South Asian autosomal structure

A recent study finds "five" components, although in practice they can be reduced to three.

Analabha Basu et al., Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure. PNAS 2015. Freely accessible → LINK [doi: 10.1073/pnas.1513197113]

Abstract

India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform.

One of the components, very distant from the rest, is the Andamanese one (Jarawa, Onge), but the isolated islands are not really in South Asia, rather in SE Asia (south of Myanmar, belonging to India only because of historical accident), what reduces the structure of South Asia to what we can see in the following graph:

Fig. 2.

(A) Scatterplot of 331 individuals from 18 mainland Indian populations by the first two PCs extracted from genome-wide genotype data. Four distinct clines and clusters were noted; these are encircled using four colors. (B) Estimates of ancestral components of 331 individuals from 18 mainland Indian populations. A model with four ancestral components (K = 4) was the most parsimonious to explain the variation and similarities of the genome-wide genotype data on the 331 individuals. Each individual is represented by a vertical line partitioned into colored segments whose lengths are proportional to the contributions of the ancestral components to the genome of the individual. Population labels were added only after each individual’s ancestry had been estimated. We have used green and red to represent ANI and ASI ancestries; and cyan and blue with the inferred AAA and ATB ancestries. These colors correspond to the colors used to encircle clusters of individuals in A. (Also see SI Appendix, Figs. S2 and S3.)

It is quite apparent that the AAA (Ancient Austroasiatic) component behaves as the ASI (Ancient South Indian) one but with a tendency towards the ATB (Ancient Tibeto-Burman) one, strongly suggesting it is basically product of admixture and not a truly autonomous ancestral component. 

This may be more apparent in the wider pan-Asian context:

Fig. 3.

Approximate “mirroring” of genes and geography. Genomic variation of individuals, represented by the first two PCs, sampled from 18 mainland Indians combined with the CS-Asians) and E-Asians from HGDP, compared with the map of the Indian subcontinent showing the approximate locations from which the individuals and populations were sampled.

In this wider mapping (would be even more clear if West Asian populations were included), we see that:

1. ANI (Ancient North Indian) strongly tends to the West. In other analyses it is very similar to the Caucasus modal component and therefore a logical conclusion is that we are before a Neolithic immigrant element, much as happens in Europe.
2. ATB (Ancient Tibeto-Burman) strongly tends to the East, more specifically SE Asia, and is therefore the reverse to ANI, although much less influential.
3. ASI (Ancient South Indian) is the true aboriginal (pre-Neolithic) component of India, better preserved in southern populations but more clinal than the sample choice allows us to perceive.
4. AAA (Ancient Austroasiatic) is very similar to ASI but has some SE Asian admixture, as is logical to expect, being Austroasiatic a SE Asian language of likely Neolithic expansiveness. 

So ASI and AAA are basically the same thing and that's why I say that the "five" components can be simplified to just three. Said that, it is indeed possible that there is underlying complexity within the ASI+AAA component but this study does not help us to clarify that. 

It is true that the K=4 (after exclusion of Andamanese, K=5 with them) fits the parsimony criterion best but the K=3 is also a good fit and shows AAA exactly as I describe them: largely ASI ("aboriginal") with a significant ATB (Eastern) component. The AAA component can therefore be perceived as consolidated, homogenized, ancient admixture. Prove me wrong on this and I'll eat my words. 

Caste apartheid stopped genetic flow

Quite interestingly, the authors also dwell on how the admixture process was stopped by the Gupta laws (Middle Ages) that imposed apartheid (caste system) enforced endogamy and caused the now apparent genetic isolation of the multiple groups.

We have provided evidence that gene flow ended abruptly with the defining imposition of some social values and norms. The reign of the ardent Hindu Gupta rulers, known as the age of Vedic Brahminism, was marked by strictures laid down in Dharmaśāstra—the ancient compendium of moral laws and principles for religious duty and righteous conduct to be followed by a Hindu—and enforced through the powerful state machinery of a developing political economy (15). These strictures and enforcements resulted in a shift to endogamy. The evidence of more recent admixture among the Maratha (MRT) is in agreement with the known history of the post-Gupta Chalukya (543–753 CE) and the Rashtrakuta empires (753–982 CE) of western India, which established a clan of warriors (Kshatriyas) drawn from the local peasantry (15). In eastern and northeastern India, populations such as the West Bengal Brahmins (WBR) and the TB populations continued to admix until the emergence of the Buddhist Pala dynasty during the 8th to 12th centuries CE. The asymmetry of admixture, with ANI populations providing genomic inputs to tribal populations (AA, Dravidian tribe, and TB) but not vice versa, is consistent with elite dominance and patriarchy. Males from dominant populations, possibly upper castes, with high ANI component, mated outside of their caste, but their offspring were not allowed to be inducted into the caste. This phenomenon has been previously observed as asymmetry in homogeneity of mtDNA and heterogeneity of Y-chromosomal haplotypes in tribal populations of India (6) as well as the African Americans in United States (34). In this study, we noted that, although there are subtle sex-specific differences in admixture proportions, there are no major differences in inferences about population relationships and peopling whether X-chromosomal or autosomal data are used. We have also found our inferences to become more robust when our data are jointly analyzed with HGDP data.

