Category Archives: India

Middle Paleolithic industries of African affinity of the Thar Desert go back to c. 96 Ka ago

Again Team Petraglia revealing fascinating evidence on the Middle Paleolithic dispersal of Homo sapiens, and one that fits well the genetic data (speculative “molecular clock” excluded), as well as with the climatic data.
James Blinkhorn et al., Middle Palaeolithic occupation in the Thar Desert during the Upper Pleistocene: the signature of a modern human exit out of Africa? Quaternary Science Reviews, 2013. Pay per viewLINK [doi:10.1016/j.quascirev.2013.06.012]


The Thar Desert marks the transition from the Saharo-Arabian deserts to the Oriental biogeographical zone and is therefore an important location in understanding hominin occupation and dispersal during the Upper Pleistocene. Here, we report the discovery of stratified Middle Palaeolithic assemblages at Katoati in the north-eastern Thar Desert, dating to Marine Isotope Stages (MIS) 5 and the MIS 4–3 boundary, during periods of enhanced humidity. Hominins procured cobbles from gravels at the site as evidenced by early stages of stone tool reduction, with a component of more formalised point production. The MIS 5c assemblages at Katoati represent the earliest securely dated Middle Palaeolithic occupation of South Asia. Distinctive artefacts identified in both MIS 5 and MIS 4–3 boundary horizons match technological entities observed in Middle Palaeolithic assemblages in South Asia, Arabia and Middle Stone Age sites in the Sahara. The evidence from Katoati is consistent with arguments for the dispersal of Homo sapiens populations from Africa across southern Asia using Middle Palaeolithic technologies.

Possibly the most strikingly unmistakable evidence for a Homo sapiens affiliation of these findings is the Aterian-like tanged point, which is almost identical to another one found previously in Jwalapuram:

Fig. 4. 1) Tanged point from Jwalapuram 22 (adapted from Haslam et al., 2012); 2 & 3)
Tanged point from Katoati.
Not just Aterian: the, visually less obvious, Nubian technology is also present:

Two Levallois cores from S4 and one from S8 exhibit a mixture of distal divergent and lateral preparation of the flaking surface to produce a distale medial ridge resulting in the removal of prepared points (Fig. 3). These reduction schemes are consistent with descriptions of Nubian Levallois technologies (Rose et al., 2011; Usik et al., 2013).

A single flake from S4 presents a combination of distal divergent and lateral removals on the dorsal surface and a prior removal of a pre-determined pointed flake,indicative of the use of Nubian Levallois strategies (Fig. 3).

Table 2. I added at bottom (red) median OSL ages from table 1.

Zhirendong jaw

In synthesis: groups of unmistakably Homo sapiens with obvious African techno-cultural heritage were already within the modern boundaries of the Indian Federation around 96,000 years ago (CI: 109-83 Ka). This totally debunks Mellars’ and Mishra’s recent claims, the usual “molecular clock” nonsense (that so many people seems willing to believe at face value), and widens significantly the earliest plausible dates for the colonization of Asia (beyond Arabia-Palestine-Persian Gulf) making findings like Zhirendong jaw (the oldest non-Palestinian H. sapiens remains out of Africa, dated to c. 100,000 BP) much more credible.

Until today I was very much in doubt about accepting dates of c. 100,000 years ago for the Asian colonization but since right now I am adopting this model as the most likely one. In other words: it seems clear that the people already settled in Arabia and the Persian Gulf “oasis” did not wait for climatic pressure at the end of the Abbassia Pluvial to send them out in search of new lands: they did it when the pluvial period was still holding the arid gates of Asia open for them.
All the evidence adds up well now. 


Note: the full paper was available at at the time of writing this:  HERE and HERE.

