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Monthly Archives: January 2012

Egyptian autosomal genetics in the regional context (quick ‘Admixture’ run)

[Important caveat: apparently both Egyptian samples are from the Delta region, the one most affected historically by Eurasian influence. The one labeled Egypt or Egypt (1) is Henn’s sample (n=18), while the one labeled  egyptan (sic) or Egyptian (2) is Behar’s (n=12)].

Some readers questioned whether the strong Iberian affinity apparently found in Egypt in the previous Admixture run focused on North Africans was actually masked Highland West Asian or otherwise non-Peninsular Arab West Asian influences. I was initially skeptic because I had expected by default that Saudi Arabs would represent better all possible West Asian influences than Iberians.

I was mostly wrong as shown here.

Methods: I just run Admixture for K=4, K=6 and K=8 on a selection from the 1000 Genomes sample, following GNXP’s instructions and using the following populations: both Egyptian samples (n=18 and n=12), plus 10 individuals from each of the following populations: Spaniards, Moroccans, Maasai, Ethiopians, Saudi Arabs, Palestinians, Turks and Kurds. The selection of Maasai and Ethiopians to represent Tropical Africans was made because previous research (mine and Henn’s) showed these two being, of the available samples, the ones to best represent ultra-Saharan influence in Egypt specifically. 

Results: I am showing only the K=8 results because the lower K levels do not seem overly informative (if anyone wants them, feel free to ask).

1. The K=8 graph:

2. The K=8 numerical apportions (same as above but in figures, minimally edited by me to improve visualization):

3. The K=8 ADMIXTURE summary, showing Fst distances between components (‘pops’), minimally edited to improve quick understanding (component ‘ethnic’ labels):

Highlights:
Egypt:

There is (and I could eventually detect) an Egyptian-specific component, of West Eurasian affinity (look at the Fst table), what implies that it’s surely descendant of the pre-Neolithic Egyptians of Asian origin. Paleolithic Egyptians that I presume existed based on other genetics (mtDNA X1, M1 and such), as well as Eurasian-like iconography like the Qurta rock art, similar to materials from SW Europe and Anatolia (but admittedly the Egyptian Paleolithic, with a few exceptions, is not well known on archaeological grounds being such a sedimentary and then desertic area overall, and also because archaeology in Egypt has been largely focused on the quite impressive pharaonic period). 

This Egyptian-specific component represents 29% of one sample but only 19% of the other one, being also of some relevance in Ethiopia (9%). This and other differences between the two samples suggest some structure to be unveiled within Egypt but I lack the means (diverse enough samples) to do it. Anyhow the two samples are only somewhat different.

Besides this component, Egyptians show a diverse array of external influences, possibly Neolithic immigrants (?). The most important ones are the Kurdish or Highland West Asian component (17-20%) and the two Arab components together (14-25%) but others (Berber, Palestinian, East African) are also quite influential. The Iberian influence was largely a mirage (although still weights 4-8%).

East Africans:

Among the other populations, the most interesting finding of this run is that the Maasai appear, unlike in other research, to be 96% themselves (but still less distant from Eurasians than the average Tropical African, which is in the Fst=0.2 range), with at most residual admixture from Eurasians (mostly Egyptian/Palestinian). Ethiopians in turn appear here as somewhat admixed Maasai, with North African (mostly Egyptian) and peninsular Arab influences. However my previous relevant exercise showed that, at sufficient K-depth (or with a different sample strategy), Ethiopians eventually converge in their own specific and dominant genetic cluster (91%), which, as in the Fulani case, is similarly distant (and not too distant) to West Eurasians and Tropical Africans, indicating (I understand) very ancient homogenized intercontinental admixture. It surely requires an specifically designed run to understand these matters well enough. 


Arabian-Egyptian (Arab 2) very distant component:

Also notice the Arab 2 extremely distant Fst values, in the >0.2 range. On first impression I thought they were the Maasai component for that reason but nope. We may be here before another OoA remnant, which is very relevant in Arabia peninsula and also in the second Egyptian sample (c. 12% in both cases) and totally absent in Iberia instead.

