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514px-Major_crop_areas_IndiaThere seems to be a deep and ancient connection between the populations of Southeast and South Asia, most evident in the substrate of the Cambodians. In First Farmers the author relays an early report about a farming community in northern Vietnam where morphological and ancient DNA evidence both pointed to a stabilized coexistence between a classically East Asian majority population and another which he terms “Austro-Melanesian.” This latter group has been predominantly absorbed today, but seems to persist in isolated tribes such as the Senoi. But these are most certainly residual elements, near extinction, and it seems the dominant genetic heritage of major ethnicities such as the Khmer derives from agriculturalists who left southern China over 4,000 years ago. Only in eastern Indonesia does the Melanesian component of ancestry in Southeast Asia begin to increase to a non-trivial component, and this area is truly as much or more part of Oceania than maritime Southeast Asia.

Freida Pinto

Freida Pinto

Nguyễn Linh Nga

Nguyễn Linh Nga

The Indian subcontinent has also characterized by a synthesis between outsiders, who likely brought farming technologies, and the native inhabitants. These ancient populations had very distant connections to the ancestors of the hunter-gatherers of the Andaman Islands, and no doubt with the peoples of pre-agricultural Southeast Asia, and further on toward Oceania. This is not to say that the zone between the South China Sea and Indus was homogeneous. Rather, like Northeast and Northwest Eurasia, it was likely a region where peoples diversified from an original Pleistocene element which arrived ~50,000 years ago, and retained broad affinities through gene flow and common ancestry. But whereas the farmers in Southeast Asia came from the north, those in India came from the west. Additionally, it seems clear that the fraction of ‘indigenous’ ancestry is far higher in South Asia, on the order of ~50% across the subcontinent. The equivalent figure for Austronesians, Daic, Burman, and Austro-Asiatic populations of Southeast Asia of Pleistocene hunter-gatherer is probably closer to ~10% (higher in the Austro-Asiatic, least among the Daic).

Ggas_human_soc So I have decided to offer up a hypothesis: the agricultural toolkit which West Asian farmers brought to the northwest fringe of the Indian subcontinent was far more constrained in its ability to expand than the equivalent for the rice farmers from southern China. Though there is still debate, it seems that the dominant Indian cultivar of rice has an East Asian origin. Though wheat plays an important role in Pakistan and northwest India, rice is the staple crop for the preponderance of the South Asian population. Though I hold to the proposition that the Austro-Asiatic populations of South Asia are recently intrusive (i.e., they are not the primal inhabitants as some would argue), for geographic reasons, it seems that east to west migration across the difficult north-south mountains separating South and Southeast Asia served as a check on migration from farmers in that zone. Ultimately it was South Asian rice farmers, a hybrid population, that pushed south and east and absorbed the tribal hunter-gatherers who remained in their fastness (the current Indian tribes are not descendants of the original hunter-gatherers, but admixed populations at the margins of Sanskritic civilization; both genetics and their mode of production suggest this). The long pause in the northwest due to the limitations of their agricultural toolkit may explain the difference between South and Southeast Asia in the completeness of their demographic assimilation. Where the rice farmers from southern China swept across all of Southeast Asia rapidly in a singular sweep, the West Asian farmers were halted for many generations at the limits of their ecological range, absorbing genes from the hunter-gatherers on their frontiers. The analogy here would be the Xhosa, Bantus at the edge of their range of expansion which have absorbed a great deal of genetic material (~25% of their ancestry) from Khoisan populations. Once the proto-Indians of the northwest had accumulated enough cultural adaptations their distinctive West Asian genetic signal may already have been substantially diluted by gene flow from the hunter-gatherers to the south and east. The subsequent expansion into the forest zones was likely a demographic disaster for the old natives, but the newcomers themselves were already partly cousins.

• Category: Science • Tags: India Genetics 
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  1. I understand that South China is almost tropical already.

    IIUC, you suggest South Chinese farmers were more successful in Southeast Asia than Northern Indian farmers in South India, because their agriculture was better suited to the new environment.