Indian Microlithic industry almost contemporary of Western initial UP and LSA

Mehtakheri toolkit
That is what a new study has found, albeit on just one date. Based on that they argue that the recent claim by Mellars et al. (see also here) about an extremely late date for the migration out of Africa (OOA) becomes more plausible.
Sheila Mishra et al., Continuity of Microblade Technology in the Indian Subcontinent Since 45 ka: Implications for the Dispersal of Modern Humans. PLoS ONE 2013. Open accessLINK [doi:10.1371/journal.pone.0069280]
However considering the pivotal role played by South Asia in the genetics of Humankind after the OOA it is still impossible that this microlithic industry corresponds with that process, because the migration and successive Eurasian expansion must:
  1. Have minimal dates of well before 60-55 Ka ago, time when the presence of H. sapiens becomes undeniable from Palestine to SE Asia and Australia
  2. Go at least largely through South Asia; because the distribution and basal diversity of mtDNA M and R, as well Y-DNA F demand it without any reasonable alternatives. 
The authors themselves acknowledge that the finding is inconclusive in this debate but they choose to lean for a revised Mellars-style interpretation on their own subjectivity.
Their hypothesis is not exactly like Mellars et al. These proposed an extremely late (c. 40-35 Ka BP) OoA, which would imply also extremely late colonization of East Asia and Australasia by Homo sapiens (via South Asia). In order to “explain” the lack East Asian blade-like technologies (necessary for the old professor’s ideas about “modern human behavior”) they proposed that the Eastern colonization was led by small populations who somehow lost the technology. But well, as I discussed back in the day, the hypothesis does not stand.
Mishra’s revised hypothesis is somewhat more coherent (but still very unlikely): she proposes that East Asia and Australia were actually colonized with Middle Paleolithic technology (neither blades nor microblades) in the time demanded by archaeological data and that South Asia instead was not colonized by our species until c. 45,000 BP, possibly because there was some kind of intelligent archaic hominin (Hathnora?), which blocked the expansion of our species initially.
However the hypothesis is still plagued by problems:
  1. As I said above, any model that dictates that South Asia was not central to the expansion of Homo sapiens in Eurasia and surroundings must be wrong: genetics demand otherwise. A settlement of South Asia that is posterior to that of East Asia, Papua and/or West Eurasia (other than the initial Arabian trailblazers or boaters) simply does not make any sense.
  2. The African microblade technology is still quite older (70-60 Ka BP) than the South Asian findings and the similitude may well be a mirage or a matter of convergent evolution. Not the only time that people reinvent the same thing separated by time and space: look for example at Neolithic, which was developed at least in four separate regions of the World, maybe more; or look at the Solutrean style of retouch, used in many different Paleolithic cultures separated by time and space (Africa, Europe, America, etc.)
  3. It would require that Homo sapiens would travel through Altai and all the evidence in this North Asian keystone region, a necessary corridor for transcontinental travel before the domestication of camels (or at the very least horses), indicates that it was inhabited by “archaic” hominids (Neanderthals, H. erectus/Denisovans) until c. 47 Ka BP, when industries related to those of West Asia and Europe show up (at later dates associated to H. sapiens remains).
The facts:
A C14 date was obtained for the site of Mehtakheri (near Barwah, Nimar region, Madhya Pradesh) annotated as: >42,900 BP, > 46,555 calBP, >45,028 – 48,081 (68% CI range for the calBP date). Another C14 date from the same site is much more recent (34,380 ± 991 calBP).
They also obtained five of OSL dates for section 2 ranging from 41.6(±3.3) to 47.0(±4.9) Ka ago. Another date for this unit of 55.5(±5.8) was not used by the authors because it corresponds to an unstudied layer.
Section 3 has older dates (65-78 Ka) but it corresponds to the Middle Paleolithic.
The microlithic industry seems to continue in South Asia until the Iron Age, suggesting that Neolithic and later developments did not substantially alter the demography of the subcontinent. 
All this is very informative but the conclusions suggested don’t seem to make any sense. It is much more logical to infer that H. sapiens left Africa with an MSA-like Middle Paleolithic toolkit that was not related to the Nubian culture (the dead horse being beaten once and again by both Mellars and Mishra) but to other ill-defined groups of possible South African affinity (as claimed by Petraglia). Insisting on the Nubian techno-complex, when we do not know it reaching beyond Dhofar (i.e. they did not reach the Persian Gulf “oasis”, unlike Petraglia’s trailblazers or Armitage’s Jebel Faya findings) is taking the part for the whole, as if there was not already a much more widespread and diverse African Middle Paleolithic (MSA, Lupenbiense, Aterian) in those times already.
Instead these data may indicate a relation of some sort with West Eurasian Upper Paleolithic and African Late Stone Age, which are of roughly those dates. This tentative relationship does not imply migration but would just need some cultural contact. 
It would be interesting to know more about the MP-UP transition in the area around Arabia Peninsula in order to develop better theories on this tripartite interaction between the West Eurasian early UP, the African early LSA and the South Asian early microlithic industry. These very possible cultural interactions fit well within the wet phase of the Mousterian Pluvial (c. 50-30 Ka ago).

Update (Jul 11): “microliths” that are not microliths

I just looked for the first time at the technical issue of what is a microlith (~1 cm long, ~0.5 cm wide) and the published toolkits only seem to have one microlith senso stricto: the J4 point. All the rest have lengths of 2 cm or larger, often 5 cm or more.

The presence of some microlith-sized pieces (usually points) in early UP cultures is almost standard: Emirian, Chatelperronian, Aurignacian and Gravettian all them have occasional “microliths” (measured by size) an in all cases these are points, exactly as happens in Mehtakheri.

So these toolkits seem to have more relationship, if anything, with Western Eurasian early UP ones, which are roughly contemporary (Emirian is the only clearly older one).

Furthermore, archaeologist Millán Mozota sees even similitudes with Mousterian flaking style (see comments):

Bladelet flaking is a typical flaking strategy for this blank type
(small pebbles). Specially if the raw material itself is of good enough

It has been documented, for high quality quartz on
Mousterian sites, like in Grotte Breuil and, if i recall correctly,
other sites in that area of the Italian Peninsula.

