October 30, 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.

October 29, 2010

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.

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.

October 28, 2010

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).

October 27, 2010

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.

October 26, 2010

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.

October 24, 2010

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.

October 23, 2010

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).

October 21, 2010

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.

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.

October 20, 2010

African ancestry of the Noir Marron of the Guianas

The Noir Marron are a population of African descent from Suriname and French Guiana. Their history is defined by their origins as slaves but also by their successful rebellion that allowed them to live freely most of the time in the Amazon jungle. They are one of the largest surviving maroon communities of America.

The people have 99% African ancestry by the maternally-inherited mitochondrial  DNA and more than 97% by the paternally inherited Y-DNA and retain high genetic diversity (unlike other maroon groups, such as those of Honduras). However there are gender-bias differences on the most common apparent origins in Africa.

While for both unilineages the main ancestry seems to be in the Eastern part of West Africa, between Ivory Coast and Nigeria, the patrilineages show a secondary strong preference for Westernmost Africa (around Senegal and Sierra Leone), while the matrilineages have a strong component from SW Africa instead. Their traditions have most in common with the Fanti-Ashanti ones of modern Ghana and surroundings.
mtDNA affinity (Fst)
Y-DNA affinity (Fst)

Maternal lineages (mtDNA, table 2) have the strongest ancestral pools in middle West Africa ('Gold Coast and the Bight of Benin'), 29%, and SW Africa, 26%. While other regions had some founder roles too, there are no shared lineages with North Africa, South Africa, East Africa nor Pygmies.

Paternal lineages (Y-DNA, table 3) show instead a strong preference for West Africa with 'Gold Coast and the Bight of Benin' at 28% and 'Windward Coast, Senegambia and Sierra Leone' at 25%. Again no Pygmy, North, East or South African lineages are detected.

More Neanderthal controversies

A couple of important Neanderthal-related news found at Archaeology in Europe:

The big teeth of Neanderthal toddlers

At 18 months, Neanderthal children already had big teeth, larger than those of modern humans. The new finding of a lower jaw, at a Belgian cave, by Isabelle Crevecoeur, belongs to the youngest Neanderthal specimen ever found and already possessed Neanderthal traits, such as a strong jaw and big teeth. 

While the kid had thinner enamel than would be found in modern humans of similar age, it already shows a clear early growth spurt in comparison to our species, starting this development maybe as early as 12 months old.

The research is scheduled to appear in the Journal of Human Evolution and has already the blessings of famous Neanderthalist Erik Trinkaus, who thinks that the conclusions are well-reasoned and reasonable.

Sources: Discovery News (via AiE), Yahoo News.

Were the ornaments of Grotte du Renne made by Neanderthals?

Ornaments from Grotte du Renne
According to Randall White the layers are so mixed and convoluted that it is impossible to say. However João Zilhão argues that White's evidence says exactly the opposite. Zilhão has in the past also clashed with other researchers on stratigraphic issues related to Chatelperronian, Neanderthals and the MP-UP transition in SW Europe.

Critically the earliest research of this cave, by Leroi-Gourham, found many Neanderthal teeth in the Chatelperronian layer, that is arguably intermediate between Mousterian and Aurignacian. However recently there has been some questioning of the attribution to Neanderthals of the Chatelperronian industry.

The case is that dates obtained from Chatelperronian materials range from 49,000 to c. 21,000 years ago, when Neanderthals are already thought to have been completely extinct for some 10 millennia (longer locally).

If this interpretation of White is correct and Chatelperronian effectively happens to be an industry of Homo sapiens, then it would be a lot easier, specially with such late dates as 21,000 BP, to trace the origins of Gravettian industry, whose closest relative is no doubt Chatelperronian (both were originally described as Perigordian and only lack of direct evidence for continuity broke down that category in two eventually).

Zilhão's counter-argumentation seems to go along the lines of most dates at Grotte du Renne being consistent with known Neanderthal presence (i.e. in the oldest range). I would say that, if the oldest date is just 49,000 BP, this fits completely well in the model that argues that all UP technologies in Europe, including Chatelperronian possibly, are the work of our species, because these technologies only appear since c. 49-48,000 calBP and more strongly since c. 44,000 calBP.

