Bonobos fall partly within Chimpanzee genetic variability

That is what a new paper has found after studying extensively Pan sp. genetic diversity:

A. Fischer, Bonobos Fall within the Genomic Variation of Chimpanzees. PLoS ONE, 2011. Open access. 

Abstract

To gain insight into the patterns of genetic variation and evolutionary relationships within and between bonobos and chimpanzees, we sequenced 150,000 base pairs of nuclear DNA divided among 15 autosomal regions as well as the complete mitochondrial genomes from 20 bonobos and 58 chimpanzees. Except for western chimpanzees, we found poor genetic separation of chimpanzees based on sample locality. In contrast, bonobos consistently cluster together but fall as a group within the variation of chimpanzees for many of the regions. Thus, while chimpanzees retain genomic variation that predates bonobo-chimpanzee speciation, extensive lineage sorting has occurred within bonobos such that much of their genome traces its ancestry back to a single common ancestor that postdates their origin as a group separate from chimpanzees.

This is very easy to appreciate in fig. 2, showing 50% majority consensus tree for mtDNA (mt) and each of the fifteen nuclear regions (a to o):

Red: bonobos - Other colors: several chimpanzee populations

We can see that Bonobos are monophyletic for all categories but that chimpanzees retain much more of the shared ancestral diversity for many of them. 

We see:

• strict bonobo/chimp dichotomy in mtDNA and nuclear regions b, d, e and i only
• bonobos as one of several branches of the the greater Pan family in nuclear regions c, f, h, k and o
• bonobos as derived within an otherwise chimpanzee branch in regions a, g, j, l, m and n. 

This unequal relation between the two Pan species may serve as reference when considering other speciation processes, including those leading to ourselves. 

Update (Jul 1): a somewhat related paper (which I am not going to comment) was just published:

G. schubert et al., Male-Mediated Gene Flow in Patrilocal Primates. PLoS ONE 2011. Open Access.

Epipaleolithic dog burial found in Portugal

The finding took place at Poças de São Bento (Alcácer do Sal, Portugal). The burial was found near an Epipaleolithic settlement and necropolis dating to some 8000 years ago near the River Sado.

Older dogs are known to have lived with humans in Europe however, for example in Anton Koba (Basque Country, 13 Ka), two sites in Ukraine (18 Ka) or Goyet (Belgium, 32 Ka), which is the oldest domestic dog known worldwide. 

Sources: Universidad de Cantabria (via Pileta de Prehistoria) and M. Germonpré 2009.

Asian Homo erectus in the spotlight

Two recent news conspire to claim that the affinity with us of Asian Homo erectus was less like us than we used to think.


Beijing brain

On one side the so-called Peking Man, Sinanthropus or Homo erectus pekinensis (right), one of the most representative fossils of the species, has seen its brain throughly researched and the researchers conclude that:

Compared with modern humans, Peking man’s brain casts have small brain size, low height and low position of the greatest breadth, flat frontal and parietal lobes, depressed Sylvian areas, strong posterior projection of the occipital lobes, anterior positioning of the cerebellar lobes relative to the occipital lobes, and relative simplicity of the meningeal vessels.

(...)

The anatomical structures of Peking man’s brain maybe differs from the modern human, suggesting that Peking man had no ability to communicate with each other in the form of language.

Open to interpretation, I guess. Remember that chimpanzees have to at least some extent a language-ready brain, it may not be as simple.

Source: PhysOrg (via Archaeology in Europe).


Java terrace's datings

On the other hand there are new datings of the river trench where the remnants of Homo erectus soloensis (aka Ngandong man) have been found.

Previous measures (Swisser 1996) produced dates of 25-57 Ka ago on bovid bones collected near the human specimens. However this new paper dates certain geological features (pumices) of the terraces that the authors consider a more reliable reference. These produce dates that are internally inconsistent (c. 546 Ka with the argon method and c. 143 Ka with the ESR/uranium one) but clearly older than the ones of Swisser.

Again open to interpretation and debate, I'd say.

E. Indriati, The Age of the 20 Meter Solo River Terrace, Java, Indonesia and the Survival of Homo erectus in Asia. PLoS ONE 2011. Open access.

Found via Dienekes.

Fig. 2, showing the H. erectus finding sites and the pumice now dated

Çatalhöyük: people buried together probably not related

As you probably know, Çatalhöyük (near Konya, Turkey) is one of the most emblematic sties of Middle Neolithic. 