Being also puzzled because the inventories described suggest a strong blade/bladelet component, instead of microblades. 


Mellars challenges the ‘early out of Africa’ model

I do not have yet access to this potentially key paper, so first of all I want to make an appeal here to share a copy with me (→ email address). Thanks in advance. Update: got it (thanks to all who shared, you people are just great!) I will review it again as soon as possible.

Update (Jun 18): complementary review of the full paper now available here.

Paul Mellars et al., Genetic and archaeological perspectives on the initial modern human colonization of southern Asia. PNAS 2013. Pay per view (6-month embargo) → LINK [doi:10.1073/pnas.1306043110]


It has been argued recently that the initial dispersal of anatomically modern humans from Africa to southern Asia occurred before the volcanic “supereruption” of the Mount Toba volcano (Sumatra) at ∼74,000 y before present (B.P.)—possibly as early as 120,000 y B.P. We show here that this “pre-Toba” dispersal model is in serious conflict with both the most recent genetic evidence from both Africa and Asia and the archaeological evidence from South Asian sites. We present an alternative model based on a combination of genetic analyses and recent archaeological evidence from South Asia and Africa. These data support a coastally oriented dispersal of modern humans from eastern Africa to southern Asia ∼60–50 thousand years ago (ka). This was associated with distinctively African microlithic and “backed-segment” technologies analogous to the African “Howiesons Poort” and related technologies, together with a range of distinctively “modern” cultural and symbolic features (highly shaped bone tools, personal ornaments, abstract artistic motifs, microblade technology, etc.), similar to those that accompanied the replacement of “archaic” Neanderthal by anatomically modern human populations in other regions of western Eurasia at a broadly similar date.

A review has been published at Live Science.

South Asian artifacts from ~30-50 Ka BP.

By “genetic evidence” they obviously mean “molecular clock” nonsense, so it is not evidence at all but mere speculation. However I am indeed very interested in knowing in detail what they mean by “archaeological evidence”, because they seem to get into direct confrontation with much accumulated evidence, first and foremost all of Petraglia’s research in both India and Arabia but also with the quite strong evidence for pre-60 Ka human presence in Australia and growing evidence for pre-60 Ka modern humans in SE Asia (in some cases even as old as 100 Ka). 
It must be said that Paul Mellars has been criticized before a lot for several reasons but very especially for his adherence to the quite speculative “modern human behavior” conjecture and, relatedly, bigotric attitudes against Neanderthal intellectual capabilities, based on nothing too solid. Therefore I’m generally skeptic about what Mellars has to say on this matter because this kind of conclusion is what one would expect from him. 
However Mellars is certainly a distinguished academic and, even if prejudiced and stuck to his own old-school and somewhat Eurocentric interpretations, he knows his trade as archaeologist and prehistorian. So he may be onto something, even if it is not exactly what he wants us to believe. 
For example, it is not impossible that this research may have, unbeknown to the authors, found evidence of a secondary OoA wave (maybe related to the spread of Y-DNA D and mtDNA N?) or even a distinctive evolution in Southern Asian technology prior to the expansion of Western Eurasia. 
It is interesting that they suggest that the 80-60/50 Ka toolkits of India would have been made by Neanderthals, when they are not describing them at all as Mousterian, the almost exclusively Neanderthal techno-culture, or Mousterian-related.
I have some difficulties judging before reading the whole study. However the supplemental material (quite extensive) is freely accessible and for what I can see there:
  1. They dedicate much text to attempt to justify a particular version of mainstream “molecular clock” hypothesis, which are clearly broke in my understanding. The kind of arguments “rebated” are more or less what I have been putting forward since many years ago. Ironically their “molecular clock” estimates make N and R much older than M, what I absolutely oppose (just count mutations downstream of the L3 node).
  2. No real attention is given instead to the geographical structure/distribution of major mtDNA haplogroups, only mentioned in relation to “molecular clock” speculations.
  3. The criticism of the African affinity of the Jwalapuram (Jurreru Valley) cores (Petraglia 2007) focuses on dismissal of any possibility of comparison, rather than on alternative comparisons. 
  4. Another “criticism” is that there is no apparent connection between Jwalapuram and the Nubian Complex (why there should be any?, it is not the only East African techno-culture, nor the only group that shows indications of traveling to Arabia in the Abbassia Pluvial).
  5. Also it is “criticized” that the most comparable African culture, Howiesons Poort) is not recorded before c. 71 Ka BP (what IMO may indicate late cultural dispersals to Southern Africa from East Africa, for example, but, hey!, Mellars is fencing off balls like crazy at his conservative goal). 
  6. They find clear similitudes between Indian and African microlithic industries (apparently related to the development of “mode 4” in both areas, as well as in West Eurasia). Indian industries are dated to c. 38-40 Ka BP, while African ones are dated to c. 49 Ka BP (Kenya) or later. However West Eurasian ones have dates as old as 55 Ka BP (not for Mellars, who remains stuck in older date references which he describes as ∼40–45 ka [calibrated (cal.) before present (B.P.)]), what really suggest that we are talking here not of the “out of Africa” but of the West Eurasian colonization process (necessarily from further into Asia, genetic phylo-geographic structure demands) with offshoots to the nearby regions. 
  7. Another element of late Africa-India “similitude” they find is “the remarkable, double bounded criss-cross design incised on ostrich eggshell”, dated in India (Patne) to at least ∼30 ka (cal. B.P.), much earlier in South Africa. For Mellars this is beyond the range of either pure coincidence or entirely independent and remarkably convergent cultural evolutionary processes. Hmmm, really? Or are we before a clear case of wishful thinking as happens with the Solutrean-Clovis relationship hypothesis? Isn’t it 30 Ka BP anyhow well beyond any reasonable expectations for the OoA time frame, including Mellar’s own conjectures?
  8. Mellars accepts the paradox that the geographical limits of these highly distinctive microblade and geometric microlithic technologies are confined to the Indian subcontinent, with no currently documented traces of these technologies in regions farther to the east. And then makes up excuses for it, such as biological and cultural bottlenecks caused by “founder effects”, mysteriously leading to a loss or simplification of cultural and technological know-how, as well as fininding new and contrasting environments (in the same latitudes?!)
  9. Even in the case of Arabian colonization, Mellars shows to be in a very defensive attitude, admitting only to the reality of the Palestinian sites with clearly modern skulls, as well as to the area of Nubian Complex colonization (on whose peculiarities he insists a lot, as if it would be the only expression of the wider MSA techno-complex), disdaining all the other MSA colonization areas and, often ill-defined, variants.
In brief, for what I could see in the supplemental material, along with some potentially interesting references to the relative cultural community spanning from East Africa to South Asia at the time of emergence of “mode 4” industries, it seems that Mellars and allies are essentially putting the cart (their models) before the horses (the facts), what is bad science. 
In 2008, Zilhao and d’Errico angrily accused Mellars of being an obsolete armchair prehistorian (different words maybe, same idea). Back in the day I was tempted to support Mellars but nowadays I must agree that he is clearly stuck in a one-sided interpretation of prehistory whose time is long gone. Whatever the case I welcome the debate and can only hope that will help to produce even more evidence to further clarify the actual facts of the Prehistory of Humankind.

