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Monthly Archives: June 2011

Bonobos fall partly within Chimpanzee genetic variability

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

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.

 
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Posted by on June 30, 2011 in bonobo, chimpanzee, Genetics

 

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. 
 
 

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

Sinathropus pekinensis

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
 
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Posted by on June 30, 2011 in China, East Asia, Homo erectus, Indonesia, mind

 

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. 
 
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Posted by on June 29, 2011 in Anthropometry, death, Neolithic, religion, Turkey

 

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.

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…
 
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Posted by on June 29, 2011 in European origins, molecular clock, mtDNA

 

Chad basin mtDNA

In a recent discussion a reader mentioned this paper that somehow I have missed:
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.
     
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    Posted by on June 29, 2011 in Africa, African genetics, mtDNA

     

    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:
    In other languages:

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