I can't but find quite curious how, once again, Indian and European histories behave so similarly: in Europe also a simpler but also "god-sanctioned" caste system (designed by Agustin of Hippo) was imposed upon the collapse of the Roman Empire (very similar dates). However popular revolutions gradually but systematically destroyed it. The same is happening in India now but with a delayed timeline. Instead Muslim West Asia (and surroundings) had no caste system and that's probably why it was so successful back in the day: because it allowed relatively more freedom and intellectual pursuit than other neighboring social systems. Of course, this stopped being the case after the Mongol conquests, roughly coincident with European Renaissance, when Islam cocooned itself into reactionary mode, leading to stagnation and eventually to colonial subservience.

Caucasus and Swiss hunter-gatherer genomes

I know I'm late for the party but better late than never, right?

A recent study sequenced three hunter-gatherer genomes from Georgia and one from Switzerland, expanding our understanding of the pre-Neolithic genetic landscape of West Eurasia.

Eppie R. Jones et al., Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nature Communications 2015. Open access → LINK [doi:10.1038/ncomms9912]

Abstract

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ~45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ~25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ~3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

Figure 1: Genetic structure of ancient Europe.

 (a). Principal component analysis. Ancient data from Bichon, Kotias and Satsurblia genomes were projected¹¹ onto the first two principal components defined by selected Eurasians from the Human Origins data set¹. The percentage of variance explained by each component accompanies the titles of the axes. For context we included data from published Eurasian ancient genomes sampled from the Late Pleistocene and Holocene where at least 200 000 SNPs were called^{1, 2, 3, 4, 5, 6, 7, 9} (Supplementary Table 1). Among ancients, the early farmer and western hunter-gatherer (including Bichon) clusters are clearly identifiable, and the influence of ancient north Eurasians is discernible in the separation of eastern hunter-gatherers and the Upper Palaeolithic Siberian sample MA1. The two Caucasus hunter-gatherers occupy a distinct region of the plot suggesting a Eurasian lineage distinct from previously described ancestral components. The Yamnaya are located in an intermediate position between CHG and EHG. (b). ADMIXTURE ancestry components¹² for ancient genomes (K=17) showing a CHG component (Kotias, Satsurblia) which also segregates in in the Yamnaya and later European populations.

The Swiss one (Bichon, Jura) is maybe less of a novelty, roughly falling within the already known parameters for Western European hunter-gatherers of Magdalenian tradition (WHG in the jargon) but the three samples from the Caucasus (CHG) are really a much needed new data-point, different from everything else that what we knew and surprisingly close to modern Caucasus populations. 

They are however very distant from all other known ancient West Eurasian samples. Fig. 2 shows an estimated divergence with early Neolithic Europeans (EEF, Stuttgart) dating from before the Last Glacial Maximum, to 24,000 years ago. The divergence of this composite West Asian macro-population (EEF's Paleoeuropean admixture is accounted for separately) with the pre-Neolithic Europeans seems to be of c. 46,000 years, what is consistent with early Upper Paleolithic (the large error margin allows for a secondary Gravettian genesis contact anyhow). On the other hand the divergence between Bichon and Lochsbour seems to fit with the Magdalenian time-frame as one would expect.

CHG are surprisingly close to modern Caucasus population, particularly to Georgians. CHG also appear to be an excellent candidate population for the formation of the early Indoeuropean Yamna people, which fit best as a mix of CHG and EHG (Eastern European hunter-gatherers). 