Source: Science (free article).

Oldest European door found in Switzerland

The door is dated, using dendrochronology, to c. 3063 BCE, more than five thousand years ago, in the Chalcolithic (or late Neolithic) era. It has been found in an emergency dig in Zurich city and is not the only one of its kind: it has a close relative from nearby Pfaeffikon and yet another one, this one made of a single plank, may be as old as c. 3700 BCE.

This door is made of several poplar planks and archaeologists find remarkable the method for keeping them together in a single unit. It has well preserved hinges.

The finding is part of a context of five newly-found lake-dwelling Neolithic villages. As always we are surprised by the persistence of the old ways of doing things, as doors much like this one can still be found in veteran rural homes.

Evidence of flour production in Gravettian Europe.

Mundo Neandertal[es] informs us today that of the discovery of evidence of food processing, specifically grain and rhizome milling, by Paleolithic Europeans some 30,000 years ago.

The three sites where this activity has been documented are Billancino in Italy (1), Pavlov-VI in the Czech Republic (2) and Kostenki-16 (Uglyanka) in Russia (3). They belong to the Gravettian and Gorodtsovian cultures (Gorodtsovian is the most "modern" culture at Kostenki, the one with needles, see here and here).

This is not at all the oldest evidence of food processing or milling anyhow, the record corresponds to a Mozambican sites of the Middle Stone Age, some 105,000 years ago. Still it illustrates by means of factual evidence that Paleolithic Europeans already used technologies that would allow them to have some short-term reserves and easy to transport high caloric food such as breads.

Ref. Anna Revedin et al.,  Thirty thousand-year-old evidence of plant food processing. PNAS 2010. Pay per view (depending of where you are and when you try to access - supp. materials freely available).

October 18, 2010

On the high mobility of mtDNA macro-haplogroups in Eurasia

This review of Eurasian mtDNA is triggered by some rather interesting debate in this other thread. Not really unexpectedly, the structure of the scatter of mtDNA N is being questioned by an habitual reader, who seems to prefer (without any evidence I know of) a "northern route" for the migration of this haplogroup. 

Here I just visually depict the main patterns of earliest scatter of the three pan-Eurasian mtDNA macro-haplogroups: M and N, both directly derived from African L3, and R, derived from N.For that I use exclusively those basal sublineages of these three macro-haplogroups which are one control region (CR) mutation downstream of the main node. Why? For simplicity and because these sublineages are the ones that show, most likely, the earliest sub-expansions of each of the three macro-haplogroups. 

Also, if you look at the other sub-lineages, you do not see strong deviations from the general pattern described here and, when that happens, it can and must be attributed to peculiar histories at the stem of those sub-haplogroups. This is for instance case of mtDNA A, a basal sub-lineage of N, which expanded in NE Asia but that shows a rather long stem with 6 CR mutations, indicating a lengthy "invisible" history of its own between the N expansion and that of A.

However I must emphasize that, in spite of the similitude in their spread patterns it is rather likely that the three patterns of diffusion were not simultaneous. At least seen from the viewpoint of the shared ancestral L3 node (East Africa), M is only detached by 3 CR mutations, while N counts 5 and R 6 (the five of N plus one of its own). This is at least suggestive of successive rather than strictly simultaneous process but we cannot totally exclude that the three expansions were more or less simultaneous (or separated only by short periods) because the so-called "molecular clock" is not actually bound to tick with strict regularity but actually has some strong uncertainty.

For the source of the information used to build these maps (ultimately from the reference mtDNA site: PhyloTree), see Leherensuge: Reconstruction of mtDNA spread in Eurasia (again), which shows also a possible time structured sequence based on a hypothetical strict ticking of the "molecular clock" and also those haplogroups derived from M, N and R at longer CR mutation counts (presumably later in time).