In any case, it is again evident that different sample strategies can produce quite different results and therefore it is good to look at these matters with an open mind and many complementary perspectives.

Update: K=4 and K=6 graphs, for the record and because some kind of speculation may have some use for them:

Update (Feb 1, after realizing that both samples are from the Delta):
The finding of an Egyptian-specific component may be even more relevant further South. If some areas of the Delta have retained some 30% of this component, it’s probable that it’d be even better preserved towards the interior. On the other hand I’d also expect more Tropical African influence further South but that should be at least balanced by a significant decrease of (post-)Neolithic West Asian influences.
Of course only real samples will provide real answers.
 

Annnouncement of study claiming that Baztanese are genetically continuous since at least 6000 years ago

Sorginetxoa dolmen (Baztan) (source)
Sadly enough the paper does not seem to be available anywhere yet but it was announced on Thursday to the press that a new study by the BIOMICs department of the University of the Basque Country (UPV-EHU), the same who delivered the recent research on the genetics of the Basque diaspora, claims to have found that modern Baztanese (and by extension modern Basques) are direct descendants of the people living there 6000 years ago (and maybe even earlier). 
From what has been published in the media, the conclusions appear to be an exercise of molecular-clock speculation but it’s also possible that rare lineages have been detected or that the authors are linking the results of their research with aDNA extracted elsewhere.
In any case I must remain cautious until the study is effectively published. This is just a heads up for whatever it may come.

Sources (all in Spanish):

Thanks to Neandertalerin for the mention.

 

‘Portuguese Prehistoric Enclosures’ blog: what a great find!

I just stumbled, lead by a note at Pileta, with a most fascinating archaeological blog that goes by the name of Portuguese Prehistoric Enclosures. Where the term enclosure may be a cattle pen… but it may well mean a big city or more commonly a walled village of some size.
I’m almost drooling like a Pavlov’s dog before the huge amount of information that this Portuguese archaeologist, A.C. Valera, is sharing with the World… and in English! As he mentions in his post #13, the phenomenon of enclosures in the Iberian peninsula has remained largely a local concern having almost no international projection.
Just yesterday, he produced a wonderful map of the known enclosures of Portugal, which is located in a separate page (and will be updated as needed).
I will probably use that blog in the future as source for my own posts but by the moment I am overwhelmed by the large amount of information that has been published and that I knew nothing or almost nothing about until now. So I’ll just list by the moment some eye candy for you to follow the corresponding link (in the caption) if that’s what you wish:

004 – Fraga da Pena walled enclosure

008 – Santa Vitória ditched enclosure

009 – Leceia walled enclosure
016 – Castro de Santiago walled enclosure
030 – A long way from home (imports)
039 – Burning rituals
044 – Enclosures and funerary context: Perdigões recent evidence

049 – The first wood henges in Iberia
050 – Castelo Velho walled enclosure: a milestone
054 – Santa Justa walled enclosure

057 – Beaker and ditched enclosures
068 – Plurality of funerary practices in ditched enclosures

070 – Neolithic ditches and rectangular houses
072 – Águas Frias ditched enclosure
Also very interesting (although in Spanish language) is this video on the archaeological findings of Marroquíes Bajos, Jaén (from 028 – Going public on large enclosures):

Remember: Portuguese Prehistoric Enclosures blog.

 

Out of Africa migration was coincident in time with an internal expansion in Africa of mtDNA L3

Ethio Helix mentions today a rather interesting study (potentially, as it is behind a paywall) on the expansion of mtDNA L3 in Africa and its relation with the migration Out of Africa of L3-derived lineages M and N.


Pedro Soares et al., The expansion of mtDNA haplogroup L3 within and out of Africa. Molecular Biology and Evolution, 2011. Pay per view.