Figure 4: The relationship of Caucasus hunter-gatherers to modern populations.

a). Genomic affinity of modern populations¹ to Kotias, quantified by the outgroup f₃-statistics of the form f₃(Kotias, modern population; Yoruba). Kotias shares the most genetic drift with populations from the Caucasus with high values also found for northern Europe and central Asia. (b). Sources of admixture into modern populations: semicircles indicate those that provide the most negative outgroup f₃ statistic for that population. Populations for which a significantly negative statistic could not be determined are marked in white. Populations for which the ancient Caucasus genomes are best ancestral approximations include those of the Southern Caucasus and interestingly, South and Central Asia. Western Europe tends to be a mix of early farmers and western/eastern hunter-gatherers while Middle Eastern genomes are described as a mix of early farmers and Africans.

I find notable that the CHG component (do not confuse with the African one of similar color) is still apparent in the Indian subcontinent, something that was already detected in other analyses. The CHG component seems to be the core of the so called "ancient North Indian" (ANI) component, also known as "Gedrosian" or "Caucaso-Baloch". What they call in the above analysis "South Asian" would be approximately the also known as "ancient South Indian" (ASI) component, which is presumably pre-Neolithic. 

"Farmer" means European Early Farmer (EEF) and already implies some Paleolithic European admixture, until we have some Levant and Mesopotamian genuine first Neolithic samples, we should not assume that all the Fertile Crescent Neolithic people were just like that, although some may have been close. In fact, I tend to think that the CHG or a similar "highlander" component was probably important in the Zagros Neolithic and consequently in the Mesopotamian and Iranian one, reaching eventually to South Asia. See here for more details on how the Neolithic expansion in Europe and India were largely parallel but not identical at all in source populations. 

To illustrate this early Neolithic complexity, still apparent to some extent in West Asian genetics and, as I just said, in European and South Asian ones, the following archaeo-cultural map should help:

Source: Eleni Asouti 2006 (red color annotation is mine)

I strongly recommend to read the full source study, because it is very informative about what were some of our ancestors¹ doing when farming and herding were being developed in West Asia, but the map above alone gives a very good glimpse of the ethno-cultural complexity of these ancient West Asian populations. 

My understading is that the mainline (Thessalian or Aegean) European Neolithic founders must have originated within the PPNA/B complex, although uncertain about which specific culture within it (most likely not Harifian because that one is surely at the origin of Semitic languages but almost any other one would do, notably those close to the Mediterranean coast: Sultanian, Aswadian and Mureybetian). Instead the populations affecting Eastern European, Mesopotamian-Iranian (Sumer and Elam) and Indian Neolithic are most probably rather linked to what is here called as M'lafatian or Zagros Neolithic, which in turn were most likely linked one way or the other to Caucasus hunter-gatherers and in general to the "highlander" West Asian element apparent in other studies in contrast to a more EEF-like "lowlander" one. 

________________________________________

¹ Sure: I'm thinking mostly of Euro-Mediterranean and Central-South Asian peoples but even if you are East Asian or Tropical African it's still very probable that some random ancestor comes from this crucial paleo-historical knot (or almost from anywhere else: admixture never ends and we are all related, even if thinly, within the last millennium or so).

South Asian first Neolithic and its relation with West Asia

Informative compilation of dates for West and South Asian Neolithic sites.

Kavita Kangal et al., The Near-Eastern Roots of the Neolithic in South Asia. PLoS ONE 2014. Open access → LINK [doi:10.1371/journal.pone.0095714]

Abstract

The Fertile Crescent in the Near East is one of the independent origins of the Neolithic, the source from which farming and pottery-making spread across Europe from 9,000 to 6,000 years ago at an average rate of about 1 km/yr. There is also strong evidence for causal connections between the Near-Eastern Neolithic and that further east, up to the Indus Valley. The Neolithic in South Asia has been far less explored than its European counterpart, especially in terms of absolute (¹⁴C) dating; hence, there were no previous attempts to assess quantitatively its spread in Asia. We combine the available ¹⁴C data with the archaeological evidence for early Neolithic sites in South Asia to analyze the spatio-temporal continuity of the Neolithic dispersal from the Near East through the Middle East and to the Indian subcontinent. We reveal an approximately linear dependence between the age and the geodesic distance from the Near East, suggesting a systematic (but not necessarily uniform) spread at an average speed of about 0.65 km/yr.

We must be warned that the study dwells on statistical data, mostly ¹⁴C and other archaeological dates and not in pottery typology and such. So there are probably a lot of nuances to be added to what the authors conclude. However the study is a major effort to systematize West and South Asian Neolithic dates (details in the extensive supplementary materials) and that must be acknowledged as very useful on its own.