New rock art findings of India

A new rock art site has been found by the Archaeological Survey of India on the Satpura mountain range, near Batul, at the Maharastra-Madhya Pradesh border. The site includes nothing less that 71 rock shelters with paintings and engravings dating from c. 12,000 years ago (Late Upper Paleolithic) to recent times.

Decors comprise petroglyph’s in various forms, such as engravings,
bruising, pecking and pictographs in various colours, viz red, various
shades of red, white, black and green. The pictographs or paintings
usually illustrate human, animal, bird, tree and abstract geometric
figures and are depicted by stick figures, outlines, solid and X-ray
figures. he engravings usually exhibit elements of natural world as well
as abstract themes. The decorated shelters are spread in an area of
approximately 40 square kilometres, Sahu said. 

No pictures are available.
Source: Indian Express (via Pileta).

Very skeptic on claim of Neolithic flow from India to Australia

I feel quite skeptic about the claims held by this paper but in any case it is worth mentioning.
Irina Pugach et al., Genome-wide data substantiate Holocene gene flow from India to Australia. PNAS 2013. Pay per view (6-month embargo, then freely accessible) → LINK [10.1073/pnas.1211927110 ]


The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early “southern route” migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India. 

The evidence for this claim is all derived exclusively by statistical inference on autosomal DNA. Suspiciously enough, even if the authors claim admixture levels of as much as 11% and as recent as a mere 4000 years ago, no patrilineage (Y-DNA) nor matrilineage (mtDNA) [correction: see update below] has been ever detected that could be associated with this purported migration. 
Additionally c. 4000 years ago Southern India, the alleged origin of the genetic flow, was already immersed in a flourishing agricultural economy and it looks very strange that the migrants, people who were exchanging crops with Africa for example, would not carry a single element of this new economy to the island continent. Of course this inconsistency could easily be fixed by merely arguing that the molecular clock estimates used tick too quickly, which is a general problem anyhow and therefore no real surprise.
If the hypothesized migration happened earlier, in the Epipaleolithic or Late Upper Paleolithic, then it would also be easier to explain that, with smaller populations, genetic drift could have caused the extinction of whatever Indian uniparental markers that the migrants carried with them initially. It still causes my eyebrows to rise instinctively. 
Even then, if this was the case, we should be able to identify some sort of techno-cultural elements that the migrants may have carried with them, like microlithic stone technologies or whatever. As far as I know nothing of the like exists. 
The only techno-cultural burden that the migrants might have brought with them to Australia would therefore have been the dingo, but this dog has lots of relatives in Island SE Asia, where the authors could not detect any significant Indian admixture.
So the hypothesis looks weak to me. Let’s see the evidence they present:

Above we can see the ADMIXTURE K=4 result, probably not the optimal one (which would probably produce an Australian-specific cluster (mostly but not fully masked as Papuan) and surely two different Indian ones, partly masked as European and Onge affinity) but the one the authors decided to show us as evidence for their hypothesis.
Not only this is surely not the optimal clustering level but also Australian Aborigines are comparatively undersampled, while Indian weight is overwhelming. This is a clear example of how NOT to design a scientifically useful sampling strategy for ADMIXTURE-like comparisons like this (because oversampled populations tend to overshadow the rest just by the weight of numbers). 
As it is, this graph proves nothing but rather suggests that some Indian affinity is part of Australian Aborigine ancestral or founder specificity, when compared with Papuans. This may have many explanations first of which is a mere artifact by reason of a poor sampling and depth design of the experiment. ADMIXTURE is a powerful neutral tool, just a like a test tube or the Geneva particle accelerator, but what we do with it may well not be neutral, either by reason of mischievous manipulation or mere error.
In this case I find the test very poorly designed and executed. If I have some time later in the weekend, I may try to perform an alternative test according to my humble possibilities – I promise nothing however.
A complementary test that the authors perform used Tree Mix. As I have discussed elsewhere, TreeMix often produces very strange results and I do not consider it a reliable tool at all, but for whatever is worth here it is what they got:

While the purported migrations generated by the Tree Mix algorithm appear to suggest a secondary genetic flow from India to Australia (orange arrow at C) the data on which such result is based (D) only gives the most tenuous level (green) of extra genetic affinity between Southern Indians (DRA) and Australian Aborigines (AUA). Meanwhile the highly questionable algorithm identifies Dravidians and North Chinese (CHB) as being genetically very close (blue), when they are not in fact.
So what do I get from this paper? TreeMix’ usual senseless noise and apparent mismanagement of ADMIXTURE, a powerful tool when used properly.
Less than inconclusive, I’d say. But your take of course.

Update: G Horvat (see comments) points me to Kumar 2009 (so far unchallenged at PhyloTree)  for a shared mitochondrial lineage between Australia and India, known as M42. This haplogroup has the following structure (each → indicates a coding region mutation according to PhyloTree, Kumar originally listed a few more):
    • → M42’74 
      • → M42 
        • →→→→ M42a (Australian Aborigines)
        • → M42b (India)
      • →→ M74 (South China, Vietnam, India)
This allows for a potential mtDNA backing of this purported connection, however it is a very small lineage and Kumar claimed that M42 coalesced long ago, in the context of the first colonization of Asia and Australasia by Homo sapiens:

The divergence of the Indian and Australian M42 coding-region sequences suggests an early colonization of Australia, ~60 to 50 kyBP, quite in agreement with archaeological evidences. 

Yet the relatively long stem leading to M42a does allow for a later time-frame of arrival to Australia. Neolithic anyhow looks still most unlikely to me.

Update (Jan 18): Dingo DNA:

An important element to consider here are the origins of the dingo as the Australian wild dog is known. This dog variant suffered a strong founder effect upon arrival to Australia described mainly by two variants of the haplotype A29. This lineage only links to East Asia however, having arrived almost without doubt, via Indonesia from mainland East Asia (either Indochina or China or both).

It is clearly not related to Austronesian expansion and could have arrived either within the early Neolithic of ISEA (arguably Austroasiatic in language) or even earlier. At least one of the papers I checked rather supports a pre-Neolithic introduction and certainly before the archaeologically supported age of c. 3000 years ago.

The Y-DNA of dingos also shows a strong founder effect (only two haplotypes, with overlapping but distinct distributions) and again the most obvious connections seem to be in SE Asia.

See (freely accessible):

Update (Jan 18): It is probably interesting also to mention that Australian Aborigines show no difference with Papuans in their overall amount of Denisovan ancestry. This also appears as contradictory with the idea of significant external admixture, which should have diluted at least minimally that Denisovan component (Indians have none).

Update (Apr 7): A new “working paper” has been published on this matter, sharing my critical stand towards the sloppiness of Puhach’s team but still considering plausible a Holocene gene flow from India. I have commented in a new entry.