As genetic research was fruitless (bone contamination, degradation), a study of dental morphology was done in order to estimate if people buried together were related, because close relatives should have close dental morphology. The result was negative for all but (maybe) one tomb, strongly suggesting that the Çatalhöyük community did not give any importance to relatedness at least for funerary rituals and related beliefs. 

Source: Live Science (found via Unreported Heritage). 

Mitochondrial DNA and 'molecular clock'

There is a new paper discussing in some good depth with the peculiarities that the irregular mutation patterns of mtDNA, particularly in the macro-haplogroup R, show and its implications and complications for the idea of a molecular clock that can estimate the age of the various haplogroups, so dear of some and so much hated by others.

While I do not necessarily agree with what the authors conclude in this paper, I do applaud their critical approach in general and I do recommend the (mostly free access) bibliography for those interested in digging deeper in the matter.

Denis Pierron et al., Mutation Rate Switch inside Eurasian Mitochondrial Haplogroups: Impact of Selection and Consequences for Dating Settlement in Europe. PLoS ONE. Open access.

Probably figure 3 illustrates quite well the problem:

As you can see the actual number of mutations found in each of the sublineages of R varies a lot! Some sublineages have accumulate as many as 16 mutations, while others barely have four. Also the excess or defect of mutations follows some obvious patterns along haplogroups.

The authors suggest that there are two issues: in the case of J1 (only), they find that there must be a selective constrain of some sort that blocks further neutral evolution.  But this does not apply to the rest of JT nor to the big problem child: R0 (notably HV and specially H under it).

They conclude that there must be some other circumstance such as the lack of mutations for some lengthy period at each lineage.

My caveat

I must say here that I found this argument faulty because the problem is not, I understand, absolute lack of novel mutations but lack of effective mutations (i.e. those that survive and forge new lineages). I understand that this was surely caused because the corresponding haplogroup was already solidly established and therefore novel mutations had no room to fructify in most cases, being reabsorbed by the dominant ones in a totally normal drift process (where the most common lineages almost invariably succeed).

We can say this is the cannibal mum model... though nobody had to actually eat anyone in reality, just "daughter" lineages with novel mutations were systematically drifted out in most cases.

Instead where populations were very low, all lineages, novel or ancestral had similar chances of survival, so the effective mutation rate was increased instead.

I reached to this conclusion because I noticed that it is actually the haplogroups with large star-like structures, notably M and H, which suffer from this symptom most intensely. As star-like phylogenies are clear indicators of sudden expansions, I concluded that it was the success of mum what aborted that of the daughters, delaying and even nearly stopping the process of accumulation of new mutations.

That is why, when doing molecular clock exercises myself, I count mutations from the root and not present day haplotypes. This last makes sense only when the number of mutations is so huge and common in all generations that every newborn has some novel mutations inside. This is true for nuclear and Y chromosome DNA but not mtDNA, which has such a small genetic chain that each mutation probably only happened every many dozen generations.

It is easy to understand, I believe, that, with so rare mutation events, the novel mutation lineage (not the carrier!) had in most cases very very low chances of survival, unless the population was so tiny that it was one among a handful and not one among hundreds or even thousands.

Back to the paper

I am not sure at the moment on what Pan-Homo divergence estimate they have used (this is one of my greatest criticisms to the usual molecular clock guesstimates and does not seem to be clarified in the paper) but, regardless, I am favorably surprised by the age estimates they have been able to calculate.

Naturally (my method is too different) I am not really in agreement but at least they have come with age estimates with some plausibility. They are all in table 5 but here there are some examples:

• R2'JT - 53 Ka
• J2 - 28 Ka
• T - 27 Ka
• R0 - 41 Ka
• V - 17 Ka
• H - 28 Ka
• H1 18 Ka
• H3 17 Ka
• U - 44 Ka
• U4 - 25 Ka
• U5 - 20 Ka
• U6 - 25 Ka
• B - 43 Ka

I still think that these dates are too recent in most cases and the reason is probably that they are still counting the age estimates, in spite of all corrections, from present backwards and not from the root to the relevant node.

Of course my method requires some other point(s) of calibration (instead of present), something like an archaeological event (for example equating the colonization of Europe c. 40 Ka with the H star-like node) and that is a point of controversy on its own...