Fig. 2 synthesizes the findings of this study:

Figure 2. A linear envelope fit to the data using the weighted dates yields the average Neolithic dispersal speed km/yr.

The filled circles (red) and triangles (magenta) show the archaeologically dated sites from Iran and the Indus valley Civilization, respectively; filled circles (black) and open triangles represent sites with multiple and single ¹⁴C dates, respectively.

[Note: Gesher is one of the earliest PPNA sites, located in Northern Palestine].

The graph is a bit misleading because there are places in South Asia with ¹⁴C dates older than the apparent 7000 BP baseline (see Appendix in the study). Ayakagytma has several dates nearing 6000 BCE (i.e. ~8000 BP), while Merhgar is dated to as early as 8520 BCE (~10,500 BP), which overlaps the oldest sites of West Asia. These oldest Neolithic sites of South Asia are hardly recognizable in the graph, as they are shown as mere dots, whose only distinction is that they are ~3000 km away from Gesher. I had to investigate the Appendix to spot them.

The Merhgar ¹⁴C date is just one but it does not seem the authors felt compelled to discard it for any reason, so it should stand in principle.

Actually, rather than explain South Asian Neolithic as West Asian derived, the data in this study only offers an interesting overview of the dates but as such demonstrates nothing. Actually, if, as they argue, we are to consider always the oldest regional date (unless unreliable), then the expansion of Neolithic to South Asia was very fast. What was rather slow was its expansion within West Asia apparently.

Said that, there are many reasons to think that there was at least an important West Asian contribution to South Asian Neolithic, if nothing else because of the important presence of several important Western Y-DNA lineages (R1a, J), which seem somehow related to Neolithic spread, as well as the so-called "ANI" component, of clear West Asian affinity. Also many crops and animals were obviously imported from West Asia.

In this regard, a reader pointed to me weeks ago to a study that claims that sheep were independently domesticated in South Asia. However I found their conclusions far fetched so I never discussed it... until now.

Sachin Singh et al., Extensive Variation and Sub-Structuring in Lineage A mtDNA in Indian Sheep: Genetic Evidence for Domestication of Sheep in India. PLoS ONE 2013. Open access → LINK [doi: 10.1371/journal.pone.0077858]

What this study did find is a very specific founder effect of sheep lineages in India. However this cannot be accepted to be caused by an independent domestication but rather looks like a founder effect after domestication, which almost certainly owes to West Asia, where the ancestors of domestic sheep lives.

Figure 3. Neighbor-joining tree of domestic sheep based on 432 bp of control region mtDNA.
(A) Neighbor-joining tree of mtDNA sequences of Indian sheep (330) along with representative samples of five lineages (▲), namely; A, B, C, D & E. Indian sheep show three lineages, namely; A, B and C. (B) Neighbor-joining tree of mtDNA sequences of the Indian (330), Chinese (129), Central Asian, Caucasian and European (406), Portuguese (161), and West Balkan (60), sheep along with representative samples of five lineages (▲), namely; A, B, C, D & E . The sequences of wild Ovis species have been used as outgroups. MEGA 5 version 5.0.1.102 was used to construct the trees using Tamura-Nei model with 10,000 bootstrap. Numbers above a given branch represent bootstrap support for the branch as a percentage out of 10,000 re samplings.

Notice please how the root of the tree is at the bottom, where the various wild species of sheep are listed by their names. So the dominance of lineage A in South Asia surely owes to a founder effect and not local domestication.

Lions also migrated out of Africa

A quick excursion from the humano-centric focus of this blog, in this occasion to the paleohistory of that fascinating social predator: the lion.

Ross Barnet et al., Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis. BMC Evolutionary Biology, 2014. Open access → LINK [doi:10.1186/1471-2148-14-70]

Abstract

Background

Understanding the demographic history of a population is critical to conservation and to our broader understanding of evolutionary processes. For many tropical large mammals, however, this aim is confounded by the absence of fossil material and by the misleading signal obtained from genetic data of recently fragmented and isolated populations. This is particularly true for the lion which as a consequence of millennia of human persecution, has large gaps in its natural distribution and several recently extinct populations.