    Posted by on January 17, 2013 in Australia, autosomal DNA, India, South Asia


    Y-DNA from Tamils and South Indian Tribals

    This is the second attempt at discussing a very interesting paper which has been hurt by an editor error in publication (a key informative element, table 2, has its columns all swapped). 
    I realized that something looked quite wrong and notified the authors, who are now awaiting for PLoS to correct the problem. In the meantime they have been so kind as to provide me with a copy of the original PDF manuscript so I could properly collate the haplogroup data and share it with readers of this blog. 
    Ganesh Prasad Arun Kumar et al., Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System. PLoS ONE 2012. Open accessLINK [doi:10.1371/journal.pone.0050269]
    As I said back in the day:
    The authors took special interest into sampling tribes, some of which
    are still foragers and a reference for all kind of anthropological
    research of South Asia, all Eurasia and even beyond. They also sorted
    the various populations into groups or classes based on socio-economic
    reality (and language in some cases) rather than the, arguably
    overrated, varna (caste) system.
    The categories used are:
    • HTF – Hill Tribe Forager (foragers of Tamil or Malayalam language)
    • HTK – Hill Tribe Kannada (foragers of Kannada language)
    • HTC – Hill Tribe Cremation (tribals who cremate their dead, not sure if silviculturalists)
    • SC – Scheduled Castes (castes traditionally discriminated against, Dalits)
    • DLF – Dry Land Farmers 
    • AW – Artisan and Warrior related castes
    • BRH – Brahmin-related castes with irrigation farming economy
    And, as I said then, the bulk of the data is in table 2, which I have the privilege of sharing with you as it really is (in two blocs, as it was in the PDF):

    And now finally I can get to discuss the details with the certainty of talking about real data.

    Haplogroup C

    As the authors note, 90% (66/74) of all the C-M130 samples belong to C5 (M356), while the rest (8/74) tested negative for both C5 and C3 (M217), so I guess we are here before at leas one other subhaplogroup of C (because the likelihood of being Japanese C1 or Australasian C2 or C4 is practically zero).
    The eight C* individuals are scattered (table S1) among several groups (all of which also display C5, as well as F*) but notably concentrated among the Piramalai Kallar (4/5 within C), which are a DLF group (corrected upon comment).
    Besides C*, which may well be a remnant of either the early Eurasian expansion or of the first backflows from SE Asia (a likely not-so-likely candidate for the origin of macro-haplogroup C), the very notable presence of C5 among tribals and some farmers may well indicate that the origin of C5 is in South Asia, even if the clade also has some presence in Central and West Asia.
    Haplogroup C has a high variance in this study (0.80), greatest among DLF (0.89) and HTF (0.81).

    (Update: see also appendix below).

    Haplogroup E

    As we should expect, this lineage of African origin (with important presence in West Eurasia) is only found at low levels among farmers (DLF). It may well be a remnant of early Neolithic flows, being strongly linked with Neolithic in the case of Europe for example.

    Paragroup F*

    The most striking thing about Paragroup F*, i.e. F(xG,H,J,K), is that it is found at such high numbers and very especially so among the hunter-gatherers, where it is often the main lineage (or lineages). It is also important among dry land farmers and the Valayar (AW class) but it is rare to non-existent among the other caste groups, which may represent relatively recent arrivals.
    Something that this confirms, along with other older data about F basal diversity, is that the main Eurasian Y-DNA haplogroup, which is of course F itself, coalesced necessarily in South Asia. 
    Said that, I cannot underline enough how relevant is to find rare F sublineages (i.e. F* – so rare that have not even been properly identified by downstream markers yet) among the last forager peoples of South Asia, often as dominant clade.  
    Haplotype neighbor-joining exercise was performed however, indicating founder effects (possible new haplogroups to be yet described) among tribals:

    Figure 3. Reduced median network of 17 microsatellite haplotypes within haplogroup F-M89.
    network depicts clear isolated evolution among HTF populations with a
    few shared haplotypes between Kurumba (HTK) and Irula (HTF) populations.
    Circles are colored based on the 7 Major Population Groups as shown in
    Figure 1, and the area is proportional to the frequency of the sampled
    haplotypes. Branch lengths between circles are proportional to the
    number of mutations separating haplotypes.
    However it is also obvious that there is a lot of diversity as well. In fact, paragroup F* does have a high variance in Tamil Nadu (0.81), being highest again among the DLF class (0.85).

    Haplogroup G

    Haplogroup G does exist in South Asia and this paper makes it evident. More so, its distribution in Tamil Nadu includes some foragers and other tribals, although it is more common among “Neolithic” classes. 
    Among these the Ivayengar (BRH) show almost 27% (3/11), however other BRH populations do not show any G, while the DLF ones instead all have relevant G. Therefore this lineage may tentatively be associated in Tamil Nadu with the Neolithic.
    Haplogroup G, suggested by the authors to be a Neolithic arrival, has an strikingly high variance in Tamil Nadu (0.83) with top level among the following classes: AW (1.05), SC (0.94) and BRH (0.82). 
    Even if the distribution corresponds well with a Neolithic inflow the diversity is surprisingly high and it tells me that more research is needed about this lineage in South Asia. After all it is one of the basal descendants of F, whose coalescence took place no doubt in the subcontinent.