What I find most interesting in these three maps is the similitude of the main pattern for all three macro-lineages from NW South Asia to New Guinea, via SE Asia. 

The differences are as follows:
  • M shows a clear distinct early trend northwards along the East Asian coast, which probably also carried the ancestors of mtDNA A. 
  • Instead R shows an early trend westwards, which is probably quite more recent than the M expansion, and does include, once you look at more derived sub-lineages (not shown here), three other N subclades (N1, X and W), two other R subclades (U and JT, the one shown is R0), and at least one M subclade (M1). The fact that all these Western lineages are rather derived, also suggests a later time-frame for the expansion of R, some time (10-20,000 years?) after that of M.
It is interesting also that N(xR) shows no scatter peculiarity of its own, in spite of having left a notable legacy.  It is also interesting to see that all three macro-haplogroups left an early mark in Melanesia, what suggests that they did indeed have some decent boating skills from early on, and is indeed supportive of the "rapid coastal migration" hypothesis, regardless of whether this model is not needed to explain some other aspects of the Eurasian spread.

October 17, 2010

A little homage to Benoît Mandelbrot

Benoît Mandelbrot was one of the great geniuses of our era, comparable to Einstein, Hawkins, Maldacena and very few others. He died on October 14 at the venerable age of 85.

Of Jewish ethnicity, born in Poland, raised in France, living in France, Switzerland and the USA, he stands as a universal genius by all standards.

He like no other helped us to discover the beauty and importance of Chaos mathematics and its physical implications. He is best known for defining the concept of fractals, a pillar of Chaos theory.

His best known quote, which is a beautiful synthesis of poetry and deep intellectual provocation is this one:

Clouds are not spheres, mountains are not cones, coastlines are not circles, and bark is not smooth, nor does lightning travel in a straight line.

A quote I just love.

In spite of his unique greatness he never received the Nobel Prize, what says nothing good about this media-hyped Scandinavian honor. He did receive many other prizes and honors in his life however, all well deserved.

To the left, photo of the deceased genius (2007, from Wikipedia) and some magnifications of the famous Mandelbrot set, arbitrarily chosen for their beauty (M=10⁻¹, M=10⁶ and M=10⁹). All from The Chaos Hypertextbook.

October 14, 2010

Some population structured SNPs and also one epigenetic factor

Another more complex, yet still interesting, paper related with population structure in this last issue of PLoS ONE is:

Jingyu Liu et al., Identification of Genetic and Epigenetic Marks Involved in Population Structure. PLoS ONE 2010. Open Access

They have detected some SNPs, mostly related to appearance, that seem to weight specially high in population structure at global levels. Interestingly they have also located an epigenetic marker that weights somewhat in the European+African vs. East Asian+Native American axis.

The most relevant population structure SNPs are by this order:
  1. Rs16891982, strongly related to the West Eurasian type of depigmentation (SLC45A2), and logically structured along the West Eurasian-Others axis in an almost true/false type of structure, excepting admixed populations.
  2. Rs535878, not yet reported at SNPedia. It is structured along the Native American vs. African American+East Asian axis, with West Eurasians and admixed populations being intermediate (but closer to Native Americans). So Native Americans (and West Eurasians to some extent) seem to have the derived allele.
  3. Rs13013484, again not reported in SNPedia yet. The structure runs between African Americans and East Asians. With other populations being intermediate (but except Latinos all closer to African Americans). So East Asians (specially) have the derived allele. However notice that the East Asian sample of just one individual is somewhat inconclusive.
There are more SNPs pondered (see table 1) with factor ranking 22nd being 48 methylation sites in 44 genes of 18 chromosomes, affecting specially West Eurasians and Native Americans in opposite senses. In particular the PM20D1 methylated site seems to have some weak but significant selective pressure among West Eurasians (and admixed populations) - see fig.2B.

