Monthly Archives: May 2011

Clovis impact theory: scam?

That is what seems to be all that noise in the end, reports John Hawks following Miller-McCune.
It is a long story but essentially there seem to be a key person who deceived them all, including his colleagues: someone by the name of Allen West, formerly Allen Whitt, a former convict for pretending to be a geologist and scamming municipal authorities out of that. 
After getting out on probation he began working on the comet theory and changed his name legally. Then somehow he managed to be part of both teams that have published anything defending the Clovis impact theory (mentioned by me here and here).
In the second case I thought it was a different team working in a different part of the World. And it was indeed but one person at least was part of both teams: Allen West.
His carbon spherules, sometimes called nanodiamonds, appear to be just graphite and not older than 200 years old.

Posted by on May 26, 2011 in America, Clovis, Upper Paleolithic


Sudanese autosomal genetics

Location of the samples
There is a new paper dealing with Sudanese genetics, which is  of some interest, in my opinion:
Most interestingly they spot a cline and divide (both) between Egypt and Tropical Africa and differential genetics for Somalis, one of three outgroups (the other two being Egyptians and Ugandans from Karamoja region (Nilotic ethnicities).

Fig. 5 (blue: my annotations)
The structure shows (as much as a mere three components allow) a duality of some clinal value (i.e. not absolute but relative) with a divide cutting across Sudan: not just between North and South according to the latest political split but also placing Darfur, Kordofan and the Nuba along with Tropical Africa as well. 
Instead Central, North and Eastern Sudanese look much like Egyptians. Somalis are clearly different however but you’d never know based only on K=2. That’s why it is important to explore these analysis to some depth, greater than K=3 in any case, a very shallow depth for such a diverse region. 

PC Analysis:

Fig. 6A
Fig. 6B

Notice that PC2 and PC3 are of similar values. PC1 however is more than double in importance and marks a cline between Egypt (and the Sudanese Copts) and the Nuba. PC2 and PC3 only show distinctions between Copts and Egyptians and Copts and Somalis respectively. 
I wonder if this last is caused because of random peculiarities of the 15 ancestry informative markers used in this study, which seem a bit too few not to cause random distortions, specially in such a poorly understood region as is East Africa.

Posted by on May 26, 2011 in African genetics, autosomal DNA, Sudan


Neolithic of Nerja and the "almagra" pottery mystery

I take this occasion to introduce this excellent Spanish-language academic blog dedicated to the Iberian Neolithic: Neolítico de la Península Ibérica. You may have already spotted it in the blogroll (they recently discussed Northern Moroccan Neolithic for example) but I imagine they will feature more and more in entries like this one.

location of Nerja cave

Today they discuss García Borja 2010 (Zephyrus), which deals with the important Andalusian site of Nerja cave. According to García, the reference C14 dates (uncalibrated) are:

  • 10860 ± 160 BP and 10040 ± 40 for Epipaleolithic (microlaminar or Azilian, NV-4)
  • 7610 ± 90 and 7240 BP for a transitional phase (NV-3), dominated by a hunter economy
  • 6590±40 BP in a sheep bone from NV-2 (but intruding by means of digging into the NV-3 zone) 

Of particular interest is the lack of Cardial pottery as such and the existence instead of an impressed one with burnished decoration known in Spanish as “a la almagra”. There has been a lot of confusion on this matter of non-Cardial, notably because the ages appear to be at least several centuries older than the earliest Cardial Neolithic and there is no known precedent. 
In this particular case of Nerja at least, the pottery displays very variable patterns of impressions and incisions (none with the Cardium edulis shell) with strong importance of red coloring (Cardial is usually colorless) both in incrustations as in burnishing (almagra).
The ages, as already mentioned, do not allow for this, as other earliest Iberian Neolithic sites to be part of the expansive process of Cardial culture. In another case (Mas d’Is, Alacant, Valencian Country), they argue for a Ligurian Neolithic arrival (and then: what did this Ligurian Neolithic arose from?) but in the case of Nerja, they know of no precedent, so they speculate about an arrival from North Africa and Sicily (with weak typological basis). 
They are anyhow trapped in the idea of “colonization”, when numerous caves from the area have clear continuity sequences from Epipaleolithic, showing how lithic industries are retained from that period. A good example is La Pileta cave, discussed here.
Still, the paper has interest in that it totally dilutes the meaning of Mediterranean Neolithic: from a more or less monolithic Cardial culture as only vector to a much more plural and diverse array of cultures as illustrated in this map:

However the full understanding of what these diverse cultures mean may have to wait a bit.

