interesting (to me) reports from Spencer Wells:

– Using a sample of more than 2,000 Hungarians they found 2-3% Asian mtDNA haplogroups. I would be curious about this number set against the basal Central European rate.

– “DNA evidence is showing that the Indian caste system is older than Indo-European influence.” This is intriguing. Using ADMIXTURE genome bloggers have adduced that high caste non-Brahmins in South India, who are unlikely to have any Indo-European ancestry, can be distinguished from low caste groups. There does seem to be a separate “European-like” element which is found among South Indian Brahmins and Indo-Aryan speaking groups. And yet David Reich’s group seems to be poised to come out with a paper arguing for the large demographic role of Indo-Europeans in the ethnogenesis of modern India.

– ‘…farmers replacing hunter gatherers in Central Germany and mtDNA Haplogroup U5, which Spencer called “the hunter-gatherer haplogroup”. They found different frequencies of haplogroups from samples at different layers. He says that the debate about the age of R1b has not yet been resolved.’

– “1 in 17 men now living in the Mediterranean descend from Phoenician traders.” I have a hard time believing this on the face of it, but not totally implausible in light of “super-Y” lineages you see now and then.

– “East Indians have the most Eurasian diversity.” There’s a lot of circumstantial evidence pointing in this direction. The major question is whether this is an artifact of the relatively recent admixture between two very distinctive populations which gave rise to South Asians. I think not. The “Ancestral South Indians” probably have deep roots in the subcontinent, and have been reservoirs for genetic variation for a long time due to the region’s relative shelter from the Ice Ages.

  • CeCe Moore

    Thanks for quoting my blog. Please note that the “1 in 10” number in regard to the Phoenician traders was a typo. It should have been 1 in 17. I apologize for the mistake.

  • Dienekes

    The 1 in 17 Phoenician figure comes from the Genographic Project’s deeply flawed 2008 study

    There _are_ Carthaginian/Phoenician bones lying around. It’s time to test them, instead of making up stories based on modern populations, which, as we have seen, are not always the best representatives of the ancient ones inhabiting the same lands.

  • Eurologist

    @ point (1): Remember, the recently tested early neolithic LBK and pre-LBK Hungarian samples showed a high percentage of Asian mt_DNA (in my view, from the known Caspian –> Black Sea water flow and connection). One would need to see details (haplogroups), here, but I am curious how much of this is recent history, and how much of this could be evidence of a gradient ~9 millennia old…

    @ point (2): I find myself repeatedly emphasizing that pretty much from the beginning of possible AMH settlement in the subcontinent (~125,000 – 70,000 ya), until well after LGM, with very brief intervals of exceptions, there were two very distinct and well-separated ecological niches, due to the severe aridity of the mid-sector (almost everything from the Thar desert region through most of India except the Himalayan foot hills and a thin strip along the southern and eastern coast). As such, people in N/NW India/Pakistan at the time clearly had a West Asian/European affinity (they largely were their parents), while the Southern and extreme Eastern population of the subcontinent have a SE Asian affinity (and, much later, with the introduction of rice farming, East and Northeast Asian contact). ANI does not equal late West Asian / European influence – much of this affinity could have happened 40,000 years ago.

  • Razib Khan

    ANI does not equal late West Asian / European influence – much of this affinity could have happened 40,000 years ago.

    i’ve talked to nick patterson about this (one of the authors on ‘reconstructing indian history’). there’s just no way that it’s 40,000 years old in terms of separation. the “ANI” has an Fst WAY too close to northern europeans. so you’re very wrong about this specific issue (unless genetic change is mysteriously slower than all geneticists assume). at the least there had to be lots of gene flow to equilibrate allele frequencies between ANI and europeans/west asians.

