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Category Archives: out of Africa

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 viewLINK [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.

B. Bernot & J.M. Akey, Resurrecting Surviving Neandertal Lineages from Modern Human Genomes. Science 2014. Pay per viewLINK [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.

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 accessLINK [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:

 
 

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 thisLINK [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 accessLINK [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:

 
 

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 viewLINK [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

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


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

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

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

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

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

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

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