Complexity arose from protein "weakness"

I find this twist on our understanding of evolution as quite interesting. It may still be true that only the fittest survive but fit means whatever actually works, not strongest or otherwise simplistically, linearly more.
If the weakest works best for whatever reason, then the weakest survive.
In this case we are before a case of proteins that work worse… and by working worse, they begin to interact and therefore create complexity.
That is what, for researchers Ariel Fernández and Michael Lynch, caused the rise of biological complexity: the evolution from prokaryote to eukaryote and so on: errors in proteins, weaker proteins… which eventually caused protein binding and compelxity.
Ariel Fernández and Michael Lynch, Non-adaptive origins of interactome complexity. Nature 2011. Freely accessible.
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Posted by on May 22, 2011 in biology, evolution


Oldest mine in America

The oldest known mine in America was, it seems, a iron oxide mine from Chile, dated to as early as 12,000 years ago. 
The mine in Taltal, in today’s Northern Chile, was used first between 12,000 and 10,500 years ago and then again since 4300 years ago. More than 500 hammerstones dating to the first use of the mine reveal an unusual interest for such an early exploitation. 
Source: Science Daily. (Paper to be published in Current Anthropology next month).

The mine was previously mentioned, in greater extent, here.

Update (May 26): in the comments’ section it was mentioned that another, no so old, quarry is known to have existed in Virginia, where the first inhabitants extracted red jasper. The site is dated to c. 10 Ka BP and you can read about it here and (if you have a Science subscription) also here.


News May 20

A hyper quick review of some news that I may not have time (or even knowledge) to discuss in further depth:
Biology and genetics
  • Human RNA often does not match DNA to the letter. Why? We do not know yet. -> SD
  • Packing and unpacking DNA -> SD
  • Did smell lead to larger brains in mammals -> SD
Archaeology and prehistory
  • Niaosung culture (1400-550 BCE) findings in Taiwan -> The China Post

Major upheaval of human Y-DNA phylogeny: we are all ‘A’ now

Fascinating: reality never stops surprising us. All the basal phylogeny of human Y-DNA has been revised quite radically.

Now super-haplogroup BT, Y(xA) or (my personal favored name) B’CDEF is just a branch, a sublineage of A. And not just of A but of a fraction of a fraction of it:

Fig. 1
To the left we have the new basal phylogeny of the human Y-DNA. Please ignore the “time” axis. I’ll get to that later.
We can well ignore the proposed nomenclature and begin talking of A as the pan-human lineage or “Y-DNA Adam”. This primeval lineage split then into A1b (found at 8.3% among Bakola Pygmies and 1.5% among Mozabites) and A1a-T (or  Y(xA1b) or A1a’2’B’CDEF, using mtDNA’s “superglue” nomenclature’s fix-it-all method), which includes all the rest of the World’s population. 
Don’t worry too much about the nomenclature because it will obviously cause an upheaval in the naming conventions of at least A. All these names are surely just provisional.
Anyhow, this second lineage is yet split between A1a and A2’3’B’CDEF (A2-T in the graph). A1a is found mostly in Niger: among the Fulbe (14.9%) and their Tuareg neighbors (4.5%), as well as among Middle Atlas Berbers of NE Morocco (2.9%).  
Importantly Sudan and other large areas of Africa SE Africa, much of Middle Africa, were not sampled. But I’d say that this distribution is suggestive of an origin near Chad Lake in relation with the expansion of mtDNA L1. But I’d wait until we have results from Sudan because Sudan, notably the South, hosts huge Y-DNA diversity and a lot of Y-DNA A, so it cannot be ignored so easily. 
Using Wikipedia as quick reference, we can see that Y-DNA A1a has also been reported among several peoples of Guinea-Bissau (2.8-5.1%), notably the Mankanha speakers (7.8%). Also 5% of Mandinka from Senegal and Gambia, 2% of Dogon from Mali, 3% of Moroccan Berbers and 2% of unspecified Malians. Basically we can say that A1a is somewhat common (always at low frequencies) through West Africa. 