Results

We sequenced mitochondrial DNA from museum-preserved individuals, including the extinct Barbary lion (Panthera leo leo) and Iranian lion (P. l. persica), as well as lions from West and Central Africa. We added these to a broader sample of lion sequences, resulting in a data set spanning the historical range of lions. Our Bayesian phylogeographical analyses provide evidence for highly supported, reciprocally monophyletic lion clades. Using a molecular clock, we estimated that recent lion lineages began to diverge in the Late Pleistocene. Expanding equatorial rainforest probably separated lions in South and East Africa from other populations. West African lions then expanded into Central Africa during periods of rainforest contraction. Lastly, we found evidence of two separate incursions into Asia from North Africa, first into India and later into the Middle East.

Conclusions

We have identified deep, well-supported splits within the mitochondrial phylogeny of African lions, arguing for recognition of some regional populations as worthy of independent conservation. More morphological and nuclear DNA data are now needed to test these subdivisions.  

 

 

Modern lions originated somewhere in Africa, possibly towards the East or South of the continent, and spread from there. Asian lions originated in North Africa and migrated Eastwards more or less like humans did. However, according to the study's molecular clock estimates, they did so only in the Mousterian Pluvial and not in the Abbassia Pluvial, as we did. 

The cave lion is a different (sub-)species, used in this study to root the phylogenetic tree.

Phylogenetic analyses of lion sequence data. A) Median network of 1051 bp of cytb for all 88 lion individuals identified from GenBank plus those generated in this study. Panthera leo spelaea was used as an outgroup. Circles are proportional to haplotype frequencies and black circles represent hypothesized intermediate haplotypes. The number of links represent the number of mutations between haplotypes. Haplotypes are labelled from A to S and correspond to sequences labelled in Table 1 and Additional file 3: Table S1. B) Phylogenetic tree from a Bayesian analysis of combined cytb and control region data for all lion taxa where available (n = 54). Posterior probabilities of supported clades are shown at nodes. Estimates of divergence times: (a) 124,200 years (95% credibility: 81,800-183,500); (b) 61,500 years (32,700-97,300); (c) 51,000 years (26,600-83,100); (d) 81,900 years (45,700-122,200); (e) 57,800 years (26,800-96,600); (f) 21,100 years (8300–38,800). Branch colours correspond to reconstructed ancestral geographic states (Purple, South Africa; Yellow, East Africa; Orange, West Africa; Red, Central Africa; Teal, North Africa; Blue, South Asia; Green, Near-East). Tip colours correspond to origins of samples.

Reconstructed distribution of the modern lion at different times. Estimates of spatial diffusion pathways at Marine Isotope Stage (MIS) time points: A. MIS5 B. MIS4-MIS3 C. MIS2-MIS1 D. Estimated natural distribution prior to anthropogenic disturbance. Black arrows show estimated spatial diffusions, with thicknesses proportional to Bayes factors. Movement from East Africa to South Africa (4.83), from South Africa to East Africa (4.66), from West Africa to Central Africa (3.00), from North Africa to South Asia (4.37), from South Asia to North Africa (4.50), from North Africa to Middle East (21.03). Tropical rainforest is shown in light grey (present distribution), maximal extent during humid periods (black dashed line), and minimal extent during arid periods (white dashed line). The Great Rift Valley is shown in dark grey. African rivers are shown in blue. Co, Congo; Ng, Niger; Ni, Nile; Se, Senegal.

Y-DNA R1a spread from Iran

While this conclusion was something more or less reachable with previous data (see HERE for example), a new study adds some fine detail for us to reconstruct the paleohistory of this major Eurasian lineage.

Peter A. Underhill et al., The phylogenetic and geographic structure of Y-chromosome haplogroup R1a. EJHG 2014. Pay per view → LINK [doi:10.1038/ejhg.2014.50]

Important: supplemental materials are freely available.

Abstract

R1a-M420 is one of the most widely spread Y-chromosome haplogroups; however, its substructure within Europe and Asia has remained poorly characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-chromosomes and analyzed them to a highly granular phylogeographic resolution. Whole Y-chromosome sequence analysis of eight R1a and five R1b individuals suggests a divergence time of ~25 000 (95% CI: 21 300–29 000) years ago and a coalescence time within R1a-M417 of ~5800 (95% CI: 4800–6800) years. The spatial frequency distributions of R1a sub-haplogroups conclusively indicate two major groups, one found primarily in Europe and the other confined to Central and South Asia. Beyond the major European versus Asian dichotomy, we describe several younger sub-haplogroups. Based on spatial distributions and diversity patterns within the R1a-M420 clade, particularly rare basal branches detected primarily within Iran and eastern Turkey, we conclude that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran.