  • http://India Indrajeet Kashyap

    Are not ANI and ASI heterogeneous then why they are used as if they are homogeneous ancestral populations?
    Also it gives wrong impression by naming them ANI as if it certainly have originated within India . is it to do with politics within India where Hindu fundamentalists are bitterly opposing anything similar to Aryan migration?
    would it not be better to compare ANI with Central Asians and West asian population giving more clarity.
    Also May be this ASI represents hunters and gatherers of Indian subcontinent and south east asia when it is totally covered with forests.
    Then Many waves of ANI migration came from North West which marzinalised these groups even their languages
    May be what we called Dravidian languages of South India were based out of India and they themselves have marginalised these tribal groups much before ‘Indo European” migration.
    The ANI which is shown in these tribal groups of south india may be due to this dravidian influence.
    certainly ANI does not necessarily mean Indo european languge speakers.
    May be dravidian speaking ANI component are dark complexioned Caucasians which may have brought agriculture to India
    Then continuous migration of ANI related people must have been coming to India giving Indian populatuion the current shape.
    Also i want to say that caste system must have originated due to race difference ( differnce in skin colour) which could be due to Dravidians or Indo european speakers one doesnt know
    Also lactose intolerance and sickle cell disease must be used to get a more clear picture
    eg. sicle cell in India map
    also one can look at central and eastern indian geography of highlands and forests in which tribals reside to get more clear picture
    also these NW SE axis is due to difficult and forested terrain of Central- South east india which is inhabited by mainly tribals which were protected from Northwest influence.
    I am not an expert but i hope for some response to some of my questions after ignoring my obvious layman mistakes.

    From India

    P.S. English is not my first language

  • http://India Indrajeet Kashyap

    some things more i want to say
    about austro asiatic tribals( a part of larger central and eastern india tribal groups) they must be ASI tribals admixed due to austro asiatic speaking tribals from south east asia as they have clearly some distinct facial feature from rest of neighbouring tribals.
    Also GOVT of India has done some aberrations in Tribal list adding some non tribal groups like Meenas of Northwest India and omitting some real tribal groups from tribal list so one has to be careful with govt identified tribal list as there is some poliics in it because some groups have fallsely included themselves into it to gain from affirmative actions
    also govt doesnt differentiate between tribals of Nort east india and Central and eastern India which have differnt ethnicity.

  • Eurologist

    “at the least there had to be lots of gene flow to equilibrate allele frequencies between ANI and europeans/west asians.”


    No doubt. But I also believe this (not complete but efficient) separation within the subcontinent was present from the beginning (some time 125,000 to 70,000 ya) and persisted until some time after LGM. ~45,000 ya is just the first time of consequence with regard to West Asia and Europe, of course gene flow persisted, also significant back-migration even along the southern coast, during opportune times (e.g., y-DNA haplogroups G, IJ, L, T).

    I am not denying some people moved into the area from the West during neolithic or bronze age times – I am just saying I suspect there is a *significant* – and perhaps dominant – effect from the persistent split within the subcontinent itself.

  • Aren



    Pre-ANI-ASI split stage, the Ancestral Indians, located diffusely from Gujarat/ Sind to the South Indian tip. Yet one of its limb extended along Narmada, to the Sone river. Then along Sone to Ganga, then along Ganga to Brahma-Putra. Then Along BrahmaPutra river into Tibet. That is why we get some of the oldest genes like Y-hg D in Tibet.The other limb proceeded coastally to Kerala, then reached Andhra coast, then Orissa, then Bengal and then moved into the SEA. The Indian tribes (Austro-Asiatic Speakers) originated at North Andhra-Orissa-Chattisgarh-Jharkhand region. The northwest Indians evolved the Indo-European languages, and the South Indians developed the Dravidian languages.

    ANI is thousands of years older than (contemporary) Europeans and Central Asians, and ANI is not any existing gene pool, but a re-constructed hypothetical gene pool, just like the Proto-Indo-European language. Now if we assign the term “Ancestral Indians” or AI to the first Indian settlers they were the first Eurasian people outside Africa.

    Soon they expanded to fill the whole of India. Because of geo-climatic barriers within India, this population developed regional genetic diversions/mutations/ features, and these genetic changes can now be identified by means of DNA technology, because we can determine the age of the DNA mutations. For example mitochondrial DNA haplogroup M2 should be considered to have originated within ASI and M3 within ANI from Ancestral Indian M*.However, we get a mixture of both ANI and ASI genes or DNAs in modern Indian population.

    The European, West Asian and Central Asian DNAs match with DNAs identifiable with ANI. This is because these populations emerged out from the population inhabiting North India before ANI and ASI admixture took place in India. These migrations took place between 55,000 years and 30,000 years back. With a more recent migration out of India into central asia, and europe, with the onset of agriculture.


    Human Genetics at the University of Michigan, conducted genetic analysis of Indian-born individuals in the US. Their studies of 1,200.’We were struck both by the low level of diversity amongst people spanning such a large geographical region, and by the fact that people of the Indian sub-continent constituted a distinct group when compared to populations from other parts of the world,’ said Pragna I. Patel.