    But is it possible that the South Chinese themselves were better adapted, e.g. in terms of resistance to tropical diseases?

    How could one distinguish between the two?

  2. Rice yield is proportional to water availability (needs more than 1200 mm water) and hours of sunlight. Many parts of India have less than 700 mm of water availability annual and about 12 hrs per day of sun. The yield potentials are poor. Rice was Not a staple crop of a majority of Indian population until about 50 years ago. Sorghum (jowar) and Bajra and other dryland crops were. Rice was a staple crop in the lowlands. It was only after the green revolution that rice came in and swept aside the traditional dryland crops. You can compare the share of rice + wheat from 1951-200 in this table from Planning commission.

    Table 6. Rice and Wheat Production

    Production (million tonnes)

    Year Rice Wheat Foodgrains R+W as % of Foodgrains
    ____________ million tonnes _________________
    1950-51 14. 8 8.9 50.8 46.8%

    1970-71 40.80 20.86 108.4 57.4

    1980-81 49.91 34.55 129.6 65.4

    1990-91 72.78 53.03 176.4 75.0

    1996-97 81.74 69.35 199.4 75.0

    To a large extent, more than 65% of the food grains produced in India until 1950 was wheat (grown without irrigation), jowar and bajra, which were all dryland crops. Rice was a post 1960s innovation.

    Whereas, all you say about farmers pushing aside is true, I just question that a majority of South Asian farmers were rice farmers; they grew a lot of “Lost” african crops like sorghum and pearl Millet. May be, the farmers who pushed aside the hunter-gatherer were rice farmers in Bengal, but not in other states. Even in my lifetime, I have seen these crops disappear, and I am sad because they are such frugal consumers of water. Who knows, may be by the time I die, all the water will be gone and it will back to Jowar and Pearl millet again for Indians.

  3. IIRC, there was a study of genetics in Eastern Indonesia which found the majority of the “Negrito” ancestry there was actually Papuan. This isn’t really surprising, given it’s known that Papuan languages (deeply nested within Trans-New Guinea Phylum) are found in Timor and other nearby islands.

    Regardless, your overall point seems plausible. IMHO this is one reason to still view Greg’s latest hypothesis with a grain of salt regarding Europe. We know “First Farmers” there left some hunter gatherers largely alone for thousands of years, and prior to both crop innovations (oat domestication, for example), and genetic adaptations (lactase persistance)

  4. I understand that South China is almost tropical already.

    actually, correcting for latitude south china is far colder, as it is not as shielded from siberian blasts. the difference is rainfall, and rainfall regime (northwest india starts shifting to a pseudo-mediterranean winter rainfall maximum). so the gist of the argument is that india is bifurcated between qualitatively different ecosystems, and west asia resembles only the northwest fringe. in contrast southeast asia and southern china are very similar, with one (southern china) just being a cooler version of the other.

    vijay, what you say sounds plausible. interesting bengal seems to be one area where recent southeast asian ancestry is ~10%. everywhere else there’s basically not outside of the himalayan fringe (the low east asian fractions are deep shared ancestry).

    IIRC, there was a study of genetics in Eastern Indonesia which found the majority of the “Negrito” ancestry there was actually Papuan.

    yes. they aren’t really negrito at all, in that they aren’t smaller. basically just melanesian. i’m pretty sure that the negrito phenotype is not reflective of ancient hunter-gatherers. the andamanese of sentinel island are not notably small. perhaps farmers chop down the ‘tall trees’ of HG populations?

  5. Yikes, I misunderstood this completely; what you are saying in bullet points is this (correct me if I am wrong):

    1. There were people residing in India who were farmers in the northwest, before 4000 BP that grew some crops like millet and cotton and sesame, but not rice.

    2. Hunter gatherers were distributed all over India. They may have had a lot of ASI.

    3. About 4000 years BP, monsoon patterns shift East to create a favorable situation for growing crops in the eastern part of India, but what crops to grow?

    4. People arrive through Khyber carrying 9000 year old Japonica; they somhow convert that to Indica in the Gangetic plain and east. They intermarry the hunter-Gathererss and former refugees from the Indus valley.

