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Mellars 2013: second round

As I mentioned before, I have already got copies of the controversial study by Paul Mellars et al., which argues for a very late colonization of Eurasia. It includes some aspects not dealt with in the first round, when I could only access the supplemental material. 
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]
Maybe the most important is the very striking visual comparison between proto-LSA African microlithic industries and post-UP South Asian microlithic ones:

While it is maybe easy to dismiss the patterns drawn on ostrich shells in Africa and South Asia as not really looking the same at all and therefore likely coincidence, the visual comparison of the industries is much harder to reject. It does indeed pose a mysterious apparent link similar to others that are hard to explain like the similitude between Chatelperronian and Gravettian (not so long ago treated together as “Perigordian”) or the hammering insistence by some rather marginal academics on the similitudes between the SW European Solutrean culture and the (much more recent) North American Clovis industry. 
Sure: impressive and intriguing. But when it comes to chronology the Mellars hypothesis seems to fail terribly. While the African microliths are pre-LSA and therefore from before ~49,000 years ago in all cases, the South Asian ones only show up mostly since c. 34-38,000 years ago, more than ten millennia later. Mellars makes this figure 40-35 Ka and then just 40 Ka for the following graph, which in fact misrepresents Petraglia’s model and data in a key issue (see below):

It must be emphasized here that Petraglia’s data and model, at least for what I know it, implies an hiatus between c. 110 Ka and c. 80 Ka BP, hiatus for which there is no archaeological data of any kind in South Asia. Therefore neither side graph should suggest continuity to the past before ~80 Ka, allowing at most for a highly hypothetical dotted line (as in Petraglia 2010):

Also there is nothing in Petraglia’s work that could suggest discontinuity at the Toba ash layer, as suggested by Mellar’s version, rather the opposite: continuity is very apparent in Jwalapuram:

Jwalapuram industries (from Petraglia 2007)

Quite conveniently Mellars ignores Petraglia’s data again, which suggest continuity before and after microlithism in Jurreru Valley and then also finds a transition towards UP (“blade and bladelet”, as well as “backed artifacts”) technologies since c. 34 Ka BP. 
But regardless, I’m pretty sure that Prehistory-savvy readers have already noticed a major issue in all this chronology: we are talking of dates that are almost 20,000 years after the colonization of West Eurasian by H. sapiens with “Aurignacoid” technologies, which are dated to before 55 Ka BP in Palestine (OSL), to c. 49 Ka BP in Central Europe and to c. 47 Ka BP in Altai (C14 calibrated). 
And those who are also familiar with Eurasian population genetics are by now shaking their heads in disbelief and claiming to heaven and hell alike. Because West Eurasians derive, at a late relative date, from Tropical Asians and therefore, if our core ancestors were already separated before 55 Ka BP, there is just no room for the Tropical Asian (and Australasian) expansion that must have preceded the Sapiens colonization of the West Eurasian Neanderlands.
(Those unfamiliar with the basics of Eurasian population genetics, see here).
So there is no way that the Out of Africa migration could be dated to just c. 55 Ka BP, as Mellars does (after grabbing hard the burning nail of conjectural coastal sites now under the sea, which would have to account for some 15-20,000 years of Eurasian prehistory on their own).
In fact it is also impossible from the viewpoint of Australian chronology, which again needs to go after the settlement of Tropical Asia but surely before that of West Eurasia. 
So, regardless of the striking visual comparison between African and Indian industries, which is no doubt the “bunny in the hat” here, the Mellars hypothesis simply doesn’t stand. 
Was there another cultural (surely not demic) flow from Africa to South Asia c. 40-35 Ka BP? Maybe. Or maybe it is just one of the many hard-to-explain coincidences in stone industry design. But whatever it is, it just cannot be the Out-of-Africa migration, unless one is ready to accept that Aurignacian and related European rock art, as well as Australian rock art, for example, are the product of archaic homo species (something that I am sure that Mellars won’t admit to: it just goes against his “modern human behavior” prejudices). And, even then, it just doesn’t add up either.