    Costa Rican genetics

    I was thinking to title this post El Día de la Raza (The Day of the Race), as Oct 12 is still called in some countries, but it'd need too give many explanations that I will deliver anyhow but in the article's body. The word race here has nothing to do with people, animals or cars running competitively but with ethnography: stock. However it is a very Latin understanding of the concept of race as ethno-linguistic and not truly biological reality, so it makes total sense... if you are from a Latin culture.

    After all, what the Germanics (wrongly) think as races are nothing but residual peripheral popuations of the only true mestizo human (and Spanish-speaking) race... or something like that. A good example, as good as any other, I guess, are Costa Ricans.

    As usual in this type of papers, they estimate the tricontinental admixture in Costa Ricans of Guanacaste Province (NW Costa Rica, bordering Nicaragua).

    The results show that this Central American population can well be described on average as 43% European, 42% Native American (38% NA+ 4% East Asian components) and 15% African by ancestry. Individual apportions and even local averages may vary somewhat but that is about it:

    Eigenvector analysis with some localities (fig. 6)

    None of the individuals sampled clusters too tightly with either reference "purebreed" HapMap samples. However in the Structure analysis (below) you can see maybe more clearly that a few (not too many anyhow) do not seem to have any African ancestry and that individual admixture ratios vary somewhat, of course.

    STRUCTURE analysis (k=4)

    Somewhat anecdotally they talk about a subpopulation that would be closer to genuine Europeans (60%) but I don't think the case is very clear, just tendencies within a continuum. The perfect cladistic scenario in fact.

    October 13, 2010

    Danubian Neolithic ancient mtDNA N1a is (mostly) European by origin

    This is a very important paper without doubt for two reasons:
    1. It further develops the phylogeny, distribution and molecular clock age estimates of mitochondrial haplogroup N1a, with possible side implications of its "niece" I, and N1 as a whole.
    2. It dismisses the idea that the N1a lineages found among Central European early Neolithic people (Western Linear Pottery culture, alias Danubian Neolithic) are, with some possible exceptions, of West Asian origin. Instead they appear as Eastern, Southern or local Central European lineages.


    In 2005 an ancient mtDNA research by Haak et al. on Central European farmers found six individuals with the N1a haplogroup, a very rare clade nowadays in Europe but somewhat more common in West Asia, specially in Arabia Peninsula. Four (4/11) of the six N1a individuals belonged to the oversampled Elbe group of East Germany (a rather peripheral offshoot within Danubian Neolithic context), however another one was found in the Rhine area (1/10) and yet another one in Hungary (1/1), where it has also been detected in later periods (Middle Ages).

    Another individual with a N1a lineage was recently found in a Megalithic burial in West France.

    This appeared to favor the idea that Central European early farmers were at least partly of West Asian origin, specially when contrasted with diverse hunter-gatherer groups, where haplogroup U (U*, U5 and U4) was clearly dominant.


    The current research has unveiled several subhaplogroups within N1a and traced their possible origins, which are in several parts of Europe. These includes four of the six Danubian N1a individuals from Haak 2005. The other two belong to still undefined N1a* which does indeed have greatest diversity in West Asia, specifically in Arabia Peninsula but is also somewhat common in Mediterranean Europe (Greece, Italy) as well as in the Eastern part of the continent.

    The evidence from phylogeographic analysis of N1a lineages emphasizes that European farmer N1a lineages might have been originated from different sources- from eastern Europe (for N1a1a1), from Near East via southern Europe (for N1a1b and perhaps for N1a1a3), and from local central European source (for N1a1a2). It is thus clear that Neolithic farmers’ migration into central Europe did not occur in a uniform way; indeed these results indicate that the Neolithic transition process was more complex in central Europe and possibly the farmer N1a lineages were brought in through the ‘leapfrog’ colonization process.

    Detail from fig.1: new phylogeny of N1a.

    The authors say that we suppose that the farmer lineages-DEB3, FLO1, and HAL2 might be derived from local communities and that they would have adopted the farming culture indigenously.