    5. However, the people who arrived from the northwest were not original rice growers in their homes; they are not great rice growers in their new digs.

    6. The remaining people who dispersed, continued to grow African-origin millets and Sorghum in the rest of India.

    It gives an idea; may be the distribution of ASI vs. ANI should be related to rice growing castes/groups versus sorghum/pearl millet/cotton growers versus Hunter-gatherers (to the extent you could be one in India)? If you looks the ANI/ASI percentage among the caste groups it does not vary in a region (say, between Kayasthas and Kurmis and Koeris in Bihar) but between Velalars versus Irulars (who are even more hunter-gatherish).

  6. A secondary confirmation of farmer spread into the gangetic plain growing rice is the arrival of Bos Indicus (not causation, though). Rice fields need tilling because of the clay pan formed by repeated flooding. Tilling was by bulls. The bulls were probably prized more for labor than the cows for milk, given that lactase persistence was rather low still. Bos Indicus arrives in the Gangetic plain 4000-3000 years BP although it originated at the Indus Valley 7000 years BP. (

    I still do not understand the “jungli abides”; the ASI were also possibly farmers growing millet cotton and sesame using the Bos Indicus for draught in 7000 BP in IVC and 5000 years BP in South India. Alternately, they may have also been admixed population, with pure ASI left only in the hunter-gatheres at that time.

  7. Doesn’t it evoke the differences between the US and South-Central America? Less admixed by both native pre-colonization populations and African vs. much more admixed? Yet the hypothesis that both inadequate agri-practices and susceptibility to tropical diseases checked the European advance in the South may not be fully sufficient.
    For example in Argentina, European crops and cattle fit perfectly well, and malaria wasn’t more common than in Italy where most immigrants hailed. Yet the resulting degree of admixture is qualitatively similar. Does it mean that you have to account for different cultural practices of the newly-migrated populations to explain the different admixture outcomes?

    PS: Looking forward to your review of “Son Also Rises”!

  8. Christ…I thought I closed up without posting my last comment, which was incomplete. I suppose the remainder should be obvious – large portions of northern Europe were likely not very hospitable to Near Eastern crops either immediately, and the pause seen in the archaeological record for agriculturalists suggests there could have been some significant admixture between first farmers and hunter gatherers in Europe. It is true that it seems the later expansion of Indo-Europeans might have accounted for much of the 50% which is “hunter-gatherer,” but even in that case, there are some similarities with the Indian situation, insofar as the Proto Indo-Europeans themselves were a culture on the margins of farming society with a great deal of hunter-gatherer admixture which happened upon their own, superior, agricultural toolkit for Europe.

  9. As an aside, the very early interchange of crops between the Indus Valley and Africa has always intrigued me. I mean, we know the Indus Valley Civilization was fairly wide ranging for its time, given they seemed to trade with Sumeria, and possibly even Crete and Egypt. But it still sort of boggles my mind how sorghum got to India, considering the Sahel doesn’t come anywhere near the Indian ocean, and during the time period in question the Bantu expansion hadn’t introduced it to coastal East Africa.

    A further aside from Vijay’s comment. At first the idea of rice being introduced from the Khyber pass seems ridiculous, given it’s very much the long way around, and would require some movement through pretty ecologically hostile areas (like the Tarim basin) to get there. But the one advantage to it is the expansion of agriculture that way – it actually seems to follow the thrust of Indian culture, which only seemed to expand out of the Indus Valley (e.g., the area well suited to wheat) during the period of decline roughly coterminous with the Aryan migrations. If rice really came from the east, you should have expected that the “rice zone” was mostly settled by Southeast Asians well before South Asians could adopt it into their own package.

  10. “There seems to be a deep and ancient connection between the populations of Southeast and South Asia, most evident in the substrate of the Cambodians.”

    Cambodia is the English version of Kampuchea and Kampuchea derives from the Sanskrit word Kambuja

    and Kambuja might be derive from the ancient sanskrit name of Kambojas in Mahabarata

    There may or may not be a genetic connection between them.

