Category Archives: South Asia

Questioning the India-Australia link and timeline

Darshi Arachige recently made me aware of a study of his authorship, which is broadly coincident with the criticisms I made to Pugach 2013:
Darshi Arachige, Do the Estimated Admixture Times Confirm the Proposed Holocene Gene Flow from India to Australia? Social Science Research Network 2013 → LINK


This paper argues that the current estimates for the time of influx of Indian genes into some sections of Australian Aboriginal population during Holocene bear large uncertainties which make elimination of the probability of a more recent gene flow less likely. It also highlights that indications for the plausibility of a later gene flow exist and can also be placed in a likely archaeological perspective.

My own very brief synthesis of the criticisms (all very legitimate) is as follows:
  • Excessive conclusions come from subjective interpretation the PC (eigenvector) analysis. 
  • Too large, diverse dataset: Pugach et al. use an excessively broad dataset, what tends to hide important information unless you look at great depths, which they do not.
  • Confidence intervals were hugely underestimated (a way too common academic malpractice).
  • The arbitrarily wrong interpretation of the Holocene techno-cultural changes in Australia, which in no way are related to India but to SE Asia.
  • Ignoring Kumar 2009, whose estimates for the South Asia – Australia gene flow is of 60-50 Ka BP. 

Intriguingly however, Arachige mentions the Aboriginal legends about the Bajini, which he considers as possible Dravidian migrants, with all cautions. 


In the preceding discussion, it was shown that the possibility of a Holocene gene flow between Indian people and Australian Aboriginal people is real. However, the external evidence quoted to support the thesis of such genomic fusion around four thousand years ago is inadequate and does not enjoy the support of many experts in the field. Given the errors associated with the estimated times of a localised admixture between these populations, it is not impossible to find a more recent time for an encounter between South Indian migrants to South East Asia and Aboriginal people from northern parts of Australia. Such an encounter is far more plausible from the archaeological evidence available in the neighbouring islands. Even though it is not possible to link the Baijini gypsies with the Dravidians due to flimsiness of the available information about the former, it is a possibility worth pursuing.


Autosomal genetics of the Roma People

Some more information on the genetics of the Roma People.
Prija Moorjani et al., Reconstructing Roma History from Genome-Wide Data. PLoS ONE 2013. Open accessLINK [doi:10.1371/journal.pone.0058633]


The Roma people, living throughout Europe and West Asia, are a diverse population linked by the Romani language and culture. Previous linguistic and genetic studies have suggested that the Roma migrated into Europe from South Asia about 1,000–1,500 years ago. Genetic inferences about Roma history have mostly focused on the Y chromosome and mitochondrial DNA. To explore what additional information can be learned from genome-wide data, we analyzed data from six Roma groups that we genotyped at hundreds of thousands of single nucleotide polymorphisms (SNPs). We estimate that the Roma harbor about 80% West Eurasian ancestry–derived from a combination of European and South Asian sources–and that the date of admixture of South Asian and European ancestry was about 850 years before present. We provide evidence for Eastern Europe being a major source of European ancestry, and North-west India being a major source of the South Asian ancestry in the Roma. By computing allele sharing as a measure of linkage disequilibrium, we estimate that the migration of Roma out of the Indian subcontinent was accompanied by a severe founder event, which appears to have been followed by a major demographic expansion after the arrival in Europe.

The claim of “80%” West Eurasian ancestry seems quite exaggerated on light of the ADMIXTURE data, where at least 40% is clearly of South Asian origin (maybe somewhat more as NW South Asians display some West Eurasian admixture). I guess that they are just speculating on the ANI/ASI (North-South Indian) issue and attributing ANI to a West Eurasian gene pool, what is most confusing to say the least.

Figure 1. Relationship of Roma with other worldwide populations.
(click to expand)

It is true in any case that FST distances are significantly higher with Gujarati Indians (GIH) than with Europeans (CEU, TSI), the former at 0.026, while the latter at only 0.016.
Whatever the case I’d focus on the Fig 1(a) ADMIXTURE graph, because in the (b) one the appearance of European affinity among many South Asians (in my understanding, a 50,000 years-old affinity highlighted only for lack of sufficient K-depth, K=3 only!) is only a factor of confusion. Following this criterion, Roma appear to be some 60% West Eurasian and 40% NW Indian.
Something I really miss in this paper is a more detailed comparison not just with South Asians (more K-depth please!) but also with West Asians, totally absent from the study.
See also: Romani mtDNA

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).

Fundaments of curry found in Indus Valley Civilization

Turmeric (Curcuma longa)
(CC by J.M. Garg)
[Updated on Feb 8th, based on details arisen in the discussion, see comments]

While modern curry is an amalgamation of many influences some of its foundations may have been used already in the South Asian Chalcolithic and Bronze Age civilization (contemporary of ancient Egypt for example), known variedly as Indus Valley Civilization (IVC) or Harappan culture. 

Key curry ingredients, namely turmeric and ginger, have now been found in pot and cow teeth remains from the impressive South Asian first civilization, suggesting that the fundamentals of modern Indian cuisine were already there some 5000 years ago.

A carbonized garlic clover was also found. Garlic is another key component of curry.

An interesting revelation is that rice grains were among the findings, indicating that the farming of this oriental cereal had already reached India by c. 2500 BCE and was popular enough to make it not just to the modern rice-farming regions of East and South India but also as far as Pakistan.

Source: Slate (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


    Romani autosomal genetics

    French Gitanes (Roma)
    CC by Fiore S. Barbato
    If a few days ago I mentioned the study by Rai et al. of Romani Y-DNA, which locate their origins with great certainty in the NW reaches of the Indian subcontinent, specifically among the lower castes, now I must echo this other study, still in pre-publication stage, which deals with the autosomal genetics of the same European minority.
    Priya Moorjani et al., Reconstructing Roma history from genome-wide data. arXiv 2012. Freely accessibleLINK [ref. arXiv:1212.1696]
    The authors studied the nuclear genome of 27 Romani individuals from six populations of four European states: Hungary (three different populations), Romania, Slovakia and Spain. 
    A reasonable complaint at this stage could be that the size of the sample is small and very specially too concentrated in a very specific area: the Middle and Lower Danube region. But, well, let’s assume that is not too important. 
    The authors appear to confirm the NW Indian ancestral affinities of the Roma, however it seems obvious that they have been heavily admixed with Europeans since their migration a thousand years ago. 
    The tests performed on this regard find greater affinity to Romanians than other Europeans but no other Balcanic nor West Asian peoples were tested for, so some question marks remain open. Certainly it is a bit puzzling that with all the worldwide comparisons performed in this paper not a single West Asian population was included. 
    There are hence some shortcomings in the sampling and analysis strategy (why to compare with tropical Africans but not with Iranians, Turks, Egyptians or Arabs?) but the study still deserves a mention. 
    Principal component analysis:

    STRUCTURE  analysis:


    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.