PS- Petraglia himself finds Mellar’s alternative model untenable. From ABC Science (emphasis mine):

… Professor Michael Petraglia, an archaeologist from the University of Oxford disputes Richards’ and Mellars’ argument. 

Petraglia says there’s not enough evidence to rule out an earlier colonisation before the eruption of Mount Toba. 

“The research reported by Mellars and colleagues is riddled with problems,” he says. 

Petraglia says that the similarity between tools used in Africa
60,000 years ago and those from Asia dating to around 35,000 years ago
is not a consequence of direct migration.


“These toolkits are separated in time by more than 20,000 years and distances exceeding several thousand miles.” 

He questions the evidence supporting a migration along the coast. He
says that surveys of ancient shorelines have not revealed any evidence
for human settlements anywhere along the Indian Ocean shore between
55,000 and 50,000 years ago.

He also says genetic dating should be treated cautiously. 

“Most geneticists will admit that genetic dating of the out-of-Africa
event is tenuous, at best. Published genetic ages for out-of-Africa
range anywhere between 45,000 to 130,000 years ago.

Petraglia
says his team is currently conducting archaeological fieldwork in
Arabia, India and Sri Lanka they expect will show that the story of
human dispersal from Africa is complex.

“What we can agree on is that little research in these key geographic
regions has been conducted and much more evidence needs to be collected
to support or refute the different theories,” says Petraglia.

 

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]

Abstract

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.
 

Synthesis of the early colonization of Asia and Australasia by Homo sapiens (haploid genetics)

Continuing with the joint series in Spanish language with David Sánchez at his blog Noticias de Prehistoria, I have just written an article on the early expansion of Homo sapiens in Asia and Australasia after the “out of Africa” migration. 
I have in the past explored this matter on this blog and its predecessor but there has been some time since I did it the last time. Therefore it may be interesting to share a synthesis of this updated review with the readers of For what they were…
As usual the review is built upon geographic reconstructions and an overly simple “molecular clock”, in the case of mtDNA only (which is the base of the interpretation), that merely counts coding region mutations from the most recent common ancestor (the L3 node), using the latest version of PhyloTree (build 15).
The result for mtDNA are the following five maps:
Map 1: the expansion of L3 sublineages from Africa to South Asia. Molecular time: L3+0 to L3+3. 
The big M star indicates the large M star-like explosion upon arrival to South Asia.
Map 2 represents the molecular time L3+4 (=M+1). There is an evident expansion in South Asia but also into SE Asia. 
The presence of M29’Q in Papua must be taken with some caution, as always that a single lineage is involved, what has low statistical significance.
Map 3 represents the molecular time L3+5, which corresponds to the coalescence of haplogroup N, as well as many M sublineages. There is a slowing down in the number of nodes sprouting at this “time”, so I would estimate it to correspond with Toba supervolcano (c. 74 Ka BP).
Map 4 represents the molecular time L3+6, which corresponds with the coalescence of R. The rhythm of expansion recovers and the colonization of Australasia seems by now quite statistically significant.
Map 5 represents the molecular time L3+7, which shows the first indications of expansion to NE Asia and Western Eurasia (the Neanderlands), while expansion in South Asia continues very strong (this dynamism of South Asian M lineages may explain why N and R had a limited impact in the subcontinent). 
I stopped here because I did not want to stretch too much the potential of my simplified molecular clock method, surely more likely to err as we move away from the reference point (L3 node) but the tendencies outlined in map 5 clearly continue and even increase at later “moments”. 
I also made a rough age estimate of the various maps, assuming map 2 to correspond to Jwalapuram (since c. 80 Ka BP) and map 5 to the earliest Aurignacoid cultures (Emirian, since c. 55 Ka BP or maybe a bit earlier). The result is:
  1. Arrival to South Asia: c. 93-83 Ka BP
  2. First expansion: c. 85-75 Ka BP
  3. Slowing down of the expansion (Toba) and N node: c. 77-67 Ka BP
  4. Reactivation of the expansion and clear arrival to Australasia: c. 69-59 Ka BP
  5. Expansion to less hospitable areas (NE Asia, the Neanderlands): c. 61-51 Ka BP
It is in any case a rough (yet quite coherent) estimate: there is no genetic equivalent of radiocarbon or other physical methods of age calculation.
I did not even try to make any time approximation for Y-DNA, whose expansion I just split in two phases. First what could well be the overall process of expansion from Africa into Tropical Asia (roughly comparable to mtDNA maps 1, 2 and 3):

