Monthly Archives: October 2012

Propose alternative model for Neanderthal admixture in non-Africans

I must say I am totally  skeptic but just for the record:
Armando G. M. Neves & Mauricio Serva, Extremely Rare Interbreeding Events Can Explain Neanderthal DNA in Living Humans. PLoS ONE. Open Access ··> LINK [doi:10.1371/journal.pone.0047076]


Considering the recent experimental discovery of Green et al that present-day non-Africans have 1 to of their nuclear DNA of Neanderthal origin, we propose here a model which is able to quantify the genetic interbreeding between two subpopulations with equal fitness, living in the same geographic region. The model consists of a solvable system of deterministic ordinary differential equations containing as a stochastic ingredient a realization of the neutral Wright-Fisher process. By simulating the stochastic part of the model we are able to apply it to the interbreeding ofthe African ancestors of Eurasians and Middle Eastern Neanderthal subpopulations and estimate the only parameter of the model, which is the number of individuals per generation exchanged between subpopulations. Our results indicate that the amount of Neanderthal DNA in living non-Africans can be explained with maximum probability by the exchange of a single pair of individuals between the subpopulations at each 77 generations, but larger exchange frequencies are also allowed with sizeable probability. The results are compatible with a long coexistence time of 130,000 years, a total interbreeding population of order 10⁴ individuals, and with all living humans being descendants of Africans both for mitochondrial DNA and Y chromosome.
Not only the discourse of the authors is strangely ideological (strange insistence in resuscitating the dead horse of multirregionalism and denying the rather unquestionable out-of-Africa model at least in name) but also they come to admit that:

The decision of which model correctly describes the origin of Homo sapiens is obscured by the intricacies of the statistical methods proposed for evaluating the models themselves.

And so they proceed to create their own intricate model and even more intricate interpretation.
Sincerely, their model of continuous admixture would normally cause West Eurasians (at least) to have much more Neanderthal introgression than Papuans, whose ancestors have been far away from West Eurasia (the former Neanderlands) since c. 80 Ka most probably (archaeological evidence of African-related techno-cultures in India, Petraglia 2007), while West Eurasian ancestors would have been in intense contact with Neanderthals all or most of that time until the effective Neanderthal extinction of c. 35,000 years ago. 
There’s no convoluted model nor mathematical fallacy that can circumvent that: anything but a single admixture episode or process early on in the colonization of Eurasia by Homo sapiens makes no sense.

Megalithic burial found in Minorca

The naveta (Binibèquer, Sant Lluís) is one of a few in all the island, belonging to the Bronze Age (Naviform I period: c. 1750-1000 BCE). This kind of tombs are exclusive of Minorca.

The new discovery is yet to be researched or even cleared

The famous and well preserved Naveta des Tudons (for comparison)
CC BY-ND 2.0

Source: Menorca Info[es] (via Pileta).


Ancient Maori mtDNA

Terry points me to this paper:
Michael Knapp et al., Complete mitochondrial DNA genome sequences from the first New Zealanders. PNAS 2012. Open access ··> LINK [doi:]


The dispersal of modern humans across the globe began ∼65,000 y ago when people first left Africa and culminated with the settlement of East Polynesia, which occurred in the last 1,000 y. With the arrival of Polynesian canoes only 750 y ago, Aotearoa/New Zealand became the last major landmass to be permanently settled by humans. We present here complete mitochondrial genome sequences of the likely founding population of Aotearoa/New Zealand recovered from the archaeological site of Wairau Bar. These data represent complete mitochondrial genome sequences from ancient Polynesian voyagers and provide insights into the genetic diversity of human populations in the Pacific at the time of the settlement of East Polynesia.

The authors sequenced ancient mtDNA from the pre-colonial period from a museum material being returned for proper reburial. The remains belong to a population from Wairau Bar from the 13th-14th centuries, which were looted by British museums in the mid 20th century. 
Of the 19 individuals researched, only four provided valid sequences. All four Three were within the so-called Polynesian motif or haplogroup B4a1a1a, the other was Q1, a lineage of Melanesian origin also found, albeit rarely, among other Polynesians. All modern studied Maoris are B4a1a1a but Q1 is known to exist among Cook Islanders, for example. (Corrected: Q1 is mentioned but in the context of other Polynesian populations, not New Zealand).

Interestingly the authors also explain that the colonization of Eastern Polynesia was performed not in a series of small randomized migrations but in a single expansive wave in the 12th-13th centuries CE, what explains the relative homogeneity of their customs and languages. 

A recent reevaluation of the dates for the colonization of East Polynesia suggests that, contrary to earlier studies positing a relatively long (2,000 y) chronology for the region, the settlement of most of East Polynesia occurred rapidly, in the period from A.D. ∼1190–1290 (22). The authors determined that the expansion event occurred from the Society Islands, which were only settled 70–265 y previously. This rapid and recent expansion event, they argue, explains the “remarkable uniformity of East Polynesian culture, human biology and language” (22).

The cited reference (22) is:

Wilmshurst JM, Hunt TL, Lipo CP, Anderson AJ (2011) High-precision radiocarbon dating shows recent and rapid initial human colonization of East Polynesia. Proc Natl Acad Sci USA 108(5):1815–1820.


Posted by on October 24, 2012 in aDNA, mtDNA, New Zealand, Oceania, Polynesians


Blood groups A and B inherited from simian ancestors

A new study has found that blood group A and B alleles have been stable (albeit in likely dynamic equilibrium) in the primate family since… always.