Abstract

Although fossil remains show that anatomically modern humans dispersed out of Africa into the Near East ∼100–130 ka, genetic evidence from extant populations has suggested that non-Africans descend primarily from a single successful later migration. Within the human mtDNA tree, haplogroup L3 encompasses not only many sub-Saharan Africans but also all ancient non-African lineages, and its age therefore provides an upper bound for the dispersal out of Africa. An analysis of 369 complete African L3 sequences places this maximum at ∼70 ka, virtually ruling out a successful exit before 74 ka, the date of the Toba volcanic super-eruption in Sumatra. The similarity of the age of L3 to its two non-African daughter haplogroups, M and N, suggests that the same process was likely responsible for both the L3 expansion in Eastern Africa and the dispersal of a small group of modern humans out of Africa to settle the rest of the world. The timing of the expansion of L3 suggests a link to improved climatic conditions after ∼70 ka in Eastern and Central Africa, rather than to symbolically mediated behavior, which evidently arose considerably earlier. The L3 mtDNA pool within Africa suggests a migration from Eastern Africa to Central Africa ∼60–35 ka, and major migrations in the immediate postglacial, again linked to climate. The largest population size increase seen in the L3 data is 3–4 ka in Central Africa, corresponding to Bantu expansions, leading diverse L3 lineages to spread into Eastern and Southern Africa in the last 3–2 ka.

As always, take the age estimates with lots of spices: they are just educated guesses which will vary wildly depending on the assumptions made a priori, like the usually under-estimated time for the divergence of the Pan-Homo genera, etc.

But otherwise the paper appears very much coincident with what Behar and myself (based on his data) could have inferred, including a NW African specificity of L3k, it seems.

Frequency maps by subhaplogroup:

A: L3a, L3i, L3h, and L3x combined, B: L3f, C: L3e, D: L3b, E: L3d

Their reconstruction of the spread of L3:

For many more details, you should visit Ethio Helix’ original entry: The Mother of Mothers!
PS- As contrast to Ethio Helix’ “too white” (in my opinion) selection of Ethiopian portraits, I have located some real women from non-Semitic Ethiopia, which may give a better idea of how the women of the L3 clan looked originally:
Hamer girl (from the SNNPR):

Gumuz mother (from the Benishangul-Gumuz region):

Nuer woman with their characteristic scarifications (from the Gambela region and nearby South Sudan):

Oromo woman (from Oromia, the largest region of Ethiopia):

 
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Posted by on January 20, 2012 in Africa, African genetics, mtDNA, out of Africa

 

Extremely ancient introgression in Papuans

Melanesians
Neanderfollia mentions today[cat] new genetic research that has found unusual diversity in gene OAS1 among Papuans. They contend that this is caused by extremely old introgression that they estimate in more than three million years (more than the age of the genus Homo).

Abstract

Recent analysis of DNA extracted from two Eurasian forms of archaic human show that more genetic variants are shared with humans currently living in Eurasia than with anatomically modern humans in sub-Saharan Africa. While these genome-wide average measures of genetic similarity are consistent with the hypothesis of archaic admixture in Eurasia, analyses of individual loci exhibiting the signal of archaic introgression are needed to test alternative hypotheses and investigate the admixture process. Here, we provide a detailed sequence analysis of the innate immune gene, OAS1, a locus with a divergent Melanesian haplotype that is very similar to the Denisova sequence from the Altai region of Siberia. We re-sequenced a 7 kb region encompassing the OAS1 gene in 88 individuals from 6 Old World populations (San, Biaka, Mandenka, French Basque, Han Chinese, and Papua New Guineans) and discovered previously unknown and ancient genetic variation. The 5′ region of this gene has unusual patterns of diversity, including 1) higher levels of nucleotide diversity in Papuans than in sub-Saharan Africans, 2) very deep ancestry with an estimated time to the most recent common ancestor of >3 million years, and 3) a basal branching pattern with Papuan individuals on either side of the rooted network. A global geographic survey of >1500 individuals showed that the divergent Papuan haplotype is nearly restricted to populations from eastern Indonesia and Melanesia. Polymorphic sites within this haplotype are shared with the draft Denisova genome over a span of ∼90 kb and are associated with an extended block of linkage disequilibrium, supporting the hypothesis that this haplotype introgressed from an archaic source that likely lived in Eurasia.