    However, there are relationships between Munda people of India, the Khmer people of Kampuchea, Hmong people of Southern China/Vietnam,

    “O2a-M95 (including O2a* and O2a1) is the most
    frequent haplogroup in MK (87.18%) and HM (45.16%)
    populations. It is scattered in the area from Northeast India to
    Southwest China and island Southeast Asia, appeared with high
    frequencies in different ethnic phyla. This haplogroup has the
    highest frequencies in Austro-Asiatic (both Munda and Mon-
    Khmer subfamilies) and Hmong-Mien populations, while it was
    widely found in Sino-Tibetan, Tai-Kadai, and Austronesian
    populations, with no clear ethnic association but geographic

  11. Razib said above that there is a possibility that paddy came to Bengal from East Asian instructions, but the info Europeans took it and transferred to Indica. Now I think that is more reasonable, if the Tarim Basin was climatically similar to what it is now(which is not provable)

    I was wrong about sorghum also. Both sorghum and pearl millet apparently are crops transplanted to india after the indo Europeans from Africa through some Greek time trade. Sorghum is not a Sanskrit word, it is an African word. Bajra or pearl millet is an Arabic Parsi word. All of these dry crops came via modern Greek and roman galley trade.

    I have a question of my own. Cattle are big in Indus Valley and both Bo’s indicts and bubalus wAs domesticated between 8000 and 5000 bp. Did the Indus Valley people already get the lactase tolerant mutation for adults by this time? Or only the indo Europeans who arrived after 4000 bp bring it along? If the original inhabitants did not have that mutation why did they spend so much effort on dairy? Bulls and cows were big in india and were a big contribution to humanity.

  12. East Asian intrusion into Bengal

    Indo europeans

  13. Bulls and cows were big in india and were a big contribution to humanity.


    also, you do now that the genetic evidence is clear that cultivated rice is all from an east asian source? just to be clear.

    dixie, the cultural connection is well known. i’ve written about it. the genetic one too. i’ve analyzed data from PanAsian data set. looks like some indian connection did occur genetically too. the cambodian affinity is much deeper than that, and doesn’t show evidence of “ancestral north indian.” in other words, it dates to the last glacial maximum.

    also, regarding mundas, i provide links for a reason. i covered that in the post above. please make sure to check links in the future.

  14. “also, you do now that the genetic evidence is clear that cultivated rice is all from an east asian source?”

    We understand. The question remains how the plant traveled from the river valleys of China to India; was it through Yunnan and North east India to lower Bengal via East Asian intrusions to India. Were the people cultivating it prior to the arrival of the next round of north east invaders? Or, the pastoralist invaders brought the Japonica from China (through the Tarim and Taklamakan) and moved to Indo-Gangetic plain where they used the Bos Indicus and the plough to create civilization there. A book tentatively titled “Indica: How a cheap Chinese import transformed a nation of proud pastoralist/nomad/hunter/gatherers to sedentary diabetics” will be useful to understand Indian history.

  15. Hrrm…you seem to be right regarding Sorghum Vijay. I probably should have taken Bellwood’s latest book (which claimed Sorghum was introduced around 2,000 BC) with a bit more of a grain of salt here, considering how weird his whole segment regarding Indo Europeans was.

    Still, my understanding of Indian archeology really does make it seem like farming villages spread from the Indus into the upper Ganges at most only a few centuries before the Aryan migrations. The idea that Aryans brought rice with them seems a bit odd. But rice is cultivated in modern Central Asia through irrigation. Certainly this is a fairly ancient practice, as the Chinese first reported rice cultivation in Central Asia around 200 BC. It very well might have been cultivated at a low level in much of Central Asia going back to 2,000 BC – roughly the same time period as the Aryan migrations.

  16. Although this is somewhat tangential to the main thrust of this post, a note should be made concerning estimates of South Eurasian admixture in the northwestern portion of the subcontinent. ANE admixture is definitely a part of the genetic heritage of northwestern South Asians, and ANE admixture shifts populations to the “east”, despite not being actual “East Eurasian” admixture. If we take this into account, ASI admixture has probably been somewhat overestimated for the northwest. Instead of 25% ASI, I wouldn’t be surprised if northwestern Indians are actually around 15% ASI. This doesn’t make much of a big difference, but it is something to keep in mind.