Frequency of Y-DNA A per Chiaroni 2009
However no further data on the crucially basal A1b lineage is found in this article at least. Anyone?
Besides, the next division is between A2, A3 and the remainder: B’CDEF (or Y(xA) or B-T). A2 is exclusively a Khoisan lineage, while A3 is split between Khoisans and the peoples of the Upper Nile (Sudan, Ethiopia…), having greater basal diversity in this last region (A3a and A3b2 are both Sudanese/Ethiopian, while only A3b1 is a Khoisan lineage).
In any case, the pattern found now in Y-DNA seems to suggest a flow from West or Central Africa to East Africa and then to Southern Africa (Khoisan peoples). This is somewhat contradictory with the pattern revealed by mtDNA (suggesting an origin in East Africa around where the oldest fossil H. sapiens are known to have existed, by the Omo river) or the pattern suggested by some autosomal diversity measures performed recently that proposed Southern or Central-SW Africa instead.
Typically they forget to (or could not) take samples in crucial areas like Angola (other than Khoisans), Mozambique, Tanzania (not even the Haza and Sandawe) or Sudan:

Fig. S1 (see: supp. materials).  
Red: A1b, green: A1a, black asterisks locations of A1a from other papers.

The technical differences between the old phylogeny and the new one are explained in detail and best perceived in fig. 2 (below). Besides of finding a large list of new SNPs, Cruciani et al. suggest that M91 is an unstable (and hence unreliable) location, while P108 and P97 are stable but were interpreted wrongly when first described, being the polymorphisms the ancestral ones, i.e. those identical to what is found among Chimpanzees. 
Fig. 2
Time-line absurdities
The authors propose a time-line for the human Y-DNA that makes no sense. Notably CDEF (CT) is proposed to have only 39 Ka, being more recent even that Aurignacian and several findings of Eurasian remains of H. sapiens (not even considering Skhul and Qahfez). It is also contradictory with so many proposals of Y-DNA timelines that suggest a CDEF age of c. 70 or 80 Ka. (Karafet 2008 for example), which I still consider a bit too recent – mind you. 
At the moment there two possible archaeologically consistent scenarios for the Out of Africa migration, one would have happened c. 90 Ka ago, reaching South Asia by c. 80 Ka (Petraglia 2010). The other one, proposed by Armitage this year (discussed here, see also here), would have the coastal migration by South Arabia happening c. 125 Ka ago and could have reached South Asia soon after. There could even have been two successive migrations.
As Y-DNA CDEF is central to the Out of Africa migration, it must have coalesced before this one happened. Unless one would argue for a back-migration of DE into Africa, what I find hard to sustain. Even if you’d do that, CDEF would have need to be consolidated c. 80 Ka ago at the latest.
That is double than suggested in this paper. It could be triple or even more. That would make “Y-DNA Adam” (everything else equal) at least as old as 285 Ka, surely more.
Of course, I am not believing a word on Y-DNA age estimates, because the hunches are so wildly different and so poorly argued (not to mention that no scientific proof was ever provided supporting such statistical methods) that it’s a total waste of time.
The phylogeny however stands and is an invaluable piece of information.

Important update (May 27): Other possible populations with A1b

Argiedude believes that he had identified A1b lineages in a number of populations (based on other studies and using mostly STR haplotype sequences). He included this spreadsheet (should be available for a year) where the likely A1b individuals were identified by him as “A4”. See the commentaries for further details.

The populations with possible A1b are therefore expanded from just two (Bakola Pygmies and Mozabites) to several, with a peak of frequency in Southern Ghana. Also in Gabon, SE Nigeria and Cameroon, and as isolated individuals in Zambia, Ivory Coast, Burkina Faso  (and then, of course, across the Atlantic in America).