Monthly Archives: October 2010

Solutrean-style retouch 75,000 years ago in South Africa

Blombos point
Since I started reading about the MSA (Middle Stone Age, the main African Middle Paleolithic stone industry) I have been under the impression that it had Solutrean affinities.
Well, now it is confirmed that at least some MSA crafters, those from Blombos Cave, South Africa, effectively used this technique some 35,000 years before it was known in Europe.


Pressure flaking has been considered to be an Upper Paleolithic innovation dating to ~20,000 years ago (20 ka). Replication experiments show that pressure flaking best explains the morphology of lithic artifacts recovered from the ~75-ka Middle Stone Age levels at Blombos Cave, South Africa. The technique was used during the final shaping of Still Bay bifacial points made on heat-treated silcrete. Application of this innovative technique allowed for a high degree of control during the detachment of individual flakes, resulting in thinner, narrower, and sharper tips on bifacial points. This technology may have been first invented and used sporadically in Africa before its later widespread adoption.

Very few stones types (obsidian, jasper, high quality flint) can be retouched this way without previous thermal modification (heating the stone appropriately). This was the technique used at Pinnacle Point, not far from Blombos in that very same time. The technological sophistication is such that it has been compared to metallurgy.
While Pinnacle point offered the first evidence of stone preparation through heating in order to improve knapping, Blombos has the first one of pressure retouch. Other evidence of the so-called modern behavior (symbolism, art, etc.) is also abundant in the South African MSA. Even food processing is known from that time in nearby Mozambique.

Source: Science Daily.

Solutrean points (or casts):

< From Don’s Maps:  

A cast of a Solutrean “laurel leaf” spear point, over 13 inches long. These delicate and beautiful implements were prepared by delicate flaking across the surface. Many are so large and delicate that they could never have been actually used, and may have been status objects.

Photo: Man before history by John Waechter

< From Lithic Casting Lab:


Francois Bordes wrote that “The majority of these specimens (Volgu cache) were chipped by direct percussion; but for the finer ones, indirect percussion or pressure has been used.” Jacques Bordaz wrote that “The obvious fragility of some of the specimens (Volgu cache) suggest rather a ritual use, or perhaps they were simply examples of some knapper’s bravura.”

< From Wikipedia.

A more complete toolkit from Solutré-Pouilly.

Another culture that used the same technique later on was Clovis culture in Holocene North America.


Do health and reproductive drive cancel each other?

This seems to be the case in a population of feral sheep from a remote Scottish island. Individuals with better immunity, and therefore longer-lived, do not manage to reproduce as successfully as their less healthy peers. However, in the long run they compensate that by participating in more reproductive seasons over their lives.

The two tendencies in dynamic equilibrium run along families.

Full story at Science Daily.

Ref. Andrea L. Graham et al. Fitness Correlates of Heritable Variation in Antibody Responsiveness in a Wild Mammal. Science, 2010. Pay per view.


Posted by on October 29, 2010 in biology, dynamic equilibrium, immunity, Scotland, sheep


Mars water is recent

Deposits of soluble minerals under the wheels of the trapped Mars rover but not in the upper layer support that water existed in liquid form recently on the red planet, otherwise the layers should be mixed by wind erosion.

Full story at Science Daily.


Posted by on October 29, 2010 in astronomy, Mars, water


Very low mutation rate, mwahahaha!

I’ve been reading around about the publication of a paper on the 1000 Genomes Project and what seems most interesting is that the observed mutation rate in humans would be of 1.1 x 10⁻⁸, much less than usually accepted. 
John Hawks seems particularly affected by the repeated observation of this rate, which he had previously discussed in March (on another different paper), up to the point that he seems about to accept the reality of such a slow molecular clock. 

Other elements of interest may be the finding of many previously unknown alleles, which, unlike those known earlier are rarer and found often only subpopulations, rather than wildly scattered through the planet.

Also that brain-related gene duplications may be at the root of human intelligence, when compared with other great apes (see Science News).


Posted by on October 28, 2010 in Homo sapiens, molecular clock, population genetics


Kerguelen mice: a model for human expansions?

