More details on the Neanderthal legacy in modern humans

Is straight hair Neanderthal?

A quick note on two recent studies on the relevance of Neanderthal introgression on modern Humankind, notably the “out of Africa” branch.

Sriran Sankararaman et al., The genomic landscape of Neanderthal ancestry in present-day humans. Nature 2014. Pay per view → LINK [doi:doi:10.1038/nature12961]

Abstract


Genomic studies have shown that Neanderthals interbred with modern humans, and that non-Africans today are the products of this mixture1, 2. The antiquity of Neanderthal gene flow into modern humans means that genomic regions that derive from Neanderthals in any one human today are usually less than a hundred kilobases in size. However, Neanderthal haplotypes are also distinctive enough that several studies have been able to detect Neanderthal ancestry at specific loci1, 3, 4, 5, 6, 7, 8. We systematically infer Neanderthal haplotypes in the genomes of 1,004 present-day humans9. Regions that harbour a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African environments. We identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology. An unexpected finding is that regions with reduced Neanderthal ancestry are enriched in genes, implying selection to remove genetic material derived from Neanderthals. Genes that are more highly expressed in testes than in any other tissue are especially reduced in Neanderthal ancestry, and there is an approximately fivefold reduction of Neanderthal ancestry on the X chromosome, which is known from studies of diverse species to be especially dense in male hybrid sterility genes10, 11, 12. These results suggest that part of the explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal alleles that caused decreased fertility in males when moved to a modern human genetic background.

→ Synthesis at Science Daily.

B. Bernot & J.M. Akey, Resurrecting Surviving Neandertal Lineages from Modern Human Genomes. Science 2014. Pay per view → LINK [doi:10.1126/science.1245938]

Abstract

Anatomically modern humans overlapped and mated with Neandertals such that non-African humans inherit ~1-3% of their genomes from Neandertal ancestors. We identified Neandertal lineages that persist in the DNA of modern humans, in whole-genome sequences from 379 European and 286 East Asian individuals, recovering over 15 Gb of introgressed sequence that spans ~20% of the Neandertal genome (FDR = 5%). Analyses of surviving archaic lineages suggests that there were fitness costs to hybridization, admixture occurred both before and subsequent to divergence of non-African modern humans, and Neandertals were a source of adaptive variation for loci involved in skin phenotypes. Our results provide a new avenue for paleogenomics studies, allowing substantial amounts of population-level DNA sequence information to be obtained from extinct groups even in the absence of fossilized remains.

→ Synthesis at Science Daily.

I don’t have access to the papers (update: I do have the second one now) but, honestly, I don’t have time either, so, even with full access, I would have to be rather shallow, given the complexity of the matter.

Nevertheless I would highlight the following:

Fitness costs

Areas of dense gene presence tend to be more depleted of Neanderthal inheritance, meaning that, at least in many cases Neanderthal genes were deleterious (harmful) in the context of the H. sapiens genome. It’s probable that they worked better in their “native” context of the Neanderthal genome but we must not understimate the risks of low genetic diversity, a problem that affected Neanderthals as well as H. heidelbergensis (species probably including Denisovans or at least their non-Neanderthal ancestry).

Partial hybrid infertility

The areas of very low Neanderthal genetic influence include those of reproductive relevance, including genes affecting the testes and the chromosome X. This is typical of the hybrid infertility phenomenon, which is part of species divergence, making more difficult or even impossible that hybrids can reproduce. This particular item emphasizes that the differential speciation of Neanderthals and H. sapiens was in a quite advance stage already some 100 Ka ago, what does not seem too consistent with the lowest estimates for the divergence of both human species (H. sapiens have been diverging for some 200 Ka and are still perfectly inter-fertile). 

Adaptive Neanderthal hair introgression

On the other hand the Neanderthal genetic legacy has been best preserved in genes that appear to affect keratin (affecting skin, nails and hair). This bit I consider of particular interest because, based on the modern distribution of hair texture phenotypes, I have often speculated that straight hair may be a Neanderthal heritage and this finding seems supportive of my speculation.

It’s possible that straight hair conferred some sort of advantage in some of the new areas colonized by H. sapiens, maybe providing better insulation against rain or cold (the ancestral Sapiens thinly curly hair phenotype is probably an adaption to tropical climate, allowing for a ventilated insulation of the head).

Some 20% of the Neanderthal genome still lives in us

Collectively, that is. The actual expressed genes are probably a quite less important proportion anyhow and the actual individual Neanderthal legacy (expressing genes and junk together) seldom is greater than 3% in any case.

 

A western riverine route for human migration to North Africa in the Abbassia Pluvial

Interesting study on paleo-rivers of the Sahara providing insight for a likely route for Homo sapiens to cross the Sahara towards NW Africa.