This case, as well as many others, including that of its close relatives R1b and Q, illustrate why frequency is not the same as origin, which can only be inferred (if at all) by studying the hierarchical diversity of the lineage. These three lineages for example, must have spread from West Asia but they are relatively less important in numbers in that region today, overshadowed by other lineages, notably J. Instead their derived branches had major impacts in other regions (Europe, South and Central Asia, Siberia and America).

Frequencies of the main lineages

There are two main sub-lineages of R1a, which according to the current ISOGG tree version (maybe to be refitted after this study?) are known as R1a1a1b2 (Z93) and R1a1a1b1a (Z282). The first one is essentially Asian (with greatest frequencies in South and Central Asia, where it includes >98% of all R1a individuals) wile the latter is almost exclusively European (notably Eastern European but with a distinct branch in Scandinavia, encompassing together >96% of R1a individuals in Europe).

These maps give us a quite decent glimpse of the main scatter patterns of R1a but alone they can't inform us of its origins. For that we have to look at the detailed tree and the relationship of its samples with geography. 

Origins and distribution of R1a

As mentioned above, the authors conclude that R1a and R1a1 must come from Iran, where the greatest basal diversity is:

To infer the geographic origin of hg R1a-M420, we identified populations harboring at least one of the two most basal haplogroups and possessing high haplogroup diversity. Among the 120 populations with sample sizes of at least 50 individuals and with at least 10% occurrence of R1a, just 6 met these criteria, and 5 of these 6 populations reside in modern-day Iran. Haplogroup diversities among the six populations ranged from 0.78 to 0.86 (Supplementary Table 4). Of the 24 R1a-M420*(xSRY10831.2) chromosomes in our data set, 18 were sampled in Iran and 3 were from eastern Turkey. Similarly, five of the six observed R1a1-SRY10831.2*(xM417/Page7) chromosomes were also from Iran, with the sixth occurring in a Kabardin individual from the Caucasus. Owing to the prevalence of basal lineages and the high levels of haplogroup diversities in the region, we find a compelling case for the Middle East, possibly near present-day Iran, as the geographic origin of hg R1a.

Between these top tier nodes (R1a and R1a1) and the two most common sublineages described above, this study only found one paragroup represented: R1a1a1* (M417). This should be an important step in the analysis but the researchers prefer to remain silent on it. Why? I guess that the reason is that it is complicated to analyze and reach to sound conclusions. 

I spent some time today looking at the haplotypes of this paragroup mentioned in the study and I could not reach a conclusion either: the majority of the sequences are from Europe and all them (excepting a highly derived Norwegian line and including a low derived Iranian one) seem to derive from a North German haplotype. I call this group "branch A". 

However there is at least one West Asian sequence (from Turkey) which seems independent ("branch B"), while an Indian and the already mentioned Norwegian sequence could derive from either one. So my impression is that there is an specifically North European "branch A" but also some other stuff with West Asian centrality ("branch B") within this key paragroup. 

Guess that I could say a lot more about not being able to say much more on this key intermediate step but, synthetically there are two options among which I can't decide:

• Branch A went back to West Asia from where it spread again to Eastern Europe and Central South Asia.
• Branch B is actually at the origin of the two derived and highly spread subhaplogroups.

Whatever the case I understand that there are good reasons to think that these spread first from West Asia, at the very least Z93 and very likely also  Z282. 

R1a1a1b2 (Z93)

There is nothing European in this lineage: only some lesser terminal branches at the Southern Urals, roughly where the Kurgan phenomenon began some 6000 years ago. 

This detail is indeed remarkable because, if, as often argued, R1a or some of its subclades spread from there, we should expect at least some basal diversity being retained. Instead all we see are some highly derived branches. So the main conclusion must be that the expansion of R1a does not seem related to the Kurgan phenomenon, except maybe in some secondary instances. 

As mentioned before, this lineage is Central and South Asian and comprises the vast majority of R1a in those two regions. 

The detailed haplotype network can be seen in Supp. Info fig. 2.

In essence we can say that:

• Z93* has three apparent distinct branches stemming from West Asia (incl. Caucasus) and another one from South Asia/Altai (1). 
• Z95* has two apparent distinct branches:
• A small one with presence in West Asia and Southern Europe
• Another one (pre-M780?) stemming from South or West Asia
• M780 has clear origins in South Asia (incl. most Roma lineages)
• Z2125 also appears to originate in South Asia, even if it has a greater spread outside it, notably to Central Asia
• M580 and M582 appear related and surely originated in West Asia

Weighting them:

• Z95:
• West Asia: 2
• South Asia: 2
• West/South Asia: 1

Therefore the origin of Z95 should be though as West-South Asian but undecided between either region. Say Afghanistan for example. 