    They estimate that N1a coalesced some 19,600 to 23,500 years ago in West Asia. Its subclades N1a1 and N1a1a1 may have formed between 6,800 and 10,700 years ago, already in Europe, while N1a1a2 may have coalesced in a later date: 3,400-4,000 years ago, making it a good candidate for a Neolithic-specific expansion.

    Notice that I do not endorse these age estimates or any other, just mentioning them for the record - however I did arrive once to a similar estimate for N1a: 25,000 years ago. N1 was detected in an individual of Gravettian culture at Paglicci Cave in Italy.

    Related older posts from Leherensuge (my old blog):

    October 12, 2010

    Bronze Age culture discovered in the North Caucasus

    The Telegraph reports (via AiE) that a previously unknown Bronze Age civilization has been discovered in the North Caucasus, after locating some 200 sites via air photography from the Soviet era. 

    The Russo-German archaeological team found the sites all following a similar architectural plan, centered around an oval courtyard, and connected by roads. In some cases the foundations of the buildings retain up to a meter of their original height. 

    The decorations and artifact styles are clearly related to the Kuban culture (axe at the left, from the Hermitage Museum), but this one is older by some 500 years, lasting from the 16th to the 13th century BCE. The sites are located rather high on the mountains, between 1400 and 2400 meters above sea level.

    Approximate location of the findings
    The sites stretch from the Kuban river to the west to the city of Nalchik by the East, in the autonomous republics of Karachay-Cherkessia and Kabardino-Balkaria. While Russian and Turkic languages are now spoken in the area also, a natural thought is to imagine the inhabitants of these settlements speaking NW Caucasian languages.

    One detail I notice in the Wikipedia reference is that so far it was believed that the Kuban culture was derived from the, slightly older Colchian culture of Abkhazia and West Georgia, however this discovery would suggest that the opposite is true instead. This in turn may provide a frame for the migration of NW Caucasian towards the South (but notice the possible affinity with extinct Hattic), or alternatively for the arrival of Kartvelian languages maybe. It looks too recent anyhow to be related to the expansion of the Indoeuropean Hittites, which are known to have been in Anatolia since at least the 18th century BCE. This matter is admittedly complicated and surely warrants further debate in any case.

    Update (Oct 13): Jean points me to this other small article at the Kyiv Post, which includes several images of the sites and the air photos that allowed their localization:

    The phrasing of the relationship with the Kuban culture is significantly different (merging instead of precursor) and also the description of the area (eastern limit is said to be Kislovodsk instead of Nalchik), but I'd say that the Telegraph article seems better informed, even if it lacks images.

    October 11, 2010

    Stupid British law hinders the work of archaeologists

    A decision to implement the obsolete Burial Act of 1857 to the context of archaeological research, taken in 2008 by the previous government, is causing upheaval among British archaeologists.

    The law establishes that all digs of burial grounds be screened from the view of the public and worse: that all remains must be reburied within two years. 

    Scientists are not happy with either measure. Screening from the public view hinders the openness and public access that most of them want for their work (and may get the public suspicious) but the obligation to rebury in a cemetery archaeological remnants that could well be producing results many years, or even decades after their discovery is plainly idiotic.

    Full story at The Guardian. Originally found at Archaeology in Europe.

    October 9, 2010

    Important Tamil Nadu Paleolithic site discovered

    From Times of India (via Archaeo News).

    Archaeologists S. Rama Krishna Pisipaty and S. Shanmugavelu have researched what may be a key site in a dry lake bed at Singadivakkam, a village some 65 km south of Chennai (Madras). The site is known as Kancheepuram.

    The site has so far provided some 200 tools and, crucially, it seems to have no disruption from the Lower Paleolithic (thought to be work of H. erectus) and the Middle Paleolithic (maybe work of H. sapiens), unlike all other sites in the subcontinent. The tools found include hand axes, borers, scrappers, choppers and pointed tools, as well as microliths.

    Kancheepuram was ideal for early settlers with its large number of safe water bodies a lifeline for any human settlement, said Pisipaty.