    Haplogroup H

    Haplgroup H is of course very common in Tamil Nadu but it must be noticed that it is concentrated in the H1(xH1a) category, as well as some notable H(xH1,H2), which tends to weight in favor of a southern ultimate origin of this important South Asian clade (as also proposed in the recent study on the Roma People). 
    H* is distributed among many populations, the only class fully excluded being the BHR one, which is generally considered to be a recent historical arrival from the North (mostly confirmed by genetics). Some tribes have the highest values but then some others totally lack it. 
    H* has extremely high variance levels in Tamil Nadu  (1.33), being highest among the SC class (1.46), followed by the AW one (1.18) and the DLF one (0.91). This is totally consistent with a South Asian origin of H overall.
    H1* is standard issue in all populations. The highest values are among the Kannada-speaking tribals (HTK), followed by cremation-practicing tribals (HTC).
    H1a instead is only found in one population at very low levels, strongly suggesting that this clade is not from the region. H2 instead is found at low levels among many groups.
    Unlike H*, H1 and H2 have rather low diversity levels in Tamil Nadu: 0.41 and 0.59 respectively.

    Haplogroup J 

    J(xJ2) is found at anecdotal levels in a couple of lower class populations (one tribal and the other SC). It would be particularly interesting if we knew it is not J1 as well – but we don’t. 
    Most is J2(xJ2a) although J2a3 is also important among several populations.
    It is generally believed that J in South Asia is of Neolithic origin and I will not question it but still… notice how important it is among several tribal foragers: >4% in four tribes, levels on average similar to those of farmers and Brahmins.
    J2* is rather high in diversity (0.73), notably among the AW class (1.0), while J2a3 is very low instead (0.29).

    Paragroup K(xL,R)

    Or if you wish paragroups K* and P*, as well as haplogroups O and Q. 
    The always interesting K* is found at low levels among some tribals and most DLF populations. However the peak is among Viyengar Brahmins. May it be haplogroup T?, L2?
    O in this area is almost for sure O2a brought by Austroasiatic-speaking rice farming tribes in the Neolithic. It is found at low levels in some groups, including the Thoda “cremation tribals” (who look quite “Neolithic” also because of their high levels of J2).
    P(xQ,R), which is most common towards Bengal, is found in Tamil Nadu at low levels among diverse populations. On first impression I’d say it’s also a Neolithic influence although, of course, in the wider subcontinental region it must be much much older. 
    Q is found at low levels in diverse populations being maybe somewhat more common among the Scheduled Castes class.

    Haplogroup L

    Haplogroup L is an important South Asian lineage with penetration in West and Central Asia and a center of gravity around Sindh (Pakistan), although it is also very common in West and South India. 
    In Tamil Nadu L1a (L1 in the table) is common among nearly all sampled populations with peak among the dry land farmers’ class.
    Instead L1c (formerly L3) is relatively rare, peaking among the Scheduled Castes class. No mention is made of any other L.
    Both clades show low variance in the region (0.41 and 0.22 respectively), consistent with their origin being further North.

    Haplogroup R

    R(xR1a1,R2) is found in several populations at non-negligible levels: near 5% among some tribals, 8% among the Parayar (SC) and the Maravar (DLF), also 12% Mukkuvar (AW) and as much as 19% among some Brahmins (the Brahacharanam who are also high in P*). This could well be R*, R1*, R1a*, R1b, etc. and indicates in my understanding target populations for future research on the hot topic of the ultimate origins of R1 and R1a (see also here). 
    R* shows clearly high variance:  0.97 on average, being highest among the DLF class (1.25), followed by the BRH class (0.99)
    R1a1, which may well be related to Indoeuropean expansion (or just Neolithic or whatever, better resolution is needed especially in Asia) is found at very high levels among the BRH class (45%), followed by the AW one (20%) other classes show near 10% except the hunter-gatherers (HTF and HTK) who have only anecdotal presence of this lineage. 
    R1a1 shows rather low variance (0.41), rather confirming its immigrant origin from North India (incl. maybe Pakistan, Bangla Desh, Nepal…). All classes are similar for this value.
    R2 (a South Asian lineage with occasional offshoots into West and Central Asia) is common in all groups except the HTF class. The highest levels (c. 15% avg.) are among cremating tribals and artisan/warrior classes. I’d say that with the likely origin of R2 somewhat to the North of this region, it seems normal that Kannada-speaking tribals (HTK, who must be immigrants from Karnataka or at least strongly influenced by this other Dravidian country’s culture) have lots of it, while the more locally native HTF almost lack it instead.
    R2 shows mid-level diversity on average (0.65) but the HTK class displays very high diversity for this lineage (1.05).

    Different interpretations

    Notice that my take and that of the authors on the autochthonous nature of each of the lineages may vary or be debatable. They say the following:

    The geographical origins of many of these HGs are still debated.
    However, the associated high frequencies and haplotype variances of HGs
    H-M69, F*-M89, R1a1-M17, L1-M27, R2-M124 and C5-M356 within India, have
    been interpreted as evidence of an autochthonous origins of these
    lineages during late Pleistocene (10–30 Kya), while the lower frequency
    within the subcontinent of J2-M172, E-M96, G-M201 and L3-M357 are viewed
    as reflecting probable gene flow introduced from West Eurasian Holocene
    migrations in the last 10 Kya [6], [7], [16], [23].
    Assuming these geographical origins of the HGs to be the most likely
    ones, the putatively autochthonous lineages accounted for 81.4±0.95% of
    the total genetic composition of TN populations in the present study.