And then the later expansions, divided in two maps for clarity (they should be roughly simultaneous processes):

General expansion of macro-haplogroups C and D (Y-DNA)
General expansion of macro-haplogroup F and its major descendant MNOPS (highlighted in a lighter, fuchsia shade).

The continuous arrows in these two maps should correspond in essence to mtDNA maps 4 and 5 and even later in time. The dotted arrows merely indicate some important but late processes since at least 30 Ka BP up to the Late Neolithic.
In all maps there is some uncertainty about the exact coalescing location of each clade or node but overall they should be at least approximate. Particularly uncertain are the original locations of mtDNA N and Y-DNA C and MNOPS but should all have coalesced somewhere between Varanasi and Guangzhou, so to say. 
 

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.
The
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.
(A)
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
1.

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.
 

Ancient Homo sapiens from Laos (46-63,000 years ago)

Tam-Pa-Ling skull
While this is not the only nor even probably the oldest remain of the so-called anatomically modern humans (i.e. Homo sapiens, our kin) in Eastern or SE Asia, it seems to be the less controversial one so far, what should help to consolidate our knowledge of the period of colonization of the Eurasian region East of Bengal.
Fabrice Demeter et al., Anatomically modern human in Southeast Asia (Laos) by 46 ka. PNAS 2012. Pay per view (6 months embargo) ··> LINK [doi:10.1073/pnas.1208104109]
Abstract
Uncertainties surround the timing of modern human emergence and occupation in East and Southeast Asia. Although genetic and archeological data indicate a rapid migration out of Africa and into Southeast Asia by at least 60 ka, mainland Southeast Asia is notable for its absence of fossil evidence for early modern human occupation. Here we report on a modern human cranium from Tam Pa Ling, Laos, which was recovered from a secure stratigraphic context. Radiocarbon and luminescence dating of the surrounding sediments provide a minimum age of 51–46 ka, and direct U-dating of the bone indicates a maximum age of ∼63 ka. The cranium has a derived modern human morphology in features of the frontal, occipital, maxillae, and dentition. It is also differentiated from western Eurasian archaic humans in aspects of its temporal, occipital, and dental morphology. In the context of an increasingly documented archaic–modern morphological mosaic among the earliest modern humans in western Eurasia, Tam Pa Ling establishes a definitively modern population in Southeast Asia at ∼50 ka cal BP. As such, it provides the earliest skeletal evidence for fully modern humans in mainland Southeast Asia.
Some more details can be found at the press release by the University of Illinois (h/t Pileta).
There are some skulls and skull fragments from East Asia that can be actually older than this one but they may be less straightforward either in their dating or their identification as Homo sapiens:
  • Liujiang skull (at Don’s Maps, at P. Brown’s site, at Bradshaw Foundation), from Guangxi-Zhuang, is clearly a modern Homo sapiens but the exact date is not known because it was originally dug with very limited means. Recent datings of nearby sediment suggest an age of 68-139 Ka but this is hotly debated.
  • Zhirendong jaw (at this blog, at PhysOrg), also from Guangxi-Zhuang and dated to before 100,000 years ago (110,000 years ago according to first reports), is argued to be a modern Homo sapiens but its very ancient date and some unavoidable ambiguity of such limited skeletal evidence allow for some skepticism, if you are so inclined.
  • Callao cave metatarsal (foot) bone (at Leherensuge) is dated to before 67,000 years ago and comes from Luzon, the largest Filipino island, but because of its small size cannot be ascribed to any human species safely. All we can say is that they knew how to use rafts or boats – but then Homo floresiensis (H. erectus?) did too. 
  • Also some non-skeletal evidence to consider:

Whichever is your personal take, it is clear that this skull adds up in support of a very old colonization of East Asia. The question is: exactly how old?