    Epipaleolithic fish traps from Wales and Ireland

    A couple of news items again mentioned by Archaeo News:

    Archaeologist Andrew Petersen is exploring willow walls under the sea at Wales. The researcher, who recently uncovered a whole medieval town under coastal sands in Qatar, is now turning his attention to what he believes are fish traps created by Epipaleolithic 'Welsh' fisherpeople at its coasts. (Source: Wales Online)

    Gibbons at a cochill trap
    In a parallel development, another archaeologist, Michael Gibbons, is researching now fish-catching stone structures in Ireland, which apparently also date to the Epipaleolithic but, oddly enough, are still made and used by some modern coastal fishermen. They use these artificial coastal ponds to catch a fish called marine or mearachán, which seems to be a type of smelt. The traps are known as cochill and their design has been transmitted through generations till present day. (Source: Irish Times).

    Exceptionally preserved early Bronze Age burial near Perth (Scotland)

    Another Archaeo News' link, this time to The Courier.

    An exceptionally preserved burial just south of Perth, Scotland, has been dug by archaeologists. The excellent sealing of the tomb made possible that some organic materials have arrived to us, including a leather bag, unidentified wooden objects and plant matter. The tomb also had a bronze dagger with a golden hilt and the capstone is engraved in the inside, suggesting it was the resting place of some princely individual.

    The site of Forteviot seems to have been a most important ceremonial and burial place up to the Pictish period, suggestive of pre-Indoeuropean roots for this mysterious northern people. This particular tomb was discovered in 2008 but they could not investigate it until they organized the resources to lift the capstone, what has been done only this year.

    It is estimated that the burial dates from some 4000 years ago, at the very beginnings of the Bronze Age.

    The researchers also investigated part of a massive timber enclosure which was made up of some 200 huge timber posts.

    Neolithic findings in Sumatra and West Papua

    A brief note from the Jakarta Globe (via Stone Pages' Arhaeo News), detailing some Neolithic findings in Aceh, Norther Sumatra:

    Takengon, Aceh. Two archeologists from Medan have found evidence that a village in Central Aceh district had been inhabited by prehistoric humans.

    Ketut Wiradnyana and Lucas Partanda Koestoro announced on Sunday that they had found artifacts such as a a square stone axe, a niche, pottery pieces and a human skeleton inside a cave near Danau Laut Tawar, a lake in Kampung Mendale.

    “One of our latest discoveries is a human skeleton which we found in the Ujung Karang Kebayakan area, another excavation site near Kampung Mendale,” Ketut said.

    The skeleton’s exact age has yet to be confirmed, since the excavation is still ongoing.

    Ketut said the artifacts would have to undergo a carbon dating test at the National Atomic Energy Agency (Batan).

    Last May, residents of Jayapura district in Papua Province found prehistoric relics at two different locations.

    Hari Suroto, head of a research team from the Archeological Institute, said locals who were digging at Kalkote, a small village in East Sentani district, came across pottery pieces now believed to date back to 1500 BC, or during the Neolithic Age.

    The team also established that the same type of pottery was found in Vanimo, Papua New Guinea, in 1996.

    Hari said Lapita pottery was previously discovered in many places in the Pacific region and the Bismarck Islands.

    Residents of Kwadare village in Waibu district also found a bronze axe, which the archeological team said was made in 300 BC and originally came from Dong Son, North Vietnam.

    The axe was kept by the village chieftain instead of being entrusted to the Archaeological Institute.

    Hari said axe-making was introduced to Papua’s northern coastal regions by the Austronesian people.

    October 6, 2010

    Some key archaeological papers on the 'coastal route'

    Notice that I use the term 'coastal route' senso lato, meaning a migratory route in Asia (from ultimately Africa) via Arabia and South Asia, rather than Central Asia and Siberia. How strictly 'coastal' this migration was is subject to debate but the evidence is strong and growing in favor of the tropical route in any case.

    The links were provided to me by a reader (carpetanuiq) in the comments section of this previous post. They are all very valuable but specially the three I want to introduce here. All links are PDF.