This is what I have been arguing since December 2010: “denisovan” admixture in Australasian and SE Asian aborigines stems from Homo erectus (diverged from our line at least 1.8 Ma ago) or even maybe a most distant cousin (maybe H. floresiensis, argued by some to be more archaic than H. erectus in key elements like the wrist or toes). 
Yet I am a bit skeptic of the age estimate, because, unless the H. floresiensis australopithecine hypothesis could be confirmed, the date is out of bounds for Humankind proper and creates many conceptual challenges, which are admittedly hard to swallow. While the “australopithecine hobbit” hypothesis would fit this scenario, it remains hard to swallow that the two genus would still be inter-fertile just a few dozen millennia ago and then again, why would archaic admixture come from this remote relative and not the much closer H. erectus, which we know lived in East Asia until rather recently. 
Finally I am in general very skeptic of age estimates as such and their ability to be able to inform more than they confuse. Normally I find them too recent but the opposite (too ancient) can also happen, I imagine. They are in any case just estimates: educated guesses and nothing else.

Update:

Got a copy of the paper (thanks again) and I would say that these two figures are of special interest:

Fig. 2 – Median joining network of OAS 1 haplotypes

Fig. 3 Geographic distribution of the deep lineage in A) Old World populations and B)
South East Asians and Oceanians.

I find particularly notable that the haplotype has been found at very low frequencies in South Asia and nowhere else West of Wallace Line. It can be backflow but may also be indicator about the possible location of the admixture event.

Certainly nothing seems to suggests in these or other maps (1, 2) of “Denisovan” admixture that the episode could have happened in Altai or nearby areas as some readers, stubborn proponents of obsolete migration models, have insisted on. Instead all the evidence suggests that the admixture episode happened in SE or otherwise Tropical Asia, whether deep in Indonesia or more towards the mainland is debatable indeed.

See also:

 

Artistic styles of the rock art of the Cantabrian Strip

Doe of Arenaza
While it is always a pity that scientists allow modern artificial borders such as the one between French and Spanish states, to restrict their research, the information obtained can still be full of interest in spite of this undeniable handicap. This is the case of this delightful paper (only available in Spanish language) on the style and chronology of rock art in the Cantabrian Strip (Northern coast of the Iberian Peninsula):
Aitor Ruiz Redondo, Convenciones gráficas en el arte parietal del Paleolítico cantábrico: la perspectiva de las figuras zoomorfas [Graphic conventions in the rock art from Cantabrian Paleolithic: the perspective of the zoomorphic figures]. Trabajos de Prehistoria 2011. Freely accessible. 
The author reviews previous work on the stylistic differences of the rock art of the area concluding that there are three clearly distinct stylistic groups:

Fig. 4 Multivariant analysis

The three groups have not just stylistic differences but also some geographical and chronological variations:

My visual synthesis (on top of fig. 1: map of sites mentioned)

Animal type indicated only where more than 60% of all figures per tab. 1

In spite of the clear stylistic differences group 1 and 2 overlap in time, specially after considering the wide error margins of dates based mostly on accretion layers (I’m showing above only the most overlapping ones, for reference). They also overlap in the dominant motif, which is the doe (less importantly also horses in group 1, buck deer in group 2 and bison in both). These groups are considered to belong to the Gravettian or even Aurignacian periods.
On the contrary, group 3, which is the most stylistically advanced, post-dates the rest by at least the full span of the Last Glacial Maximum. According to Ruiz, there are at least six millennia between these groups and the Magdalenian rock art, which is the most famed one because of the full perspective and great realism achieved. Contradicting previous work, he suggests that there was no rock art in the region in the Solutrean and Early Magdalenian periods. 

Fig. 7 – comparison of three proposed timelines (right: Ruiz Redondo)

While the author thinks that the difference between groups 1 and 2 is chronological, I fail to see the evidence clear. Instead a geographical difference is rather obvious (see map above), with group 1 concentrated in Asturias and Western Cantabria and group 2 in Eastern Cantabria and Western Biscay.

Group 3, which is much better dated than the others, is clearly dominated by the bison, painted almost obsessively, as in the famed Altamira ceiling. Another important animal is the goat, usually painted in black, as well as the horse.

