Monthly Archives: June 2011

Coconut scatter shows that, once established, a population structure is hard to alter

You may have heard of this by now:
I was a bit perplex at first because what I have read around is that this paper somehow demonstrates that coconuts only spread with human domestication and colonizing flows. This is a most extreme claim which hardly fits the nature of this plant, which is not truly a domesticate but a widely exploited wild plant in fact. It is a very hardy plant that grows primarily at the high tide line and is naturally transported across the oceans by mere drift.
Fig. 2 has the essence of the paper
It is evident from this paper that coconuts have at least two distinct ancestral populations: one seemingly originated in South Asia and the other from SE Asia/Pacific, that its dispersal to the Atlantic Ocean happened necessarily with human help and that the East African population while essentially the Indian variety, has some admixture from the SE Asian/Pacific variants.

Coconut germinating on Black Sand Beach, Island of Hawaii
Coconut germinating at a volcanic beach
This last element is argued by the authors to signify human influence by means of the Austronesian colonists of Madagascar. While this is plausible I see no definitive argument for this logic in fact. Similarly I fail to see the hand of Austronesians in the Pacific  scatter as something cast on iron, rather as just a possibility. 
The only clear case of human intervention are the Dwarf variants because they are self-pollinating and this is not a trait you typically find in wild plants. But the Dwarf component is relatively rare and is not even present in the alleged Austronesian-mediated arrivals to East Africa and South America (Panama variant). 
So I am not really persuaded of their thesis that most of this structure was caused by humans. It is possible but very far from demonstrated in fact. 
Regardless, what eventually brought me to write this entry was after all their other discovery, which is quite solid and obvious: that in spite of the palm being so widely exploited and moved around in the Modern Era, the original genetic structure has persisted almost unaffected. 
This is quite astonishing because copra (dried coconut flesh) and palm oil, as well as the fibre and the fresh fruit, so suitable as natural preserve for the long travels of sailors of not so long ago, make the coconut a clear candidate for extensive alteration of its ancestral genetic landscape, yet it has resisted all that almost impassible in all its range from Africa to South America. 
A lesson to be assimilated by all those who happily proclaim that established populations can easily be altered. It can happen indeed but it is not easy.

Earliest art of America may be mammoth engraving in Florida

[Updated Jun 23]
Science Daily reports of the finding of a bone with a mammoth engraving. It is believed to have an age of c. 13,000 BP because that is the approximate date of extinction of these animals in North America according to the fossil record. The unusual finding was recovered from Vero Beach, Florida:

Barbara Purdy et al., Earliest Art in the Americas: Incised Image of a Proboscidean on a Mineralized Extinct Animal Bone from Vero Beach, Florida. Journal of Archaeological Science, 2011. Pay per view.

[DOI is broken so link above is direct]


A fragmented fossil bone incised with the figure of a proboscidean was recently found at Vero Beach, Florida near the location where Late Pleistocene fauna and human bones were recovered from 1913–1916. This engraving may represent the oldest and only existing example of Terminal Pleistocene art depicting a proboscidean in the Americas. Because of the uniqueness, rarity, and potential antiquity of this specimen, caution demanded that a variety of tests be used in anattempt to verify its authenticity. The mineralized bone was identified as mammoth, mastodon, or giant sloth. Rare earth element analysis was consistent with the fossil bone being ancient and originating at or near the Old Vero site (8-IR-9). Forensic analysis suggests the markings on the bone are not recent. Optical microscopy results show no discontinuity in coloration between the carved grooves and the surrounding material indicating that both surfaces aged simultaneously. Scanning electron microscopy (SEM) revealed that the edges of the inscription are worn and show no signs of being incised recently or that the grooves were made with metal tools.In addition, the backscattered SEM images suggest there is no discontinuity in the distribution of light and heavy elements between the scribed region and the surrounding bone indicating that both surfaces aged in the same environment. This is very different from an intentional mark made on the bone for comparison. Energy dispersive x-ray spectroscopy (EDXS) shows that the surface contains significant amounts of calcium, phosphorus, oxygen, and carbon typical of a mineralized bone surface. Examination of a cast and mold of the incised bone by Reflectance Transformation Imaging (RTI) also provided no evidence that the engraving was made recently. All of these results are consistent with the mammoth engraving being authentic.

I also found an available PDF (not sure how long it will stay open).

The bone itself may be one of a mammoth, though being mineralized (true fossil) we can’t expect to get DNA nor C-14 dates:

It definitely derived from a much larger land mammal than any known to have been alive in Florida during the Precolumbian Holocene interval (e.g., bear, bison, deer), and the great thickness of the cortical bone precludes a cetacean origin. Because the bone is mineralized, it is improbable that it can be identified by DNA analysis or dated by 14C. This is usually the case for Late Pleistocene fossils from Florida (e.g., Hulbert et al. 2009).

Basque-specific mtDNA lineages

Forewarning: the maps illustrating this entry are from the discussed paper BUT they seem to fail to adequately capture the actual frequencies of the discussed clades in some areas, notably the Atlantic Islands. 

