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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. 
 
4 Comments

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.
     
    5 Comments

    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
     
     

    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]

    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):

    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.