• Z93:
• West Asia: 3
• West/South Asia: 1 (Z95)
• South Asia/Altai: 1 

In this case I would say that West Asia is almost certainly the origin, although tending to Central/South Asia. For example: Iran again. 

So, regardless of whether the previous stage (M417) represents a stay in West Asia or a back-migration from Europe into West Asia, West Asia is clearly at the origin of Z93. It does not represent any Kurgan migration but an Asian phenomenon with origins towards the West (around Iran).

R1a1a1b1a (Z282)

On first sight this European sublineage seemed quite simpler: it is obvious that the bulk of it spread from Eastern Europe. However, when we look at the haplotype network, we cannot confirm this pattern for the Norwegian or Scandinavian haplogroup Z284, which is only linked to the rest via some South European and West Asian samples. 

So my conclusion must be that Z282 experienced a main expansion from Eastern Europe but only into Eastern and Central Europe and that the Scandinavian variant almost certainly represents another flow within this haplogroup, with the knot being in West Asia. 

Anyhow the main East and Central European expansion seems true. For some reason it is not centered in any obvious prehistorical locality, as could be the Volga or maybe Ukraine, but instead its center is further North around Smolensk. 

Overall reconstruction of the spread of R1a

With all the previous analysis I made this map, which also shows in discrete gray color the general pattern of expansion of haplogroup R:

We have an expansion of R into South Asia and Western Eurasia (incl. Central Asia) and even into parts of Africa (R1b-V88) from apparent South Asian (R, R1 and R2) and West Asian (R1a, R1b) origins. Related lineages Q and P* could also be integrated into this pattern of expansion but I did not want to overload the map with too many details. 

There is some uncertainty regarding the North European branches of R1a but otherwise the pattern seems quite clear. 

On these North European branches, I must say that they remind me of other odd lineages with similar geography: R1b-U106, I1-M253 and I2a2-M223. With the likely exception of R1b-U106 neither appears to have experienced any significant re-expansion since their arrival to that corner of the World, however they do seem to survive pretty well in it. 

Time frame?

Finally we seem to be entering the age of full Y chromosome sequencing and a more serious molecular clock based on it. As I have explained on other occasions (for example), the human Y chromosome is large enough to experience mutations almost every single generation, what should provide a decent molecular clock, unlike the very rough approximations used in the past. 

However the issue of correct calibration remains open. As you surely know the academy is slow to incorporate the most recent evidence, especially from fields distinct to their specialty. Hence I do not expect them to calibrate based on the obvious fact that age(CF) or at least age(F)=100,000 years. They are probably still stuck in old concepts of a "recent" out-of-Africa migration c. 60 or at most 80 Ka ago, as well as the usual Pan-Homo spilt under-estimates

I must reckon in any case that I had not enough time to study this matter in depth yet, so the previous observation is rather my idea of what to expect.

In any case in this study the authors resorted to full Y chromosome to calculate their age estimates and I applaud them for doing so. As apparent in fig. 5, all R1 derived sequences have approximately the same number of accumulated SNPs, what in principle allows for a perfected molecular clock, assuming it is well calibrated. 

Their estimate is as follows:

A consensus has not yet been reached on the rate at which Y-chromosome SNPs accumulate within this 9.99Mb sequence. Recent estimates include one SNP per: ~100 years,⁵⁸ 122 years,⁴ 151 years⁵ (deep sequencing reanalysis rate), and 162 years.⁵⁹ Using a rate of one SNP per 122 years, and based on an average branch length of 206 SNPs from the common ancestor of the 13 sequences, we estimate the bifurcation of R1 into R1a and R1b to have occurred ~25,100 ago (95% CI: 21,300–29,000). Using the 8 R1a lineages, with an average length of 48 SNPs accumulated since the common ancestor, we estimate the splintering of R1a-M417 to have occurred rather recently, B5800 years ago (95% CI: 4800–6800). The slowest mutation rate estimate would inflate these time estimates by one third, and the fastest would deflate them by 17%.

The references correspond to (4) Poznick 2013, (5) Francalacci 2013, (58) Xue 2009 and (59) Méndez 2013. This last is the Anzick study, of which at the very least we can say that they had a real calibration point in the ancient Amerindian DNA. It is also the one which provides the longest mutation rate. 