A reader points me to this paper (in Spanish with introduction in Basque):

Starting from a rather unoriginal sample (four Basque provincial samples plus Cantabrians from nearby Valle del Pas) they make some noticeable discoveries on less common mtDNA lineages. First of all they find that haplogroups U5b and J1c have their highest densities among Basques (>10%):

Regarding U5b, a particular sublineage U5b1f is mentioned as being notably frequent among Basques and also found in other sub-Pyrenean populations (Crespillo et al. 2000; Martínez-Jarreta et al. 2000; Alfonso-Sánchez et al. 2008).

The highest apportion of U5b worldwide is in Northern Navarre (15.5%).

In the case of J1c, it is mentioned in the text that a sublineage J1c2d, defined by a transition in site 16366, is common among Basques and that this particular lineage has also been found in some other populations, specifically the Irish (McEvoy et al. 2004). 
Besides these two, the most common mtDNA lineages among Basques are H1, H3 and V. Among these, this paper finds that sublineages H1j1 and V10 are notably common in the country.
Overall and based in an array of older papers, the authors feel that they must support the post-LGM recolonization theory, which would have originated from a Franco-Cantabrian refuge. However they argue that U5b1b, which has been claimed to be of similar origin for being found in remote populations such as the Berbers or Saami (Achilli et al. 2005) has not been found in their survey of (a fraction) of the Franco-Cantabrian refuge. Here I must say that while the datum is surely valid, the argument is somewhat weak however because they have not sampled all the Franco-Cantabrian refuge but just a small fraction: 2/3 of what is now France remain largely unresearched.

[Update: in the comments section, Heraus, who has deep Bearnois roots, confirms my hypothesis: U5b1b may not be found among Basques but it’s found for sure among Gascons. Himself is this particular lineage].

This is something that I cannot emphasize too much: in order to understand properly European genetic correlations France, specially the southern half, must be studied properly, because the Basque Country is only a small subregion of that Franco-Cantabrian refuge and the rest of the Iberian Peninsula is not even part of it (excepted Cantabria and Asturias) but a different, less important, archaeological province.

Franco-Cantabrian province: dots indicate rock art sites, white areas are glaciers, light green is land now submerged

Update: check the supplemental material of a previous paper by the same author. I understand from this paper’s text that the samples studied are the same ones.

Update (June 22):

U5b frequencies by Argiedude (synthesis of many diverse papers):

Click to enlarge. Figures in percentile points.

See the discussion for details. Importantly he argues that he is working in a diversity map but that preliminary data appears to show that U5b in SW Europe is more diverse than in Fenno-Scandia (I’d be surprised if it’d be the other way around, honestly, because this region was covered in ice until some 10,000 year ago).

Update (June 29): Argiedude has also worked out this map of U5b diversity (see comments):

Not sure what conclusions may be reached, if any.


Did agriculture worsen life conditions?

This is the thesis proposed by Amanda Mummert and colleagues: that Neolithic was not so good, or rather that it had at least very poor trade-offs. We tend to think having regular sources of food as something good but when that means eating mostly one or two vegetable foods all year long it may well be a problem.
Whatever the reason what Mummert discovered is that the health and size of Europeans  suffered with the introduction of farming. 
Source: Science Daily
Incidentally a couple of days ago, I stumbled upon the Wikipedia page on life expectancy and I noticed that same pattern in the list of documented life expectancy variation over time: the record before the Middle Ages was in the Paleolithic period, when newborns could expect to live 33 years. Then, with Neolithic, it fell to a mere 20 years, recovering only very slowly.

Posted by on June 18, 2011 in health, Neolithic, Prehistory, Upper Paleolithic


Ritual cannibalism among early Crimean Homo sapiens

Stratigraphic sequence of Buran Kaya III
New research about the earliest documented Homo sapiens of Crimea:
The paper deals mainly with the cave of Buran-Kaya III in the wider context of the Crimean transition from Middle to Upper Paleolithic.
Importantly the remains of several anatomically modern humans were found, mostly skulls and mandibles, which showed signs of cannibalism. The fact that these remains were treated differently from saigas (an antelope, food) clearly indicates that we are before ritual cannibalism and not dietary one. These bones have produced dates of c. 32,000 BP (almost 36,000 years ago after calibration).
Besides the issue of ritual cannibalism, the site shows a peculiar sequence with a Micoquian layer placed between a Szeletian and an Aurignacian one. While Szeletian (similar to Chatelperronian) is considered an Upper Paleolithic industry, the Micoquian with its heavy hand axes is thought of as a Middle Paleolithic one, reason why archaeologists raise their eyebrows when finding it above (after) a Szeletian layer. 
However I must say here that both cultures would probably be attributed to Neanderthals by most experts, while this would not be the case with the Aurignacian which sits on top of them. 
After the Aurignacian layer we arrive to the Gravettian one, which is the context in which the remains of seemingly cannibalized Homo sapiens were found. This layer has also produced personal ornaments made of mammoth ivory. 
Overall Buran-Kaya III has produced some 23,000 artifacts.