    Sahoo et al had actually written the following words:“The perennial concept of people, language, and agriculture arriving to India together through thenorthwest corridor does not hold up to close scrutiny.Recent claims for a linkage of haplogroups J2, L, R1a,and R2 with a contemporaneous origin for the majority of the Indian castes’ paternal lineages from outside the subcontinent are REJECTED, although our findings do support a local origin of haplogroups F* and H.” .They also rule out arrivals from Southwest Asia because West Asian haplogroups (like Y-Hg G) are not found in India.

    Kivisild’s findings (2003) too had shown that humans could not have arrived from West Asia into Indiabecause of lack of West Asian Y-hgs E, G, I, J* and J2f. Kivisild et al wrote,“When compared with European and Middle Eastern populations (Semino et al. 2000), Indians (i) share with themclades J2 and M173 derived sister groups R1b and R1a, the latter of which is particularly frequent in India; and (ii) lack or show amarginal frequency of clades E, G, I, J*, and J2f.”

    There is a fundamental unity of mtDNA lineages in India, in spite of the extensive cultural and linguistic diversity, pointing to a relatively small founding group of females in India. Most of the mtDNA diversity observed in Indian populations is between individuals within populations; there is no significant structuring of haplotype diversity by socio-religious affiliation, geographical location of habitat or linguistic affiliation.- Scientists Susanta Roychoudhury and thirteen others studying 644 samples of mtDNA from ten Indian ethnic groups.

    Dravidian” authorship of the Indus-Sarasvati civilization rejected indirectly, since it noted, “Our data are also more consistent with a peninsular origin of Dravidian speakers than a source with proximity to the Indus….” They found, in conclusion, “overwhelming support for an Indian origin of Dravidian speakers.”The frequencies of R2 seems to mirror the frequencies of R1a (i.e. both lineages are strong and weak in the same social and linguistic subgroups). This may indicate that both R1a and R2 moved into India at roughly the same time. R2 is very rare in Europe.

    Sanghamitra Sengupta, L. Cavalli-Sforza, Partha P. Majumder, and P. A. Underhill. – 2006.


    To indrajeet, you seem to think colonial bias is neutral.What i come over and over again is indians who have been educated through a colonial western biased education system, which promotes a western centric view of histoy, genetics, and civilisation. And the current indian education system needs reform as at the moment its a very biased education system created and funded by the british empire.But as history has shown us, the european expansion was the most racist, brutal system of occupation.Even terminology, such as Indo-European, would be better classified as North Indian language group. Because the western world had Military domination over Asia, it has written history in his image. So in other words, If India had conquered Europe, and Central Asia in modern times, today it would be known as a North Indian language group instead of a Indo-European classification. Lets JUST accept for one moment that European culture is derived from North Indian population. That means a direct contradiction to the religous ideology of Jews, Christians and Muslims. That changes everything,in history, in politics, in culture and most importantly it challenges the VERY basis of Abrahamic faiths, as being nothing more than a very old branch of indic culture.A connection diluted on purpose to give more support to a local middle eastern/ biblical home of jews, christians and muslims.Almost all research articles go AGAINST the fictional story created by abrahamic intellectuals in wanting to make central asia the home of civilisation, which would go nicely with the religious origins of the jews, the muslims and the christians, who all support this religous fallacy.

    ANI and ASI are genuine south asian markers. ANI is the ancestor to west asian markesr. THEIR was no migration into india that had any significant impact. No greek genome of alexander the great in india, only measurable in Afghanistan. IT was always a migration out of india. civilisation rose in india, and then abrahmic faiths through conquer and invasion rewrote history, only to be found out by genetics.

    ASI and ANI always group together, they constituted a distinct group when compared to populations from other parts of the world.

    Now the many abrahamic culture want to know their origins, you KNOW it. I say argue over yourselves who is what race, maybe start a new eugenics program.

    and Indo-european language group.Not from central asia, or europe. but again from North west India, Who always group closer to other indian groups. Indians are ONE distinct population. ITS central arabs, middle eastern, north african, southern european who are the REAL mixed breed.

  • http://India Indrajeet Kashyap

    This is what i was talking about Hindu Fundamentalists( @Aren ) similar to the Creationists of America keep on piling their ideological crap. He must be a RSS ( Rashtriya Swayamsevak Sangh ) supporter too.

  • RKM

    The Indian subcontinent, because of its pivotal position in the Eurasian landmass, has acted both as a capacitor (during glacial maxima) and as a pump (during glacial minima). Therefore, there has been immigration and emigration through the northwestern and northeastern corridors and the coasts. As data from linguistics, genetics, anthropology and archeology are integrated, a few axioms and some plausible hypotheses emerge:

    1. The Indo-European language family is descended from a proto-language that was not spoken in the Indian subcontinent (axiom). Given the overwhelming evidence supporting this, to argue for an out-of-India hypothesis is to join hands with the flat-earthers.