Update: a creative reconstruction by H. Zänder:

 

On the origin of mitochondrial macro-haplogroup N

The notion that the migration of Homo sapiens out of Africa had to pivot around West Asia has been deeply entrenched in our minds, partly because geographical common sense, partly because Eurocentrism, partly maybe because of the Judeo-Christian-Muslim religious background of most influential researchers historically… 
However in the last years this idea has been challenged by the coastal migration theory that proposes a migration mostly along the coasts of the Indian Ocean rather than through the interior of Asia. This theory was first outlined by population geneticists, who needed to explain the facts of haplogroup distribution in Eurasia, not at all more diverse towards the West, as we could expect from the classical models pivoting around the Fertile Crescent, but rather towards the East and very specially in South Asia. Later it has been also corroborated, with lesser shadings maybe, by archaeologists who have sought material support in Arabia and India and found it.
While the origin of mitochondrial macro-haplogroup M in South Asia is seldom contested, that of its “sister” N is seldom agreed upon. The reason is that it is distributed somewhat evenly through all Eurasia, Australasia and even America.
This map, from the Metspalu 2005 paper (open access), illustrates the issue and how even renowned geneticists doubted not long ago on where to place the urheimat of the haplogroup:

The phylogeny has anyhow been refined in these six and a half years and you may notice that Australasia is not even included in the map, although it does play an important role, being surely more important than West Eurasia. In any case the map is illustrative of this state of confusion. Confusion that I will try (once again and hopefully for good) to dispel in this article.
The facts of mtDNA N
Macro-haplogroup N has 15 acknowledged basal haplogroups scattered through all Eurasia and Aboriginal Australia. They have diverse numerical importance but what matters to me here is how many mutations (coding region transitions, to be more precise) they are downstream of the N node. Why? Because this is surely indicative of the timing of their respective expansions in relation with N as such. 
Looking at this measure we find the following classes of N sub-haplogroups:
  • Elder daughters: one coding region mutation downstream of N: N1’5, N9, N11, S and R. Notice that among these R holds a special place, not for any phylogenetic reason but because it has a scatter as wide as that of her mother N, suggestive of a very early coalescence and some sort of association between both expansions. 
  • Two mutations downstream of N: N10 and O.
  • Four mutations downstream of N: N2 (incl. W), A and X.
  • Extremely long stems, rare clades without any known node under N: N8, N13, N14, N21, N22.
This distinction is not very important but I have always present in any case, because it implies that the various classes of subhaplogroups expanded at different moments after the N node. Notably there is a “pause” at the place of the third mutation and then after the fourth. So we can well imagine the expansion of N as a double explosion, first the two first categories and then the third and maybe the fourth.
Representing each haplogroup as a dot, where they might have coalesced (often a hunch within the local region), the result is as follows:

1.- Estimated coalescence of basal subhaplogroups of N

The size of the dots represents only the “class”, that is: how many mutational steps they are under N, the larger the closer they are and the earlier they must have coalesced (according to the laws of probability). The peculiar macro-haplogroup R (whose approx coalescence location was estimated in the past and I will not explain here) has been painted of a lighter blue and given a slightly larger size. 
I have also outlined the cloud of N expansion at mutational steps 1 and 2 (no difference), which are followed by an apparent pause at mutational step 3, as mentioned above. The cloud has been pushed northwards a bit in East Asia in order to avoid disputes on where exactly did N9 coalesce (it does not make much of a difference if you prefer Beijing over Shanghai for this clade’s coalescence in the end).
Notice that this N cloud is almost identical as would be the M cloud (not shown but look here for a reference if you wish). Whether they were simultaneous or, as I think, N coalesced and expanded a bit after M did, their geography was the same: South Asia, East Asia and Australasia without distinctions. This T-shaped region (with the East on top) was the homeland of the first Eurasian (or more properly non-African) population of Homo sapiens (excepted those who remained in Arabia, which are another story).
The geographic origin of N
Alright, I have described the scatter of N subhaplogroups and the most likely sequence of the expansion but my main purpose here is to estimate the origin, the urheimat of N: where did the N matriarch, the ultimate matrilineal ancestor of all N people today, live?
I apply the statistical principle by which the derived basal haplogroups should tend to remain not too far away from the common origin. Being the most removed ones, exceptions and never the rule. It does makes sense, right?
Hence if we can estimate the centroid of the geometry described by the 15 haplogroups, we will have found the origin of N – or at least a raw estimate of it. There are several methods to estimate centroids but I chose to use the geometric one. In fact, for simplicity, I divided the subhaplogroups in three sets of five (so they all weight the same) and estimated their centroids by geometric decomposition. Then I estimated the centroid of the resulting triangle.
If I am correct the raw centroid of N is at the lower Mekong:

2.- Possible origins of mtDNA N (blue flowers): A – ‘raw’ geometric centroid, B – corrected against directionality.

I have argued on occasion that, in order to compensate for the directionality of the expansion, a correction can be applied to the geometric centroid or raw estimate of the origin. This correction should pull the origin towards the parent node, in this case L3 in East Africa (estimated here). How much? Maybe 1/4, maybe 1/3… this step, even if probably very reasonable, is a guess and not rocket science. Here I chose to use 1/4 and then look for the closest coast, which is that of Bengal – alternatively I can use a crooked line that follows the geography and get the same result (even less ambiguously Bengal again).
If I would have chosen a 1/3 value for the correction, it would fall in a more central part of India, if 1/5 in Burma surely. We can’t be sure of where exactly that happened but we can be more than reasonably sure that it was between India and Cambodia. 
And nowhere else: not in West Asia, not in Altai… thanks for the suggestions but I have heard that before… many times… always without a single piece of evidence nor well-reasoned backing of any sort. 
The data says otherwise: around the Bay of Bengal or even further East maybe. 
Getting R into the picture
I have said before (and is obvious for anyone interested on population genetics) that mtDNA R is peculiar. While it is not different phylogenetically from other subclades of N which are separated by just one coding region mutation, its geographic distribution is very different, because R, like its mother N, is everywhere. 
In order to show it more clearly, I drew approximate origins of all basal R-subclades (in lighter blue). The size of the circles follows the same logic as do those of N above, representing only the distance from the mother node (R in this case, what means one step further downstream in relation with N), and hence a probable order of coalescence:

3.- Scatter of N (deep blue) and R (cyan) subhaplogroups. The flower indicates the possible common origin.

The scatter of R fits very curiously within that of N(xR). They do not overlap too much maybe and it looks on first sight like R could have pushed other N around to the margins of the common expansion cloud. However this does not seem to happen with M, so maybe another explanation is needed, like undifferentiated N and R traveling together, mostly under the leadership of the latter and causing different founder effects in different locations.
Whatever the case it is worth a good meditation, because it is possible that both haplogroups (mother N and daughter R) coalesced in rapid succession in a single region (Bengal probably). 
 

Echoes from the Past (Nov 11)

There is a lot of stuff accumulating in the to do folder again. I am sure that you will find most or at least some of it interesting.
People who can only read in English may want to consider now subscribing to Pileta de Prehistoria. Until recently most of the materials were in Spanish and largely home-made but since a few days ago, they are compiling a lot of Prehistory-related news, most of them in English. Part of my queue has to do with this change in content.
Paleolithic and Epipaleolithic
Laetoli ash walkers may have been unrelated among them: the various individuals of Australopithecus afarensis who walked on volcanic ash at Laetoli some 3.6 million years ago did so in different occasions and may therefore not have been relatives ··> Live Science.
A researcher questions whether Idaltu (Herto man, reconstruction at right) was actually a Homo sapiens. I think that the questioning is very weak, with key vault-height measures that rather make Idaltu outstanding within H. sapiens range rather than approaching Kabwe (H. rhodesiensis), which had a low vault. However the paper has a long list of anthropometric data on various H. sapiens specimens (all West Eurasian ones, except Idaltu) and said H. rhodesiensis which may be of interest for readers, so worth mentioning anyhow ··> Kyle D. Lubsen’s PDF at the Journal of Contemporary Anthropology, Neanderfollia[cat].