I will today stop at a new genetic paper that does not deal with humans but with a not-so-distant relative: house mice. Specifically with mice in the remote Kerguelen islands, which have been known to humans (and hence to mice) only since 1772.

Abstract (provisional)


Starting from Western Europe, the house mouse (Mus musculus domesticus) has spread across the globe in historic times. However, most oceanic islands were colonized by mice only within the past 300 years. This makes them an excellent model for studying the evolutionary processes during early stages of new colonization. We have focused here on the Kerguelen Archipelago, located within the sub-Antarctic area and compare the patterns with samples from other Southern Ocean islands.


We have typed 18 autosomal and six Y-chromosomal microsatellite loci and obtained mitochondrial D-loop sequences for a total of 534 samples, mainly from the Kerguelen Archipelago, but also from the Falkland Islands, Marion Island, Amsterdam Island, Antipodes Island, Macquarie Island, Auckland Islands and one sample from South Georgia. We find that most of the mice on the Kerguelen Archipelago have the same mitochondrial haplotype and all share the same major Y-chromosomal haplotype. Two small islands (Cochons Island and Cimetiere Island) within the archipelago show a different mitochondrial haplotype, are genetically distinct for autosomal loci, but share the major Y-chromosomal haplotype. In the mitochondrial D-loop sequences, we find several single step mutational derivatives of one of the major mitochondrial haplotypes, suggesting an unusually high mutation rate, or the occurrence of selective sweeps in mitochondria.


Although there was heavy ship traffic for over a hundred years to the Kerguelen Archipelago, it appears that the mice that have arrived first have colonized the main island (Grande Terre) and most of the associated small islands.The second invasion that we see in our data has occurred on islands which are detached from Grande Terre and were likely to have had no resident mice prior to their arrival. The genetic data suggest that the mice of both primary invasions originated from related source populations. Our data suggest that an area colonized by mice is refractory to further introgression, possibly due to fast adaptations of the resident mice to local conditions.

The abstract alone is quite explanatory.
I must say that the reason for the refraction may not be adaptations to local conditions as much as mere demographic pressure: any new mice would be automatic minority and have poor chances of perpetuation, even in the absence of adaptations. Numbers alone make the difference, proving statistically difficult for any new arrival to leave a mark after the first population is consolidated.
Another detail worth discussing is:
In the mitochondrial D-loop sequences, we find several single step mutational derivatives of one of the major mitochondrial haplotypes, suggesting an unusually high mutation rate, or the occurrence of selective sweeps in mitochondria.
The mutation rate does not look too striking to me: 200 years for mice is like 10,000 for us maybe, as they reach reproductive maturity in a matter of months. So it’s like one (or two in a few sub-lineages)  surviving mutations downstream of the founder haplotype, which is anyhow still massively dominant.

Fig.2A mtDNA HVS haplotype network
In other words: there were some distinct founder effects of some derived haplotypes, mostly in Kerguelen itself but also overseas: in Falkland and Auckland islands and even back to Europe (Britain).
The diversity of derived basal lineages clearly indicates that this Kerguelen haplotype (yellow) exploded in the islands, regardless that it may be original from mainland Africa (black) and regardless that it has also spread overseas. This in the equivalent of 10,000 human years (very roughly).
It reminds me somewhat of what we can see in Eurasian human mtDNA, with the yellow lineage resembling human mtDNA M somewhat and the magenta one like N. And that is one reason I wanted to comment this paper, really. Of course the stage of diversification and other aspects are clearly different but it does illustrates how founder effects proceed and how demic pressure alone tends to fend off new colonizations.

East Asian jaw from 100,000 years ago is ‘modern human’