More stuff to read

As I said at the beginning one of the virtues of this paper is that it has an extensive free access bibliography on the issue of why mtDNA molecular clock is problematic. I have selected the following (not all of which I have read yet):

• A. Torroni et al., A Signal, from Human mtDNA, of Postglacial Recolonization in Europe. AJHG 2001. (link)
• Neil Howell et al., African Haplogroup L mtDNA Sequences Show Violations of Clock-like Evolution. MBE 2004. (link)
• Neil Howell et al., Relative Rates of Evolution in the Coding and Control Regions of African mtDNAs. MBE 2007. (link)
• H-J Bandelt, Clock debate: when times are a-changin': Time dependency of molecular rate estimates: tempest in a teacup. Heredity 2007. (link)
• Brenna M. Henn et al., Characterizing the Time Dependency of Human Mitochondrial DNA Mutation Rate Estimates. MBE 2008. (link)
• N. Howell et al., Molecular clock debate: Time dependency of molecular rate estimates for mtDNA: this is not the time for wishful thinking. Heredity 2008. (link)

See also the molecular clock category at Leherensuge (my old blog) and at For what they were...

Chad basin mtDNA

In a recent discussion a reader mentioned this paper that somehow I have missed:

María Cerezo et al., New Insights into the Lake Chad Basin Population Structure Revealed by High-Throughput Genotyping of Mitochondrial DNA Coding SNPs. PLoS ONE. Open access.

The paper has more data but I'd say that the essence of it is in figures 1 and 2:

Fig. 1 Map of the Lake Chad Basin showing frequencies of the main African hgs in the different ethnic groups analyzed.

What I most clearly notice in this map is that L2 is dominant North of Lake Chad, while L3 is hegemonic elsewhere in the basin.

Figure 2 (not displayed because it needs high resolution for clear contemplation) is the phylogeny and commonality of the specific lineages under the wide categories shown above. Most common lineages are:

• L0a (almost all the L0 displayed above is this sublineage). Excepting historically slave-trader nations (Arabs, Kanuri, Kanembu) it is most common south of the Lake, in North Cameroon.
• L1b is most common among the Fulani (20-26%) being very rare in other ethnicities, except the Fali and the Kanembu.
• L1c (usually associated with Pygmies but not exclusively) is found most commonly among the Hide (15%).
• L2a makes up most of the L2 above, being quite common among all ethnicities (but more in the North, as mentioned for L2 overall, reaching its highest figure among Chad Arabs: 33%).
• L2b is most common among the Mafa (11%) and Fulani (8%).
• L2c is most common among the Tcheboua Fulani specifically (10%)
• L3b is most common among the Fulani (28-30%) but also among many other ethnicities.
• L3d is frequent among several groups but rare among others without any pattern I can discern. The highest frequency is that of Chad Arabs (19%).
• L3h is quite frequent (>20%) among the peoples that live at the very shores of the lake (but the Northern ones), being most common among the Kotoko (29%).
• L3e reaches high frequencies among diverse peoples, with a peak among the Fali (38%).
• M1 is most common among the fishermen Buduma (10%) and also the Shuwa Arabs (13%).
• U only reaches noticeable frequencies among the Borgor Fulani (8% U(xU6)) and Shuwa Arabs (5% U(xU6), 3% U6).
• R0 is quite common among Chad Arabs (18.5%, all R0(xHV), surely R0a). There is some HV(xH) and H scatter but at very low frequencies.

Iruña-Veleia affair: police won't do analysis

The incrustations appear to support the authenticity of the engravings

After a whole year of institutional delays, Spanish military police corps (Guardia Civil) has apparently told the judge that they will not do and that they cannot do the analysis to the controversial shard inscriptions found by Eliseo Gil's team in the Vasco-Roman town of Iruña-Veleia and which are quite central to linguistic and historical matters.

That is what El Correo newspaper[es] (founded by dictator Francisco Franco) claims and linguist Juan Marti Elexpuru echoes in his dedicated blog[eu]. However all the rest of the El Correo's article is all lies and manipulations so it is hard to say if there is any truth in the claim.

I therefore await confirmation by a more respectable source.

If I recall properly, the civic association SOS Iruña-Veleia and Gil's defense had offered to pay themselves the necessary tests in a reputed international laboratory. This kind of physical evidence is in any case necessary to establish the truth of the matter because all that the accusation has so far are contradictory graphological studies (one of which is clearly done in bad faith) and the conclusion of an even more controversial ad-hoc academic commission, where the evidence was notable for not being apparent anywhere.

Further information in English:

• For what they were... category: Iruña-Veleia
• Leherensuge category: Iruña-Veleia

In other languages:

• SOS Iruña-Veleia [es/eu]
• Ostraka euskalduna blog [eu]
• Iruña-Veleia gezurra ala egia? blog [eu]

Location of Iruña-Veleia and other Basque towns of Roman era

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

You may have heard of this by now:

B. F. Gunn et al, Independent Origins of Cultivated Coconut (Cocos nucifera L.) in the Old World Tropics. PLoS ONE 2011. Open access.