Laure Ségurel et al., The ABO blood group is a trans-species polymorphism in primates. PNAS 2012. Pay per view (6 months embargo) ··> LINK [doi:]


The ABO histo-blood group, the critical determinant of transfusion incompatibility, was the first genetic polymorphism discovered in humans. Remarkably, ABO antigens are also polymorphic in many other primates, with the same two amino acid changes responsible for A and B specificity in all species sequenced to date. Whether this recurrence of A and B antigens is the result of an ancient polymorphism maintained across species or due to numerous, more recent instances of convergent evolution has been debated for decades, with a current consensus in support of convergent evolution. We show instead that genetic variation data in humans and gibbons as well as in Old World monkeys are inconsistent with a model of convergent evolution and support the hypothesis of an ancient, multiallelic polymorphism of which some alleles are shared by descent among species. These results demonstrate that the A and B blood groups result from a trans-species polymorphism among distantly related species and has remained under balancing selection for tens of millions of years—to date, the only such example in hominoids and Old World monkeys outside of the major histocompatibility complex.

Razib has some more details on the matter (being PPV, I haven’t read it). Still he wonders what kind of disease or otherwise evolutionary pressure may have been so virulent as to keep the whole order of primates (or at the very least all simians) on our toes all these millions of years.
The answer may well be known already: it seems that type A blood protects against the plague, while type B protects against smallpox, both great historical killers of those without enough defenses. However they may favor other less important health problems like blood clots or cancer, enough to exert a mild pressure in favor of a return to the basic type zero (“O”), which would have evolved by loss of function once and again. 
Whatever the case I find fascinating that these immune mechanisms may be so extremely persistent and I wonder if the bacterian mechanisms they confront may be more generic than just an specific disease.
See also: maps of distribution of major blood types.

Update: a pre-print copy of the paper is available at arXiv.


Alert: destruction of 8000 year-old engravings in Morocco by Fundamentalists – government denies

The Amazigh League for Human Rights denounced the destruction of several Neolithic engravings in Toubkal National Park, south of Marakesh. Among the damaged art is said to be a depiction of the Sun as a god. They date from c. 6000 BCE.

Source and more details: BBC (h/t Stone Pages’ Archaeonews).

The damaged relic (source)

Update: the Government of Morocco denies the claim with strange wording

The Moroccan authorities have denied the claim of a vandalism against a solar engraving attributed to Fundamentalists. According to an AFP report:

“This kind of incident, contrary to our values, cannot take place in
Morocco,” it said, adding that an investigation carried out with local
and regional authorities had showed that the claims were unfounded.

such sites “can suffer, like elsewhere, the effects of natural and even
human degradation, sometimes through vandalism and trafficking.”

The wording is at the very least strange: the logic does not seem sound (can’t happen because of our values) and the suggestion of other reasons for the same vandalism are at the very least suspicious. 
My reading is that the Moroccan Ministry of Culture wishes to deny all kind of militant Salafist activism but that, subtly, acknowledges the destruction, attributing it to mystery causes (either erosion or mindless vandalism) rather than Fundamentalism. 
Not too credible. 

Update (Oct 25):

Dalouh (see comments) has been gathering some more info on the matter from Arabic language sources in Facebook and it would seem that the locals chased out the fundamentalist vandals preventing greater damage, still:

Above: damage stone, below: original


Posted by on October 22, 2012 in Morocco, North Africa, rock art, vandalism


Periodization of Saharan rock art

Marnie has a most interesting blogpost today on the periodization of Saharan rock art, specifically at Tadrart Acacus site in SW Lybia. It is not a well known matter so I am recycling her entry and the materials at Amis de l’Art Rupestre Saharien[fr/en/de/it] to make a quick visual note here on the matter.
Periodization dates are based on description at UNESCO site but need not to be correct for all pieces or not all authors need to agree to them. Here I follow that lead after some thoughts just because of its simplicity, which may well be misleading. It should only be taken as a very basic introductory note, nothing else.
Naturalistic or bubaline phase (14-10,000 BP):

··> more info at AARS.

Reminds a bit of rock art from Qurta (Nubia, Egypt).

Round head phase (10-6,000 BP):

··> more info at AARS.

Bovidian or Pastoral phase (6000-3500 BP):

··> more info at AARS.

As Marnie mentions, this phase would be approximately after the date of earliest clear evidence for milking in Africa, which is of c. 7000 BP.

Caballine phase (3500-2000 BP):

··> more info at AARS.

This would be soon after the date of arrival of the Hyksos to Egypt, who brought the chariot from Asia.

Cameline phase (since 2000 BP):

··> more info at AARS.

Dromedaries were probably introduced in Egypt (and the rest of Africa) with the Persian invasion c. 500 BCE.

Large Neolithic-Chalcolithic settlement found in Antequera (Andalusia)

Burial in flexed position
Pileta de Prehistoria reports[es] on the discovery of a large settlement occupying some 150 hectares in Arroyo Saladillo (Antequera) from the transitional Neolithic-Chalcolithic period (centuries around 3000 BCE). 
The site was previously known but the archaeological research prior to the public works on the high speed rail branch Antequera-Granada have evidenced that it was much larger than believed, occupying an almost circular area, delimited with a ditch or moat, with a diameter of 1.4 Km (less than one mile across), what results in an occupation of 150 Ha., of which only a fraction has been excavated so far. 
In this research zone of 700x40m. as many as 139 silos for cereal storage have been documented, some with carbonized remains, others (four) recycled as tombs, other four newly excavated burials and also four burials of megalithic type (dolmen).
Among the materials recovered are loom weights, tuyeres (sign of incipient metallurgy), marble and shell bracelets, three idols made in shale, pottery decorated with red ochre (a material also used in burials) and imported double edged axes. 
Economically speaking, agriculture, pastoralism, hunting and fishing all seem to have been important but maybe with some dominance of pastoralism (it is a mountain area).