The Zhirendong jaw from Guangxi Zhuang (South China) was discovered in 2007 (but I did not know until late 2009). Its most striking characteristic is the chin, which is a trait typical of Homo sapiens. Now a paper co-authored by palaeontology superstar Erik Trinkaus says we are before a modern human jaw, maybe admixed with other Homo species.
Wu Liu et al., Human remains from Zhirendong, South China, and modern human emergence in East Asia. PNAS 2010. Pay per view (depending on your country and for six months only elsewhere). 
The 2007 discovery of fragmentary human remains (two molars and an anterior mandible) at Zhirendong (Zhiren Cave) in South China provides insight in the processes involved in the establishment of modern humans in eastern Eurasia. The human remains are securely dated by U-series on overlying flowstones and a rich associated faunal sample to the initial Late Pleistocene, >100 kya. As such, they are the oldest modern human fossils in East Asia and predate by >60,000 y the oldest previously known modern human remains in the region. The Zhiren 3 mandible in particular presents derived modern human anterior symphyseal morphology, with a projecting tuber symphyseos, distinct mental fossae, modest lateral tubercles, and a vertical symphysis; it is separate from any known late archaic human mandible. However, it also exhibits a lingual symphyseal morphology and corpus robustness that place it close to later Pleistocene archaic humans. The age and morphology of the Zhiren Cave human remains support a modern human emergence scenario for East Asia involving dispersal with assimilation or populational continuity with gene flow. It also places the Late Pleistocene Asian emergence of modern humans in a pre-Upper Paleolithic context and raises issues concerning the long-term Late Pleistocene coexistence of late archaic and early modern humans across Eurasia. 
Sources: NeanderFollia[cat] and Discovery News.

MtDNA stars (notes)

[Updated to include some data that showed up at the comments and I did not know initially]

On February, I wrote a ‘working note’ at Leherensuge on mitochondrial DNA stars. As I said then, star-like structures in haplogroups (stars for short) indicate rapid expansion in the time of few thousand years after a founder effect. They are in fact very hot markers in the genealogical tree.

There are the following categories of stars (slightly modified from the original February note):
  • Giant: only M and H, both around the 40 basal sublineages
  • Large: R, H1 and D4, with 15-18 basal sublineages
  • Medium: N and M4″64, with 12-13 basal sublineages (counting only CR mutations!!!)
  • Small: a host of them (5-10 basal sublineages)
All the medium-to-giant stars can be said to belong to the following two conceptual categories:
  • Early Eurasian Expansion: M, M4″64, N and R (in chronological order counting from L3)
  • Peripheral Eurasian Expansion: H, H1 and D4 (in Europe and NE Asia)
Many small stars also belong to these categories. However a number seem to happen relatively late, specially in West Eurasia (and occasionally Japan and America).

Some stars also belong to the African geography but all happen in the earlier period (simultaneous to the main Eurasian expansion) with the only exception of the mother of all Eurasians (and many Africans), L3, which is necessarily older than M and, therefore, is the first star-like structure one can detect in the human matrilineal genealogy.