    Analysis of lesser cost routes into South Asia and through it

    Fields et al., The southern dispersal hypothesis and the South Asian archaeological record: Examination of dispersal routes through GIS analysis. Journal of Anthropological Archaeology 2007. [LINK]


    This research advances a model for coastal-based dispersals into South Asia during oxygen isotope stage (OIS) 4. A series of GIS-based analyses are included that assess the potential for expansions into the interior of South Asia, and these results are compared with known archaeological signatures from that time period. The results suggest that modern Homo sapiens could have traversed both the interior and coastlines using a number of routes, and colonized South Asia relatively rapidly. Use of these routes also implies a scenario in which modern H. sapiens, by either increased population growth or competitive ability, may have replaced indigenous South Asian hominin populations.

    Key maps from this paper (there are some others also interesting):

    Cut from fig.2 Location of linear origin and the results of the least-cost route analysis into South Asia. Least-cost route is indicated by the grey [black] line.

    Fig. 3 Results of the wandering path analyses into and through South Asia. Least-cost routes are indicated by the grey [black] lines.

    The Red Sea in the Pleistocene

    Geoff Bailey, The Red Sea, Coastal Landscapes, and Hominin Dispersals. Published within M. Petraglia & J. Rose (eds.). The Evolution of Human Populations in Arabia (2009). [LINK]

    (No abstract)

    Key maps in this paper are:

    Fig. 1 showing among other things 'a simplified
    distribution of Lower and Middle Paleolithic archaeological sites in the Arabian Peninsula'.

    Fig. 5 reconstructed shoreline of Bab-el-Mandeb at different Late UP dates (cal BP)

    The Persian Gulf "oasis"



    The emerging picture of prehistoric Arabia suggests that early modern humans were able to survive hyperarid climatic conditions that periodically caused widespread landscape desiccation by contracting into environmental refugia around the coastal margins of the peninsula. This paper reviews new archaeological and palaeoenvironmental evidence from the richest of such zones in eastern Arabia: the “Persian Gulf Oasis.” These data are used to assess the role of this ancient alluvial plain, which, prior to being submerged beneath the waters of the Indian Ocean, was well-watered by the Tigris, Euphrates, Karun and Wadi Batin Rivers as well as subterranean aquifers flowing beneath the Arabian subcontinent. Inverse to the amount of annual precipitation falling across the interior of Arabia, reduced sea levels periodically exposed large portions of the Persian Gulf, equal at times to the size of Great Britain. Therefore, when the hinterland was desiccated, populations could have contracted into the Gulf Oasis and exploited the freshwater springs. This relationship between environmental amelioration/desiccation and marine transgression/regression is thought to have driven demographic exchange into and out of this zone over the course of the Upper Pleistocene and Early Holocene, as well as having played an important role in shaping the cultural evolution of local human populations during that interval.

    Key maps are:

    Fig. 2 Map of ancient drainage systems in Arabia showing the Ur-Schatt River Valley as
    the primary recipient of runoff within the regional catchment zone. Numbers indicate
    known MP/UP sites in eastern Arabia and southern Iran.

    Cutoff from fig. 5 (Palaeo-shoreline configuration, drainage systems and archaeological sites around the Persian Gulf basin during the Upper Pleistocene and Early Holocene). Shown 74-24 Ka map only. Dots are archaeological sites.

    Other relevant links mentioned in that discussion are:

    • Gahnim Wahida et al., A Middle Paleolithic Assemblage from Jebel Barakah,
      Coastal Abu Dhabi Emirate
      . (Chapter in M.D. Petraglia and J.I. Rose (eds.), The Evolution of Human Populations in Arabia, Vertebrate Paleobiology and Paleoanthropology). [LINK]
    • Marta Mirazón Lahr et al., Project: 'Searching for traces of the Southern Dispersal'. General description of the archaeological research project0 by the 'Petraglia team'. [LINK]
    • Ancient Indian Ocean Corridors. Blog of the same team, inaugurated this spring. [LINK]
    • Synopsis of Paleo India (2007). James B. Harrod. [LINK]