Tom J. Coulthard et al., Were Rivers Flowing across the Sahara During the Last Interglacial? Implications for Human Migration through Africa. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0074834]

Abstract


Human migration north through Africa is contentious. This paper uses a novel palaeohydrological and hydraulic modelling approach to test the hypothesis that under wetter climates c.100,000 years ago major river systems ran north across the Sahara to the Mediterranean, creating viable migration routes. We confirm that three of these now buried palaeo river systems could have been active at the key time of human migration across the Sahara. Unexpectedly, it is the most western of these three rivers, the Irharhar river, that represents the most likely route for human migration. The Irharhar river flows directly south to north, uniquely linking the mountain areas experiencing monsoon climates at these times to temperate Mediterranean environments where food and resources would have been abundant. The findings have major implications for our understanding of how humans migrated north through Africa, for the first time providing a quantitative perspective on the probabilities that these routes were viable for human habitation at these times.

Figure 2. Simulated probability of surface water during the last interglacial. This figure details Archaeological sites, and an annual probability that a location has surface water. The archaeological data are derived from a number of sources (including [42], [66], [67], [68]. The findspots are characterised by Aterian and Middle Stone Age artefacts such as bifacial foliates and stemmed Aterian points and/or typical ‘Mousterian’ points, side scrapers and Levallois technology. Most are represented by surface scatters but where stratified examples exist these can be shown by dating (OSL and U-series techniques) and geomorphological setting to belong within MIS 5e [41], [42].

As discussed in other occasions, it seems likely that some genetic remnants of those early migrations are still visible in at least some NW Africans.

See also:

• North African autosomal genetics through the prism of ADMIXTURE.
• Major upheaval of human Y-DNA phylogeny: we are all ‘A’ now (on some very ancient lineages shared by West and North Africans).

 

Homo sapiens was in China before 100,000 years ago!

This finding consolidates the recent dating of African-like industries of India to c. 96,000 years ago, as well as other previous discoveries from mostly China, and, jointly, they totally out-date not just the ridiculous “60 Ka ago” mantra for the migration out-of-Africa (which we know is dated to c. 125,000 years ago in Arabia and Palestine) but also the previous estimates of c. 80,000 years ago for India (Petraglia 2007).

Guanjung Shen et al., Mass spectrometric U-series dating of Huanglong Cave in Hubei Province, central China: Evidence for early presence of modern humans in eastern Asia. Journal of Human Evolution, 2013. Freely accessible at the time of writing this → LINK [doi:10.1016/j.jhevol.2013.05.002]

Abstract


Most researchers believe that anatomically modern humans (AMH) first appeared in Africa 160-190 ka ago, and would not have reached eastern Asia until ∼50 ka ago. However, the credibility of these scenarios might have been compromised by a largely inaccurate and compressed chronological framework previously established for hominin fossils found in China. Recently there has been a growing body of evidence indicating the possible presence of AMH in eastern Asia ca. 100 ka ago or even earlier. Here we report high-precision mass spectrometric U-series dating of intercalated flowstone samples from Huanglong Cave, a recently discovered Late Pleistocene hominin site in northern Hubei Province, central China. Systematic excavations there have led to the in situ discovery of seven hominin teeth and dozens of stone and bone artifacts. The U-series dates on localized thin flowstone formations bracket the hominin specimens between 81 and 101 ka, currently the most narrow time span for all AMH beyond 45 ka in China, if the assignment of the hominin teeth to modern Homo sapiens holds. Alternatively this study provides further evidence for the early presence of an AMH morphology in China, through either independent evolution of local archaic populations or their assimilation with incoming AMH. Along with recent dating results for hominin samples from Homo erectus to AMH, a new extended and continuous timeline for Chinese hominin fossils is taking shape, which warrants a reconstruction of human evolution, especially the origins of modern humans in eastern Asia.

The range of dates for the teeth is ample but the oldest one is of 102.1 ± 0.9 Ka ago. Other dates are very close to this one: 99.5 ± 2.2, 99.3 ± 1.6, 96.8 ± 1.0, etc. (see table 1), so there can be little doubt about their accuracy. 

The Huanglong teeth (various views)

 

Now, how solidly can these teeth be considered to belong to the species Homo sapiens? Very solidly it seems:

The seven hominin teeth from Huanglong Cave have been assigned to AMH
mainly because of their generally more advanced morphology than that of H. erectus and other archaic populations (Liu et al., 2010b),
especially in terms of the crown breath/length index. These teeth also
lack major archaic suprastructural characteristics listed by Bermúdez de Castro (1988)
for eastern Asian mid-Pleistocene hominins, such as “strong tuberculum
linguale (incisors), marked lingual inclination of the buccal face
(incisors and canines), buccal cingulum (canines and molars), wrinkling
(molars), taurodontism (molars), swelling of the buccal faces (molars)”
(Tim Compton, Personal communication). However, in their roots, these
teeth still retain a few archaic features, being more robust and
complicated than those of modern humans (Liu et al., 2010b).