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 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]

Abstract

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):

Sergio Cardoso Martin & Marian Martinez de Pancorbo, Los linajes genéticos de la población vasca hablan de su pasado. 2011. Direct PDF link.

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. 

Ref. A. Mummert et al., Stature and robusticity during the agricultural transition: Evidence from the bioarchaeological record. Economics & Human Biology, 2011. Pay per view.

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.

Ritual cannibalism among early Crimean Homo sapiens

Stratigraphic sequence of Buran Kaya III

New research about the earliest documented Homo sapiens of Crimea:

Sandrine Prat et al. The Oldest Anatomically Modern Humans from Far Southeast Europe: Direct Dating, Culture and Behavior. PLoS ONE 2011. Open access. 

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.

Found via Dienekes.

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: Philly.com[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.

Also:

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. 

References:

• Article at New Scientist.
• Royal Society generic entry.
• Audio of Parham's conference.

News found thanks to Neanderfollia[cat].

See also in this blog:

• Denisova hominins, Neanderthals, Melanesians and so on... 
• Explaining 'Denisovan' and also 'Neanderthal' admixture: the simplest scenario.

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. 

Very slow and variable mutation rate in humans

A direct measure of the mutation rate in two family trios (mother, father and child), one from Utah and the other from SW Nigeria, finds that the average mutation rate is of the order of one mutation per 100 million sites, what totals some 60 inherited mutations per newborn child.

There was some remarkable variation between the number of mutations inherited from each parent but the data failed to support the hypothesis that the male line was more prone to introduce mutations just because one more meiosis takes place in the production of sperm than in the formation of ovules.

Sources: Science News, Science Daily.

Ref. Donald F. Conrad et al. Variation in genome-wide mutation rates within and between human families. Nature 2011. Pay per view.

This is not the first case that real measures of the mutation rate happen to be slower that hypothesized: 

• (L) Molecular clock: two to six times slower than thought.
• (L) Mutation rate is less than half.
• Very low mutation rate, mwahahaha!

And let's not forget that we diverged from Chimps not before 8 million years ago. But way too many geneticists and other people who write on genetics ignore these facts of life, what I find pretty much unscientific (careless at best, mischievous at worst).

The various options for the migration out of Africa

I want to call your attention to the latest entry at M. Petraglia and colleagues' blog Ancient Indian Corridors. The main focus of this short entry (with open access links to the relevant papers) is the Jubbah site in what today is the terrible Nafud Desert but what really called my attention the most is this other article: Trailblazers across Arabia, where Petraglia discusses not just his own work on the matter of the migration out of Africa of Homo sapiens but also the recent one by Armitage, who proposed a coastal migration via southern Arabia some 125,000 years ago.

This map from that article really synthesizes the various options, even if the matter on when the migration happened (125 Ka ago or more like 90-80 Ka ago) remains open:

Sadly the Ice Age sea levels are not reflected, for that reason we cannot appreciate that the Persian Gulf was then above sea level, constituting a fertile riverine and swampland region that surely hosted plenty human settlements.

This was addressed by J.I. Rose in 2010 and discussed by me here, among other key papers on the migration out of Africa into Asia.  This map may help understanding better the geography implicated in the OoA:

Something that I find fascinating about all this is how we are living in such a key moment of discovery of our own prehistory and how in this particular case Archaeology is following Population Genetics. As you probably know, I am adamant of double-checking genetics-based prehistory reconstructions with archaeology when this one is minimally developed and can provide unavoidable key references. But in the case of the migration out of Africa we were until recently very much ignorant of everything: we knew with good likelihood that humankind had formed in Africa and then... well, there are nice decorated caves in Europe and some controversial skulls in Australia. Between Omo II and Cro-Magnon I, so to say, we were totally amiss (and that's like 160,000 years of prehistory, most of our history as distinct species).

But then, because of certain peculiarities of the distribution of lineages in Asia, some geneticists found themselves forced to posit the theory of the rapid coastal migration out of Africa. The theory posited that our ancestors, or at least some of them had migrated, at least partly, by taking advantage of coastal ecosystems even in relatively arid areas. This coastal specialization allowed these beachcombers and boaters to move faster that any inland route would have allowed, largely able to ignore the difficulties posed by deserts, rivers and swamps alike... and even to cross some narrow sea branches as attested by the colonization of Australia and nearby islands, colonization that must have happened (Genetics seem to say) quite early on in the human adventure in Asia. 