Homo sapiens child’s remains found in Morocco (108 Ka BP)

Artistic recreation of Bouchra (right)
The quite complete remnants of a child of our species, Homo sapiens, have been found in the site known as Smugglers’ Cave (Dar es Soltan, Morocco) in Aterian context. The child has been nicknamed Bouchra, meaning Good News in Arabic.
No paper or image of the infant’s skeleton are known, as the research is financed by the sensationalist media National Geographic, which aims to keep the exclusive. 
There are several older known members of our species in Africa (from Mozambique to Morocco) and Palestine but this one seems to be the first one dead at such a young age: approximately 8 years old. The remains have been dated to c. 108 Ka ago.

Sources:[en] and Mundo Neandertal[es].


Strong introgression of non-Sapiens antigens in ‘Eurasian’ modern humans (but not in Africa)

HLA-A11: the legacy of H. erectus in ourselves
Please read the updates below because some of the claims may not be sustainable (however others are plausible).

Prof. Peter Parham (Stanford University, USA) has found that some of the most common immunologic alleles among non-African modern humans have been adopted from other species of Homo living in Eurasia upon the migration out of Africa. 

This would be a typical case of introgression, a process in which, by means of lesser admixture highly adaptive alleles from another population are adopted. The logic here is that Neanderthals and other Eurasian hominins would be much better adapted to Eurasian-specific diseases, while our species would initially be  adapted to African-specific diseases instead. 
According to New Scientist:
One allele, HLA-C*0702, is common in modern Europeans and Asians but never seen in Africans; Parham found it in the Neanderthal genome, suggesting it made its way into H. sapiens of non-African descent through interbreeding. HLA-A*11 had a similar story: it is mostly found in Asians and never in Africans, and Parham found it in the Denisovan genome, again suggesting its source was interbreeding outside of Africa.


Half of European HLA-A alleles come from other hominins, says Parham, and that figure rises to 72 per cent for people in China, and over 90 per cent for those in Papua New Guinea.

The dominance of Denisovan alleles in Eastern Eurasia is coincident with my theory of these Denisovan specimens being hybrids of H. erectus and Neanderthals and acting actually as a proxy for H. erectus, with whom some of our ancestors would have hybridized in SE Asia, where this hominin is known to have existed until very late dates compatible with our arrival to the region.
Besides HLA, only Melanesians show some clear (albeit very minor) Denisovan admixture, but in the realm of antigens, the legacy of H. erectus has been clearly stronger. 


News found thanks to Neanderfollia[cat].

See also in this blog:

Update: John Hawks, who has also been studying HLA, has objections to the conclusion that these alleles come from Denisovans or Neanderthals. For what I could gather he has two objections:
  • Age estimates, which are high risk slippery terrain.
  • Insufficient resolution of the genetics of the archaic hominin genomes. 

Important Update (Jun 18): the “Neanderthal” allele probably Sapiens, the “Denisovan” one may stand:

Hawks (same post, updated or did I miss it in first read?) directs us to a database of allele frequencies through the World, which would seem a most useful reference site. There we get clear evidence that the “Neanderthal” allele HLA*C:0702 probably migrated with our ancestors from Africa and needs no introgression explanation at all. The allele is frequent enough in many African populations peaking among the Baka Pygmies with 15%.

More complicated is the case of the allegedly Denisovan (Erectus) alleles HLA*A11. A look at the database is very clear: no native African population (south of the Sahara) has it at all except the creole ones of Cape Verde and Sao Tome (where it has without doubt recent European origin) and, crucially, a sample from Kampala, Uganda, where it reaches 4.3%.

This sample one is the only one that could suggest an African origin for this set of haplotypes. It could be argued however that as some genetic back-flow from Asia exists in the area, this case is explained by genetic back-flow. However the apportion is rather high, almost as high as Moroccan Berbers, Italians or Macedonians. Even the largest possible Asian source (Omanis: 11.4%) does not seem to be large enough to justify this island of HLA*A11 in Kampala.

Additionally the Nilotic Nandi of nearby Kenya are reported to have 0% of the controversial alleles. It is really hard to explain how this island of HLA*A11 arose in Kampala. But on the other hand, the fact that it is such an isolated finding is equally suspicious: if the allele (essentially HLA*A11:01) was so old in Africa, we should expect it to be found at least a very low frequencies in other populations.

Fine that malaria or other tropical diseases may have played a contrary selective role, as Hawks argues, but still the allele could, should, have survived in populations not affected by this disease. Also Uganda is not less Malaria-prone than Kenya (or most other nearby countries). So this explanation is not satisfactory.

A very localized founder effect of Asian origin (or a reporting error maybe) would seem to be at the origin of this anomaly. Also no African presence of variants 02, 03 or 04 has ever been reported.

Of course, we must always await for further data and research, but on the grounds of what we have now, I would say that:

  • Claim 1: HLA*C0702 is a Neanderthal introgressed allele. Busted!
  • Claim 2: HLA*A11 (several alleles) is a Denisovan (Erectus probably) introgressed allele. Plausible (but watch that Kampala island in Africa). 

Update (Aug 26):

The reference paper is:

Laurent Abi-Rached et al., The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans. Science, 2011. Pay per view

The supplementary material however is freely available