Zhirendong jaw

Let’s not forget that further South in China, in Zhirendong, a “modern” jaw was found and dated to c. 100,000 years ago as well.

As for the so-called “molecular clock”:

The new timeline for human evolution in China is in disagreement with
the molecular clock that posits a late appearance for AMH in eastern
Asia (e.g., Chu et al., 1998).

… too bad for the “clock”, because a clock that doesn’t inform us of time with at least some accuracy is totally useless.

 

 

Nubian Complex in Central Arabia

The Nubian Complex MSA techno-culture arrived to Central Arabia, just south of Riyadh seemingly via the South

Rémy Cressard & Yamandú H. Hilbert, A Nubian Complex Site from Central Arabia: Implications for Levallois Taxonomy and Human Dispersals during the Upper Pleistocene. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0069221]

Abstract

Archaeological survey undertaken in central Saudi Arabia has revealed 29 surface sites attributed to the Arabian Middle Paleolithic based on the presence of Levallois blank production methods. Technological analyses on cores retrieved from Al-Kharj 22 have revealed specific reduction modalities used to produce flakes with predetermined shapes. The identified modalities, which are anchored within the greater Levallois concept of core convexity preparation and exploitation, correspond with those utilized during the Middle Stone Age Nubian Complex of northeast Africa and southern Arabia. The discovery of Nubian technology at the Al-Kharj 22 site represents the first appearance of this blank production method in central Arabia. Here we demonstrate how a rigorous use of technological and taxonomic analysis may enable intra-regional comparisons across the Arabian Peninsula. The discovery of Al-Kharj 22 increases the complexity of the Arabian Middle Paleolithic archaeological record and suggests new dynamics of population movements between the southern and central regions of the Peninsula. This study also addresses the dichotomy within Nubian core typology (Types 1 and 2), which was originally defined for African assemblages.

Figure 3. Levallois methods schemata: figuration of product and core shapes for each method. A: Preferential Levallois flake production with centripetal preparation; B: Preferential Levallois point production with unidirectional convergent preparation; C: Nubian Levallois type 1 with distal divergent preparation; D: Nubian Levallois type 2 with double lateral preparation; E: Nubian Levallois type 1/2 with mixed type 1 and type 2 preparation.

Figure 10. Schematic representation depicting the three main dorsal preparation types, preparation type 1, 2 and 1/2, and the proposed reduction succession discussed in the text. In order to facilitate comprehension cores, end-products and preparation by-products have been color-coded; blue equals type 1 preparation, green type 2 and yellow type 1/2.

Many more images of interest for experts or qualified amateurs are available in this high quality study. For the less specialized reader it is probably more interesting to ponder the overall extension of the Nubian Complex:

Figure 11. Distribution of main sites with Nubian cores in Eastern Africa and Arabia. Illustrated cores do not represent actual size. 1. Al-Kharj 22 (this study); 2. Aybut Al Auwal [12]; 3. Shabwa [30]; 4. Hadramawt [5], [6], [27]; 5. Aduma [112]; 6. Gademotta [113]; 7. Asfet [114]; 8. Nazlet Khater 1 [115]; 9. Abydos [66].

The authors argue that Southern and Central Arabia are the Easternmost reaches of this complex, however we cannot forget that the recent discovery of Indian sites with a complex industry, dated to c. 96 Ka ago, of Nubian, Aterian and other MSA affinities challenges this notion.

See also in this blog:

• Middle Paleolithic industries of African affinity of the Thar Desert go back to c. 96 Ka ago
• African MSA
• The Nubian techno-complex of Dhofar: yet another evidence for an early migration out-of-Africa via Arabia
• The various options for the migration out of Africa
• … and in general the categories MSA and out of Africa.