    2. There are detectable genetic differences (in both autosomal DNA and in Y chromosomal and mtDNA haplogroups) among endogamous groups within the subcontinent that are structures by geography, language and caste (strong hypothesis). This confirms a fact that is obvious to anyone with even a cursory knowledge of the subcontinent.

    3. It is beginning to appear that the Paleolithic and early Neolithic components predominate in the genetic composition of most subcontinental groups (strong hypothesis). The latter component is larger than the former, likely reflecting the demographic expansion of agricultural groups at the expense of hunter-gatherer groups.

    4. The early Neolithic group is genetically more proximal to west Eurasian populations than to east Eurasian populations (strong hypothesis). As such, this makes up the bulk of David Reich’s ‘ANI’ component (strong hypothesis).

    5. The genetic contribution of proto-historic and historic groups (i.e. Indo-Aryans, Parthians, Scythians, Parthians) is relatively small (<30%) in most groups and displays obvious north-south and upper caste (all upper castes in the northwest, mainly brahmins outside the northwest)-lower caste clines (strong hypothesis).

    6. The early Neolithic farmers came into the subcontinent from the northwest (strong hypothesis given biological discontinuity in the skeletal remains between Mehrgarh II and III, 6-7 kybp), possibly speaking a language of the Elamo-Dravidian family (weak hypothesis). The magnificient Indus Valley Civilization likely evolved from within this group (moderately strong hypothesis). This would explain a discernible difference between non-brahmin south Indian upper castes (more early Neolithic, less Paleolithic) and south Indian lower castes and tribals (more Paleolithic, less early Neolithic) and would suggest that the Indo-Aryan 'varna' system was an overlay on a pre-existing 'jati'-like system that resulted from the expansion of agriculture in the subcontinent (emerging hypothesis).

    7. The Y chromosomal haplogroup O2a is strongly associated with the Austro-Asiatic language family both within India and outside it (strong hypothesis). According to Sengupta et al, this haplogroup is likely not autochthonous to India (strong hypothesis). This may have been a male-mediated immigration of rice-farmers of the eastern Neolithic into India through the northeastern corridor (moderately strong hypothesis). Given the fluidity between marginal farmers and hunter gatherers, both groups are represented among Austro-Asiatic speakers in present-day India.

    8. The language isolate from Nepal, Kusunda, seems to be affiliated with the Indo-Pacific language family (moderately strong hypothesis) and related languages may have been much more widespread in the subcontinent among Paleolithic hunter gatherers (emerging hypothesis) prior to the arrival of early Neolithic farmers.

    Now, I am well aware of the political dimensions of this debate. No doubt colonial historiography overplayed the 'blond, blue-eyed Aryan conquerors'-bit. However, the Indian nationalist attempt to bring pre-history and history in line with the modern Western nation-building theme of 'one race, one religion, one language' seems to gloss over emerging data that may problematize the overly simplified implementation of this project . Isn't it obvious that no place in the Eurasian landmass, including Europe, has remained untouched by population movements? What does 'autochthonous' even mean any more in light of the 'Out-of-Africa' model? Acknowledgement of this in no way undermines the project of building the modern nation-state of India, which, after all, explicitly espouses a uniquely dynamic pluralism.

  • Onur

    May be dravidian speaking ANI component are dark complexioned Caucasians which may have brought agriculture to India

    They were probably as dark as Iranians at most, given the fact that the West Eurasian agriculture came to the Indian subcontinent from Greater Iran.

  • http://India Indrajeet Kashyap

    “They were probably as dark as Iranians at most, given the fact that the West Eurasian agriculture came to the Indian subcontinent from Greater Iran.”

    May be the Ancestral Dravidians were dominating that region before and why you assume that present Iranians are the direct descendants of proto Dravidians without any outside influence given the whole history of that region.

    this ANI must be further analysed to give a clear picture it must be a combination of Dravidian and Indo Aryan/ Indo european influence

  • Onur

    why you assume that present Iranians are the direct descendants of proto Dravidians without any outside influence given the whole history of that region.

    I did not say Iran has not genetically changed any since the time of Neolithic migrations. But the recent findings that ANI is genetically very close to modern West Asians (including Iranians) strongly suggests that ANI had a West Asian look (including complexion).


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


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