  17. no, ANE is no closer to east eurasian.

  18. MA-1 clusters among substantially East Eurasian-admixed Central Asians like Uzbeks, and among some of the more West Eurasian of the Hazara (his data has already been analyzed by people in the genetic genealogy community, with both PCA, ADMIXTURE, ALDER, and other software. Also, La Brana clusters among the Burusho, but he is less relevant to South Asia). Yet, he isn’t an East Eurasian, or even East Eurasian-admixed. I understand that, and I never suggested that he is closer to East Eurasians in terms of his linage or clade. I also understand that he is actually ancestral to many living West Eurasians.

    But he is outside present West Eurasian variation, and he appears significantly “Eastern” shifted, because he lacks any connection with the African-like “Basal Eurasian” element in Europe and Western Asia. So, is it not reasonable to suppose that a population with substantial ANE admixture will appear slightly more ENA than other West Eurasians, despite that excess “Eastern” pull having nothing to do with actual ENA admixture? In the case of northwestern South Asia, there is some “real” ENA admixture, probably on the order of 10%-20%, but ANE admixture should have some confounding effects. Also, based on various non-academic analyses of his genome, MA-1 has a deep connection to northern South Asia. This is somewhat evident in the paper, with his ADMIXTURE results, but that isn’t very important, you already understand the issues and caveats there. But if you calculate something like drift statistics, populations from northwestern South Asia are rather high on his list, beating all West Asians, and many European populations.

  19. i see. thanks for the clarification. makes a lot more sense. need to think on it deeper. appreciate the follow up.

  20. Hi Razib,

    No problem.

    Also, I’m truly sorry for taking so long to respond. I was waiting for a few analyses, and everything is finally set. Here is a spreadsheet created by David of “Eurogenes Ancestry Project”:

    Please do compare these results with the values found in the actual paper:

    An almost perfect correspondence! It seems very accurate. Since it seems to fit very nicely with the paper, I think the percentages of ANE are broadly correct. In fact, his spreadsheet seems, at least to me, to be more accurate, since he can infer very reasonable ENA percentages. This means better results for the Chechens.

    With all that aside, I’m pointing this out because of my results. I am:

    My ANE percentage is much greater than any other population in Eurasia. I’m almost at the Native American limit. Also, in his run, the average West Asian/Caucasian/Southeast European is 6% East Eurasian. So, I’m just 10% more East Eurasian than the average West Asian/Caucasian/Southeast European. And as this relates to ASI, this means I am likely 11% ASI. Every analysis of my genetic data puts me at 4% Siberian. In addition, this is the value obtained for me by Geno 2.0 (4% “Northeast Asian”). Also, they did construe me as 11% “Southeast Asian”, which is equivalent to ASI for Iranians, some Central Asians, and all South Asians. This would also match the 11% “Onge” obtained by Zack for the HGDP Pashtuns. In short, there is quite a gap between 30% ASI for the HGDP Pashtuns, and only 11% ASI for myself. I think ANE has a role to play here. As a technical note, this was a very intensive analysis on David’s part. He could only do it with one sample at a time. I believe he used PCA. Since he wanted to try analyses on many more samples, he had to give up on this. Instead, he tried ADMIXTURE. It was a question of accuracy versus speed, and he was forced to choose speed. Here are the ADMIXTURE results:

    This is much less accurate, but still, a rather solid analysis. My ADMIXTURE results:

    As you can see, less accurate, but it still seems reasonable. The ENA has been underestimated, and there is some SSA I’ve never seen before, but everything else seems fine. As is evident, ANE does seem to peak in South Central Asia, and Northwestern South Asia.

    But I think this can only be settled via formal academic analysis. I hope we can look forward to a fresh look at South Asia on the part of the Reich lab, utilizing the scenario constructed from ancient genomic data. Also, we have a lot to look forward to from the lab working on Farmana.

    Note: I am of Pashtun background.

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