    Mostly our differences stem on my doubts about the real origins of R1a1 (which could well be West Asian by origin) and that I imagined L1c (aka L3) as native from South Asia (uncertain now admittedly). But otherwise I agree. The hottest issue is no doubt the origin of R1a or R1a1, still unsolved. 

    PC Analysis

    A quick visual understanding of the relations between the different classes can be obtained from figure 2:

    Figure 2. Plots representing the genetic relationships among the 31 tribal and non-tribal populations of Tamil Nadu.
    PCA plot based on HG frequencies. The two dimensions display 36% of the
    total variance. The contribution of the first four HGs is superimposed
    as grey component loading vectors: the HTF populations clustered in the
    direction of the F-M89 vector, HTK in the H1-M52 vector, BRH in the
    R1a1-M17 vector, while the HG L1-M27 is less significant in
    discriminating populations. (B) MDS plot based on 17 microsatellite loci
    Rst distances. The two tribal groups (HTF and HTK)
    are clustered at the left side of the plot while BRH form a distant
    cluster at the opposite side. The colors and symbols are the same as
    shown in Figure 1, while population abbreviations are as shown in Table

    Check table 1 for population codes but essentially: squares are tribes and circles caste populations; red are the HTF class, green the HTK and yellow the Brahmin-related groups (BRH).
    These are the outliers: all the rest, including HTC, cluster together near the (0,0) coordinates.
    It is also clearly indicated in Fig. 2A how R1a1, H1 and F* are the strongest defining markers.
    Old structure
    As always, take age estimates, also provided, with utmost caution and distrust. However I must mention that the main conclusion of the authors is that the haplogroup structure in the region pre-dates the introduction of the caste system as such and is, in their opinion, of Neolithic age.

     __________________________ . __________________________

    Appendix (update Dec 2):

    Much of the discussion below has been on the origins of haplogroup C. I have been pointed to Hammer 2006 and this haplotype NJ tree (fig 4d) of what was known back in the day as C* and C1. At that time neither Australian C4 nor Asian C5 had been described yet. However Wallacean/Melanesian/Polynesian C2 and NE Asian and Native American C3 are not shown here.

    Annotations (C1, C4 and root?) by me:

    Maybe even more interesting is Fig. 3 from Redd 2002, which shows the whole C haplogroup tree and clearly annotates the likely root (branch to haplogroup B):

    While C4 is not obvious here, the fact that South Asian (Indian subcontinent) C* is central to all the haplogroup is again underlined.
    The protuberance to the top might be C5, while the one to the bottom may well correspond with the SE Asian cluster above, at least partly. The differences underline the limitations of this STR-based method alone to infer real phylogenies – but it is anyhow much better than nothing.

    Y-DNA survey of Tamil Nadu

    Fig. 1 – Sampling sites
    Warning (Dec 1): table 2 was so messed up that I had to postpone most of the commentary on this important paper. Please disregard this entry and head to the new, much more extensive and correct version HERE.

    Always welcome to find more about the genetics of India, surely one of the key geographical nodes of prehistoric human expansion (and, of course, a huge region with interest of its own right).

    Ganesh Prasad Arun Kumar et al., Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System. PLoS ONE 2012. Open accessLINK [doi:10.1371/journal.pone.0050269]
    The authors took special interest into sampling tribes, some of which are still foragers and a reference for all kind of anthropological research of South Asia, all Eurasia and even beyond. They also sorted the various populations into groups or classes based on socio-economic reality (and language in some cases) rather than the, arguably overrated, varna (caste) system. See table 1 for details.
    The bulk of the data is in table 2, an edited and annotated version of which I include here (two columns, R2 and SD, were transposed in the original, I resized for optimal visualization and annotated wildly to highlight most important clades, etc. – that’s how I read papers, rather than paying too much attention to the wording or beliving blindly all what geneticists say on age estimates and other educated hunches):

    Annotated and corrected version of table 2 (click to view in optimal size).

    As I’m not totally sure that the tabulation (even after correction) is right, I’m going to withhold judgment. Hopefully it’ll be corrected soon and we can analyze the data properly.

    Update (Nov 30): I wrote to the authors on the issue and got prompt reply. Apparently the shifted column is that of J2-M172 and not R2 as I thought first, but instead of a simple swap all columns since J2a1 shifted one place to the left (so  all that K* is actually L1, all that R* is actually R1a1, etc.)

    I am very interested on what this paper seems to have found and therefore I will wait a bit for the formal correction (which is apparently in wait for PLoS ONE editors to perform only) and write on the matter anew. Because, if nothing else, the high levels of F* and C among hunter-gatherer tribals seem very important.