This was several years ago and I recall the importance of this discovery in allowing us to understand better the most likely prehistory of our kind across Eurasia. Suddenly all the classical maps, which almost invariably included arrows across Siberia for some odd reason, became obsolete. However there was still no or almost no archaeological evidence. Arabia was not just a desertic region but also seemed an archaeological desert, with very few data, much less reliable one. Even in South Asia, when I tried to find any information on Prehistory, there was not much.

Luckily, in the last years this has changed a lot. And it is still changing: we are learning every other month something new about this key episode of our history as species. So here there go my thanks to Petraglia, Armitage, Rose and all the others who are helping so much in getting us to understand our (pre-)history, what our remote ancestors did, allowing us to be what we are.

Some quick prehistory news

P. boisei reconstruction

Quickly some archaeological or otherwise prehistorical news, mostly (but not only) from Stone Pages' newsletter ArchaeoNews.

Paranthropus sp. were patrilocal: enamel analysis finds that females were much more mobile than males in this hominin genus > SD.

Autism was maybe selected for in scattered hunter-gatherer populations > SD.

The effective population size of the first Native Americans was maybe of just 70 > Daily Mail [update: it seems to be on <a href=http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030193 >a 2005 paper</a>, not really new].

Geometric rock art and "rock gongs" in Northern Sudan (Wadi Abu Dom) may be 5000 years old > Live Science, UPI.  

Newly found Australian skull might date to as much as  25,000 years ago > ABC.

Barrows (tumuli) excavated in Dorset (England) before the sea destroys them > BBC.

Large dolmen tomb discovered at Srikakulam (Andrah Pradesh, India) > Times of India.

Languedoc Chalcolithic DNA

There is a new host of ancient DNA data, which seems to have been carefully analyzed, from the important Languedocine site of Treilles, which gives name to a whole "tribal" group of the Chalcolithic period, after the post-Epicardial Chassey culture broke up in pieces.

Marie Lacan et al., Ancient DNA reveals male diffusion through the Neolithic Mediterranean route. PNAS 2011. Pay per view (for 6 months or depending where you live).

As I do not live in India nor Argentine, for example, I would have to pay for this paper or wait six months. I never ever buy anything online, so I will do the latter. Put up with me.

Regardless, the supplementary material is freely available and most data is there. I have also read something online around what this paper has to offer. 

Y-DNA: almost all cousins!

Fig. S5 - Y-DNA G2a median joining network

The most striking finding is that almost all male members of this population belonged to a single Y-DNA lineage: G2a. Only two of them did not and they carried I2a instead. 

This speaks volumes on this population being a patrilocal one and made up of closely related men. It is not just the haplogroup but also the haplotype: all the Treilles men belong to a relatively rare haplotype within G2a (left in red).

It is also suggestive of this population being of immigrant origin. Haplogroup G2a is rather mysterious in this matter but it is one of the main candidates, along with J2 and E1b1b1a1, for being a Neolithic immigrant lineage in Europe. 

The secondary lineage I2a is also a possible case of Neolithic immigrant lineage but in this case it would come directly from the Balcans and not West Asia. However in this case a pre-Neolithic origin is also very possible, specially as I (likely I2a1) has been found in North African ancient DNA (specifically Guanche mummies from the pre-colonial Canary Islands). 

Mitochondrial DNA: quite more diversity

[Note: this section was corrected hours after writing it first time because it contained errors]

But, regardless of we may think of Y-DNA, what really supports a largely non-native origin of the population is the mitochondrial DNA, the female lineages. These (n=29) are as follows:

• H - 6 (21%)
• H1 - 3 (10%)
• H3 - 3 (10%)
• HV0 - 3 (10%)
• HV0 (undefined) - 2
• V - 1
• U - 8 (28%)
• U (undefined) - 1
• U5 - 5 (17%)
• K1a - 2 (6%)
• JT - 8
• J1 - 6 (18%)
• T2b - 2 (7%)
• X - 4
• X2 - 4 (14%)

I estimate that there is a 45% of Neolithic immigrant lineages (X, J, T and K). On the other hand, there is still at least 41% of Paleolithic aboriginal lineages (H, V, U(xK) and I), what seems to be telling us of some level of continuity in nearby areas, where the women may have originated. 

The relatively high diversity of maternal lineages reinforces the idea of this group being strongly patrilocal in any case. 