(Note: nearly all you need to know about anthropometry seems to be in this nice site).

Human bones found in Okinawa dated to c. 24,000 years ago (oldest occupation known to date) ··> M24, ABC[es].
Painted stones discovered in Hohler Fels (Swabian Jura, Germany).  The style of the stones, dated to c. 15,000 years ago resembles that of SW Europe. However no wall mural has yet been located in that region. It was experimentally demonstrated that the dots are not made with either brush or finger but with a wooden stamp ··> SD, Der Spiegel, Qué[es].

Hohler Fells painted stones
Spotted horses did exist in the Paleolithic, DNA suggests, emphasizing the realism of Magdalenian cave painters, which occasionally painted such kind of coats ··> M. Pruvost et al. at PNAS, Science, SD, Dienekes, Popular Archaeology, NYT.

The dots are not symbols but realistic depictions, it seems now

Download link for Cave of Forgotten Dreams: Werner Herzog’s documentary on Cave Chauvet (English with subtitles in Spanish).
Epipaleolithic findings in Rotterdam’s harbor. The expansion works for the largest port of Europe have located very small fragments of animal bone (some of which was burnt by human action) and flint stone. Not much but enough to demonstrate human presence in the Western Netherlands in that period, being the first known direct evidence of it ··> Dredging Today, Paleorama[es].

Neolithic & Metal Ages

Neolithic findings in Qatar are oldest known to date in the Emirate: some flint tools and Ubaid style pottery (proto-Sumerian) are complemented by animal remains of diverse significance: fish bones indicating what they captured at sea, shells used for decorative purposes (right) as well as for food, a dog’s canine and even the hearth and the hole for the main pillar of their probably sedentary residence have been found ··> Gulf Times.
No second chamber at Newgrange ··> The Meath Chronicle.
Archaeological findings in Inner Mongolia ··> Archaeology News Network (another site to follow apparently)
Humor (from Heritage in Action): Norwegian singer Vegard Ylvisåker made a freaky song on Stonehenge. While I don’t like the music, the lyrics have some great moments for laughs (in English with English subtitles, just in case):

There are also some awkward moments because any megalithomaniac worth that name knows that Stonehenge is not a henge (rondel) but a stone ring (cromlech) but well…

Archaeogenetics

The Neanderthal genome goes open access… or something like that. Millán Mozota recommends this UC Santa Cruz page dedicated to allow anyone interested to access the Neanderthal genome in full detail. I can’t but agree: an important resource.
The Genographic Project claims that our species migrated from Africa to Asia via Arabia. Better late than never ··> Marta Melé et al. at MBE (pay per view), PR Newswire, Paleorama[es], La Vanguardia[es].
From Melé’s abstract:

We also observe that the patterns of recombinational diversity of these populations correlate with distance out of Africa if that distance is measured along a path crossing South Arabia. No such correlation is found through a Sinai route, suggesting that anatomically modern humans first left Africa through the Bab-el-Mandeb strait rather than through present Egypt.

The Genographic Project’s latest elaboration is coastal migration (finally!)
Successful pioneers get some selective advantage… or so it seems from a study of Quebecois surnames (which does not count the fallen) ··> C. Moreau et al at Science (pay per view), SD.

Psychological anthropology

Neanderthal brains were strikingly asymmetric. It is unclear why but their right hemisphere was hyper-developed, at least among those from El Sidrón (Asturias) ··> Sinc[es].
Does the origin of language lay in baby apes’ gestures? Not the first time I am told that language began with gestures but, specially if you’re unfamiliar with this concept, you may want to read this article at New Scientist.