 

Homo sapiens from Central China dated to 81-101 Ka BP

I just received notice (h/t David) of this most important finding and dating:

Guanjun Shen et al., Mass spectrometric U-series dating of Huanglong Cave in Hubei Province, central China: Evidence for early presence of modern humans in eastern Asia. Journal of Human Evolution 2013. Pay per view → LINK [doi:10.1016/j.jhevol.2013.05.002]

Abstract


Most researchers believe that anatomically modern humans (AMH) first appeared in Africa 160-190 ka ago, and would not have reached eastern Asia until ∼50 ka ago. However, the credibility of these scenarios might have been compromised by a largely inaccurate and compressed chronological framework previously established for hominin fossils found in China. Recently there has been a growing body of evidence indicating the possible presence of AMH in eastern Asia ca. 100 ka ago or even earlier. Here we report high-precision mass spectrometric U-series dating of intercalated flowstone samples from Huanglong Cave, a recently discovered Late Pleistocene hominin site in northern Hubei Province, central China. Systematic excavations there have led to the in situ discovery of seven hominin teeth and dozens of stone and bone artifacts. The U-series dates on localized thin flowstone formations bracket the hominin specimens between 81 and 101 ka, currently the most narrow time span for all AMH beyond 45 ka in China, if the assignment of the hominin teeth to modern Homo sapiens holds. Alternatively this study provides further evidence for the early presence of an AMH morphology in China, through either independent evolution of local archaic populations or their assimilation with incoming AMH. Along with recent dating results for hominin samples from Homo erectus to AMH, a new extended and continuous timeline for Chinese hominin fossils is taking shape, which warrants a reconstruction of human evolution, especially the origins of modern humans in eastern Asia.

In other words: strong material evidence is quickly piling up in favor of a Homo sapiens “fast” colonization of Southern Asia (and as far NE as Hubei!) around 100 or at least 90 Ka BP. 

See also:

• Middle Paleolithic industries of African affinity of the Thar Desert go back to c. 96 Ka ago
• East Asian jaw from 100,000 years ago is ‘modern human’

 

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.

 

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.

 

Reconstructing human demographic history from IBS segments

Figure 1. An eight base-pair tract of identity by state (IBS).

Identity-by-state (IBS) segments are those located between any two SNPs (polymorphisms, letters that vary among individuals). According to this new paper, they seem to be evolutionarily neutral and therefore their length, modified by recombination events each new generation, is a good trail to reconstruct human demographic history.

Kelley Harris & Rasmus Nielsen, Inferring Demographic History from a Spectrum of Shared Haplotype Lengths. PLoS Genetics 2013. Open access → LINK [doi:10.1371/journal.pgen.1003521]

Abstract

There has been much recent excitement about the use of genetics to elucidate ancestral history and demography. Whole genome data from humans and other species are revealing complex stories of divergence and admixture that were left undiscovered by previous smaller data sets. A central challenge is to estimate the timing of past admixture and divergence events, for example the time at which Neanderthals exchanged genetic material with humans and the time at which modern humans left Africa. Here, we present a method for using sequence data to jointly estimate the timing and magnitude of past admixture events, along with population divergence times and changes in effective population size. We infer demography from a collection of pairwise sequence alignments by summarizing their length distribution of tracts of identity by state (IBS) and maximizing an analytic composite likelihood derived from a Markovian coalescent approximation. Recent gene flow between populations leaves behind long tracts of identity by descent (IBD), and these tracts give our method power by influencing the distribution of shared IBS tracts. In simulated data, we accurately infer the timing and strength of admixture events, population size changes, and divergence times over a variety of ancient and recent time scales. Using the same technique, we analyze deeply sequenced trio parents from the 1000 Genomes project. The data show evidence of extensive gene flow between Africa and Europe after the time of divergence as well as substructure and gene flow among ancestral hominids. In particular, we infer that recent African-European gene flow and ancient ghost admixture into Europe are both necessary to explain the spectrum of IBS sharing in the trios, rejecting simpler models that contain less population structure.

The most interesting graph, synthesizing the result for standard HapMap European and African proxy samples is figure 7. However I have major issues with the age estimates, which seem to be half what is needed to be realistic according to archaeological and other genetic data (unlineal haplogroup history, for example). Therefore I have annotated it with a revised timeline, so it fits better with the objective data:

Figure 7. A history inferred from IBS sharing in Europeans and Yorubans. This is the simplest history we found to satisfactorily explain IBS tract sharing in the 1000 Genomes trio data. It includes ancient ancestral population size changes, an out-of-African bottleneck in Europeans, ghost admixture into Europe from an ancestral hominid, and a long period of gene flow between the diverging populations. (Right margin annotations by Maju).

Indeed the simplest revision of the time-scale was to double it. I guess it can be refined a bit more than that, maybe pushing it a bit further into the past, but the alternative time-scale I propose fits closely enough with known archaeological data like the time of the OoA to Arabia and Palestine or the spread of Acheulean (and therefore H. ergaster, common ancestor of Neanderthals and H. sapiens) out of Africa c. 1 Ma ago to illustrate that the reconstruction seems pretty much correct overall but fails when estimating the dates (because of scholastic-autistic academic biases that are too common in the field of human population genetics).

Update: even Dienekes agrees, on his own well documented reasoning, with a x2 mutation rate being necessary for the above graph.