No milk for the shepherds

While the title of this USA Today article is very much misleading, because lactose intolerant people can perfectly eat cheese in fact (it is raw milk which they find intractable but they can have most processed dairies), one of the findings of this paper is that they did not have the common variant that, in most of Europe, signals lactose tolerance. 

This is not fully conclusive, as there are people without the gene that is lactose tolerant and vice versa, but it is highly likely correct in their conclusions.

In fact, modern Occitans are still largely unable to digest milk as adults (but they can eat cheese for sure): according to a 2001 paper, 65% of Southern French are lactose intolerant. While the exact sampling location(s) for these "Southern French" is not clearly identified, it is most unlikely that they are Basques or Gascons, because Basques are the population with less lactose intolerance on Earth (0.3%).

Who were these people of Treilles

As I haven't yet read the paper I am not very sure about the details of this necropolis, however Treilles gives name to an archaeological group (not quite a culture but almost). When the late Neolithic Chassey culture broke up c. 3000 BCE, several local groups arose from it. Treilles was one of them and maybe the most advanced and cosmopolitan one. 

Inserted in the Megalithic phenomenon since its formation and later also in the overlapping Bell Beaker one, the Treilles group was intensely connected with the Iberian cultures but very specially with that of Zambujal (or Vila Nova de Sao Pedro), a true Megalithic civilization and the first identifiable civilization on the shores of the Atlantic Ocean.

I made the following maps for your interest:

 My reconstruction of trade routes in late Chalcolithic SW Europe (green star is Treilles, solid ovals locate Iberian civilizations)

A more concise map (source of the other one) showing the various cultural elements apparently traded (see legend below)

Legend:

• Light blue dots: Palmela points (weapons originated in Portugal)
• Dark blue dots: turtle buttons (originated in Portugal?)
• Green dots: conical and Dufort buttons (likely from Languedoc)
• Orange dots: pyramidal buttons (Catalonia essentially)
• Stars indicate Treilles (green), Zambujal (blue) and Los Millares (black).

From Pellicer 1986 (himself on Harrison), several maps gathered in one here by me.

Important update: 

I got a copy thanks to a reader. Interestingly this is not a burial from nearby the modern town of Treilles, which gives the group its name (located with a star in the maps above), but from a cave further Northwest, towards the Massif Central, in the area of the Grand Causses[fr], near Millau.

The cave is named Saint-Jean-et-Saint-Paul and hosts a collective burial dated by the authors of this paper to c. 3000 BCE, early in the Chalcolithic period (though the authors prefer to speak of Late Neolithic). This kind of collective burials are the same as those found in dolmens and other megalithic structures and are usually thought as clannic tombs (which is coincident with the findings, if we accept, as we must, that clans were then patrilineal). Many areas of Europe where Megalithism never took roots, used these kind of collective (or clannic) burials in caves. This was the case in most of the East and Center of the Iberian peninsula, and also in North Italy, which had strong connections with this area in the period just before this burial (Chassey-La Lagozza fusion culture, maybe proto-Ligurian).

So we are clearly before a patrilineal clan in a rather hidden spot of post-Epicardial Occitania.

The authors argue that:

The Treilles cultural group is a well identified archeological complex of the late Stone Age period, preserved of any major late Neolithic population movements as suggested by the absence of the Bell–Beaker culture influence in the second part of the third millennium B.C. The study of this cultural group should give a snapshot of the local genetic pool of the end of the Neolithic period in southern France before all recent migrations.

While not fully rejecting this claim, I doubt that they were so much isolated and I would instead argue that they had rather intense interactions with North Italy in the previous period and Iberia in the one to come. Chalcolithic long distance trade began long before Bell Beaker (it correlates best with Megalithism in fact) and even if the early date in the context of Chalcolithic justifies some of the claims, these are poorly argued. There was also trade and cultural interaction in the previous cultural period of Chassey-La Lagozza: even if it was more restricted to the region, the interaction with North Italy cannot be ignored. 

But my most important caveat rests in the clannic (and arguably aristocratic) nature of collective burials: it is clear that we are looking at the members of a single patrilineal clan, all related by a common male ancestor (excepting of course the two I2a individuals, who could be adopted, illegitimate or whatever). In this sense no single clannic tomb can provide a good snapshot of the wider region, at least for the Y-DNA.


Update (Jun 3): Heraus has written an entry on this particular district (Causse de Larzac) at his blog dedicated to the physiognomy of French citizens Anthrofrance.