Considering that Xue 2009 is "old" (for this avant-guard aspect of this pretty young science), I find their choice of the Poznick rate quite a bit conservative. The Francalacci rate is the intermediate one of the three "recent" papers referenced and it is also quite close to the calibrated Méndez rate. 

Personally I would choose the later without a second thought. As long as CF ends up being younger than 100 Ka, it is positively too conservative anyhow.

Using the Méndez (Anzick-calibrated) rate of 162 years per SNP, I get the following corrected estimates:

• R1a/R1b split (R1 node): 33,000 years ago (CI: 26.0-42.5 Ka)
• R1a-M417 node: 7,700 years ago (CI: 6.4-9.0 Ka)

These seem fair enough to me, judging on the fact that the core R1a expansion seems to originate in West Asia (at the very least for the South/Central Asian branch), what fits much better with a Neolithic frame than with the Kurgan one.

It also fits better with my previous estimates after due re-calibration of Terry D. Robb's full sequence Y-DNA tree, although my estimates are even older, especially after a second recalibration to adjust to the recent discovery of widespread H. sapiens evidence in South and East Asia c. 100 Ka ago. 

In my understanding the R1 node is actually c. 48 Ka old (R1b: c. 34 Ka.), what, apportioning, yields a date of c. 11.2 Ka for the R1a-M-417 node. 



Update (Mar 31):best possible molecular clock estimates for R1:

Follows fig. 5 of Underhill et al. 2014, annotated by me in red and purple colors:

• Red: age estimates calibrated for age(CF)=~100Ka, which is what modern archaeological evidence overwhelmingly supports for the second phase of the migration Out of Africa (or rather out of Arabia into India and East Asia). Dots drawn to help identify the estimated nodes.
• Purple: general references of European (plus) prehistorical cultures or periods for the key ages estimated.

If I'm correct, then the expansion of R1b in Europe still corresponds in rough terms to the Magdalenian period or, more generally, the late Upper Paleolithic. This does not mean that it remained that way forever (it may well have been reshuffled later on: in the Epipaleolithic, Neolithic and Chalcolithic) but it seems to be the time-frame of its main expansion when the main lineages got established, whatever happened to them later on.

I know well that so far ancient DNA for this lineage remains to be found and that the dominant haplogroup among known Epipaleolithic hunter-gatherers was (for all we know) I2a. However this is what the refined full Y chromosome sequence molecular clock, properly calibrated according to the archaeological evidence for the settling of Asia by H. sapiens, has to say. If you wish to dismiss this and use another estimate instead, that's always up to you. I just hope that you know what you're doing.

Anyhow, if I am correct, then the expansion of R1a is neither Chalcolithic nor Neolithic but clearly Epipaleolithic. Does it make any sense? I can't say for sure because this period is not so well understood. Whatever the case, is it possible to integrate the key pre-Neolithic Zarzian culture of the Zagros (map) in this scheme of things? What about all the other question marks that fill the gaps of our mediocre knowledge of the Mesolithic of West Asia? Or is it the Balcanic Epigravettian to be blamed instead? Or both?

I really can't say with any certainty at this stage. But I am intrigued indeed.


Update (Mar 31): frequency pie charts of Underhill's data available at Kurdish DNA.


Update (Aug 2015): I must update the frequencies of the various upstream paragroups, in agreement with table S4, because I may have missed some details initially. However the overall tendency is the same.

• R1a* (M420): Italy (1), Turkey East (1), Turkey Cappadocia (2), UAE (1), Oman (1), Iran (set 2) (2), Iran NE (1), Iran South (5), Iran North (5), Azeris-Iran (5).
• R1a1* (SRY10831.2): Iran (set 2) (1), Iran NE (1), Iran South (2), Iran North (1), Kabardin (1). In addition it has more recently been found in two Epipaleolithic Eastern Europeans (EHG), from Karelia (Haak 2015) and Smolenskaya Oblast (Chekunova 2014).
• Ra1a1a1* (M417): Ireland (1), Netherlands (3), Norway (1), South Sweden (1), Germany (1), Estonia (1), Hungary (1), Turkey East (Kurds) (1), Iran (set 3) (1), India South (1). 

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 view → LINK [doi:10.1016/j.quascirev.2013.06.012]

Abstract

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 Academia.edu 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 access → LINK [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 quality.

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 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.