While the mtDNA phylogeny goes a lot deeper than L3, there is no sign of strong rapid expansion before this matri-clan. This may be a time marker and may refer to the Abbassia Pluvial, c. 120-90 Ka ago.
The chronology of stars is as follows (loosely based on this previous exploration):
  • A very long period of African coalescence and gradual expansion (almost 30 molecular clock ticks, about half of human history). No star-like structures (no node with 5 or more basal branches)
  • L3 in East Africa (Sudan-Ethiopia-Eritrea) – Abbassia Pluvial?
  • Two ticks without major events
  • M in South Asia and into East Asia and Melanesia – beginning of Eurasian expansion. Huge demic explosion
  • M4″64 in South Asia.
  • Triple expansion (good climatic moment?)
    • N, probably in SE Asia (Burma?), with expansion Westwards
    • M30 in South Asia
    • L1b1a, maybe around Chad
  • R in South Asia SE Asia with expansions to West, North and South
  • P in Melanesia and B4’5 in SE/East Asia (updated)
  • Four expansions:
    • D4 in East/NE Asia
    • M5a in South Asia
    • HV in West Asia
    • L3e1 maybe at Sudan
  • D1 in Beringia?
  • Several expansions (7 haplogroups in 4/5 regions):
    • H and V in Europe. Huge demic explosion (Aurignacian?)
    • M1a and U2’3’4’7’8’9 in West Asia (two different centers possibly)
    • Z and A in NE Asia
    • L2a1 in East Africa probably
  • Two expansions (three haplogroups but two centers):
    • H1 and H3 in West Europe with eventual penetration into North Africa
    • X2, probably from the Levant, into Central Asia and eastwards (reaching to America eventually)
  • Six haplogroups in four regions:
    • C, D4a1 and A2 in NE Asia
    • R2a in West Asia
    • H2a in Europe
    • U6a in North Africa (Egypt?)
  • A tick without anything notable happening
  • Two expansions:
    • M7a1a in Japan (?)
    • J1c in West Asia
  • I and U5b3 in Europe probably
  • W in West Asia, B2 in America (updated).
  • D4h3a in America
  • Two ticks without major events
  • T2 and K2a in West Eurasia
  • Another idle tick
  • K1a1b and T2b in West Eurasia (Danubian Neolithic?)
  • No more stars till present
Color code: purple: L3(xM,N), red: M, blue: N(xR), green: R, black: others
Size code: largest type: giant stars, large type: medium and large stars, normal type: small stars.
Note on chronology:  My understanding of the molecular clock is that you must count from up-down, i.e. from older to younger node. This is different than most geneticists would do, what explains their failure in providing archaeologically reasonable dates, because they need to average the length of downstream branches, causing massive distortions. In my understanding, large haplogroups tend to remain stable as the dominant lineages generally ‘win’ the tug-of-war of genetic drift, so mutations tend to accumulate specially in smaller haplogroups, belonging originally to small isolated populations where drift would be more purely chaotic (similar odds for all existing lineages, as they were all similarly tiny). 
However I realize that this method ’causes’ a very early founder effect in America, maybe c. 45 Ka ago, much earlier than generally claimed. I don’t know yet how to explain this well but either is a founder effect limited to Beringia or it is the genetic indicator for the somewhat ghostly Paleo-Indians (maybe with an initial limited spread along the Pacific coast of North America?)
Noticeable patterns:
  • All secondary star-like (fast) expansions of R happen in West Eurasia except P (Melanesia). The same can be said of N, except for A (NE Asia).
  • All secondary star-like (fast) expansions of M happen in NE Asia, except the first ones, which happen in South Asia.
  • There are three or four moments of geographically diverse expansiveness that may be associated to good climatic conditions and may help to calibrate. These are:
    • The expansion of N, M30 and L1b1a, soon after the beginning of the Eurasian expansion
    • The expansion of D4, M5a, HV and L3e1, before the colonization of Europe (maybe in the early Mousterian Pluvial – c. 50 Ka ago?)
    • The expansion of H, V, M1a, U2’3’4’7’8’9, Z, A and L2a1 (maybe late Mousterian Pluvial, c. 45-40 Ka ago?)
    • The expansion of C, D4a1, A2, R2a, H2a and U6a (soon after, Gravettian era?) – it is more regionally-specific than the others, as there are no Tropical African lineages involved.
That’s all for now.

Mitochondrial DNA H1 in North Africa

A new paper on mtDNA H1 has been published, detailing its presence and phylogeny in Africa.
Claudio Ottoni et al., Mitochondrial Haplogroup H1 in North Africa: An Early Holocene Arrival from Iberia. PLoS ONE 2010. Open Access. [LINK]
They ratify that African H1 is, as its sisters, of ‘Iberian’ (SW European) derivation  (something known at least for Tunisia since last year, see Cherni 2009) . They also add some detail on its phylogeny and frequencies. 
Maybe most notable is the high frequency (but low diversity) of the lineage found among Libyan Tuaregs, telling of some sort of specific founder effect. 
Of some interest is the description of three novel sublineages:  H1v, H1w and H1x, all them almost exclusive of Lybian Tuaregs (see fig. 1). 