Santimamiñe rock art

There are more interesting articles (all in Spanish however) in the same magazine: Trabajos de Prehistoria (hat tip to Pileta).
 

Echoes from the Past (Jan 18)

Again lots of short news and hopefully interesting links I have been collecting in the last weeks:
Lower and Middle Paleolithic 
Cova del Gegant Neanderthal jaw
Catalonia: Neanderthal mitochondrial DNA sequenced for the first time. The sequence, obtained from a jaw from Cova del Gegant (Giant’s Cave), is fully within normal Neanderthal range ··> Pileta de Prehistoria[es], NeanderFollia[cat], relevant paper[cat] (PDF)

Castile: Stature estimates for Sima de los Huesos (Atapuerca) discussed by John Hawks.

Upper Paleolithic and Epipaleolithic

Romania: stratigraphies and dates revised by new study (PPV) ··> Quaternary International.

Andalusia: oldest ornament made of barnacle’s shell (right) found in Nerja Cave ··> Pileta de Prehistoria[es], UNED[es], Universia[es].

England: Star Carr dig to shed light on transition from Paleolithic to Epipaleolithic ··> short article and video-documentary (32 mins) at Past Horizons.

Basque Country: archaeologists consider a barbarity that only 65m are protected against the quarry at Praileaitz Cave (Magdalenian) ··> Noticias de Gipuzkoa[es].

Yemen: 200 tombs said to be Paleolithic discovered in Al Mahwit district, west of Sanaa. Tools and weapons were also found. Other thousand or so artifacts from the same period were found in the Bani Saad area  ··> BBC

Peruvian rock art
Sarawak: Niah Cave being dug again for further and more precise data on the colonization of the region by Homo sapiens ··> Heritage Daily.

Siberia was a wildlife-rich area in the Ice Age ··> New Scientist.

Peru: 10,000 years old cave paintings (right) discovered in Churcampa province ··> Andina.

Neolithic and Chalcolithic

Iberia and North Africa: Southern Iberian and Mediterranean North African early Neolithic could be the same process according to new paper (PPV) ··> Quaternary International.
Galicia: Neolithic and Metal Ages remains to be studied for DNA ··> Pileta de Prehistoria[es].
Texas: very informative burnt hut reveals clues of the natives of the San Antonio area c. 3500 years ago.
Mexico: 2000-years old paintings found Guanajuato ··> Hispanically Speaking News (notice that the photo appears to be act of shameless journalistic low quality, being a European bison painted with European style, probably from Altamira).
Metal ages and historical period
Croatia: oldest known astrological board unearthed at Nakovana (Roman period). The cave was probably some sort of shrine back in the day, maybe because a striking phallic stalagmite. Besides the ivory astrological device, lots of pottery has been found as well ··> Live Science.

The best preserved fragment depicts the sign of Cancer (full gallery)
Basque Country: Iruña-Veleia affair:  Basque autonomous police does not have means to test the authenticity of the findings. The Commission for the Clarification of Iruña-Veleia asks for the tests to be performed in one of the few European laboratories able to do that ··> Noticias de Álava.
Cornwall: replicating sewn-plank boats of the Bronze Age ··> This is Cornwall.
India: cremation urn from the Megalithic period excavated in Kerala ··> The Hindu.

Human genetics and evolution

The six flavors
Centenarians don’t have any special genes ··> The Atlantic.
Fat is a flavor: newly discovered sixth flavor in human tongue identifies fat (and usually likes it) ··> Science Daily.
Hominin tooth found in Bulgaria dates from 7 million years ago ··>  Daily Mail.
Anthropology (senso stricto)
The journey of the Tubu women: fascinating documentary in Spanish language about these trans-Saharan trader women available at Pasado y Futuro[es].
Small capuchin monkey bands fight as well as large ones because members are more motivated and have many less defections, even in peripheral conflicts  ··> Science Daily.
Other
Horse genetics again ··> new paper at PLoS Genetics

Fig. 4 – Phylogenetic tree of extant Hippomorpha.