Fig. 2 Frequency of mtDNA H1

The authors make the leit motiv of this paper their molecular clock estimates, which they calculate between 3400 and 11,500 years ago for all H1. If anybody needed further evidence of why the molecular clock methods are unreliable this is it: the only way Europe could have got a meaningful genetic influence on North Africa (and we are talking here c. 25% of the maternal ancestry, not counting K nor V) in this period would have been the Megalithic phenomenon. However, if that would be the case, where is the Y-DNA?
The only comparable Y-DNA is R1b1b2a2, which does exist in North Africa (along with some fossil I found in Guanches), looks of European origin too, but is found at much smaller frequencies (and lower diversity) than in Europe. There are no possible inputs between Megalithism and present day, as we know that Roman and Islamic conquests had minimal demic impact (nor they look likely origins for the dominant Y-DNA E1b1b1).
Additionally there is reasonably clear evidence of the existance of mtDNA H (and in general similar frequencies as today) at Taforalt some 12,000 years ago (Kefi 2005), which argues for an older arrival, surely at the genesis of Oranian culture, in the LGM.
Only the Oranian time-frame really seems to explain the deep and extended penetration of Iberian DNA in North Africa.
R. Kéfi et al., Diversité mitochondriale de la population de Taforalt (12.000 ans bp – maroc): une approche génétique a l’étude du peuplement de l’afrique du nord. Anthropologie 2005. [PPT presentation direct download – Institut Pasteur]
L. Cherni et al., Post-last glacial maximum expansion from Iberia to North Africa revealed by fine characterization of mtDNA H haplogroup in Tunisia. American Journal of Physical Anthropology. Pay per view. [LINK]
H. Enafaa, V. M. Cabrera et al., Mitochondrial DNA haplogroup H structure in North Africa. BMC Genetics 2009. Open Access. [LINK]
For papers on H but not specifically related to Africa, see this post at Leherensuge (April 2009).

Cyprus Neolithic among the earliest ones

A Cornell University press release tell us of how the view of Cyprus Neolithic is changing as research advances.

“Up until two decades ago, nobody thought anybody had gone to Cyprus before about 8,000 years ago, and the island was treated as irrelevant to the development of the Neolithic in the Near East,” Manning said. “Then Alan Simmons (now at the University of Nevada, Las Vegas) discovered a couple of sites that seemed to suggest Epipaleolithic peoples went there maybe about 12,000 or 13,000 years ago, much earlier than anyone had thought possible. The big question started to become in the field, well, what happened in between?”

The new findings at Ayia Varvara Asprokremnos, in the central part of the island, place early Cypriot Neolithic c. 11,000 years ago (9000 BCE), totally in line with mainland Neolithic in West Asia: PPNA may be as old as 10,700 BCE, with more common occurrences after 9500 BCE. So the Neolithic of Cyprus seems to be one of the first offshoots of West Eurasian Neolithic.

… these dates mean that Cyprus, an island tens of miles off the Levantine coast, was involved in the very early Neolithic world, and thus long-distance sea travel and maritime communication must now be actively factored into discussions of how the Neolithic developed and spread.

Found via R&D, via Archaeology in Europe.

1 Comment

Posted by on October 21, 2010 in Cyprus, Neolithic, Prehistory, West Asia


Revisiting Bocquet-Appel 2005: the population of Europe in the Paleolithic.

Something I want to do in this new blog is to revisit some areas that I have explored in the past, hopefully with an improved approach. One of the key elements in understanding European Prehistory as a whole is the demographics of Paleolithic Europe.  Nothing better surely than this excellent survey of archaeological density and corresponding population estimates:
The paper evidences the demographic growth, specially after the Last Glacial Maximum (LGM), when it really explodes (from 5900 to 28,700 – average figures). 
But maybe even more interesting is the demographic tendencies of the various regions. Most outstandingly, the Franco-Cantabrian region comprises almost half of the all Europeans early on, reaching to 2/3 in the LGM.
Second is the Danube region, with 20-25% in the early period and a marked decrease in the LGM. Third is the related Rhine region with 6-9%, sharply declining to near zero in the LGM. 
These three regions are fused in the latest map (Late UP, Magdalenian), including together 95% of all Europeans some 15-10,000 years ago. These would be then something between 11,000 and 73,000 individuals, average: 29,000 (more than 27,000 in the Magdalenian area). 
Fig. 5 (2nd part). Population estimates for LGM (top) and Late UP (bottom)

Less important regions are East Europe (4% in the Gravettian era, declining after that) and Iberia (7% in the LGM, much less in the next period). Italy is not mentioned but does indeed show some sparse continuity (Gravettian/Epigravettian).
You can easily compare these maps and those of the patterns of R1b1b2a1a2; it seems clear to me that the best possible explanation for its subclades’ dispersion patterns is at the post-LGM stage.