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):

• Noticias de Navarra 
• Izaro News
• Deia
• Diario de Navarra
• Reuters

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):

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).

Fernando L. Méndez et al., Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations. Molecular Biology and Evolution 2012. Pay per view.

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:

• Neanderthal gene flow found in modern humans (on Green 2010)
• Exploring the Neanderthal admixture episode (version 1)
• Denisova hominins, Neanderthals, Melanesians and so on... (on Reich 2010)
• Explaining 'Denisovan' and also 'Neanderthal' admixture: the simplest scenario (where I first hypothesize that H. erectus and also maybe a relative of Neanderthals like the Hathnora hominin, could be the actual culprits).
• Is X-DNA lineage Neanderthal?
• Denisovan admixture widespread beyond Wallace Line, non-existent elsewhere - but then:
• Minimal Denisovan admixture in SE Asians.
• 'Denisovan' admixture may actually be from H. erectus.

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.

North African autosomal genetics (again)

Two weeks ago I performed almost the same exercise here at this blog but now a paper with academic seal of proficiency has been published at PLoS Genetics:

Brenna M. Henn et al., Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. PLoS Genetics 2012. Open access.

The basic results are very very similar if not outright identical to what I achieved. And that is because the sampling strategy was also very similar. If anything Henn and colleagues used a broader sample of Tropical African populations.

From Fig. 1 (click to expand)

The choice of North African populations is exactly the same as mine (actually the samples I used are from a previous paper by Brenna Henn, who is making a great job in exploring African genetics, and must be the same as in this paper) exception made that I included 10 HGDP Mozabites also. The choice of West Eurasian populations is different but does not seem to produce any relevant difference in the result. The main differences are in the choice of Tropical African samples, which does produces some differences.

Tunisian Berbers' endogamy

But first of all let's explain what happens with the weird Tunisia sample:

... the Tunisian Berber population displayed an excess of pairs of individuals sharing 200–1200 cM IBD. This bimodal distribution indicates that many 1st and 2nd cousin genetic equivalent pairs were present in this sample, even though donors declared themselves to be unrelated during the sampling process. Analysis of long runs of homozygosity (ROH) indicate that the Tunisian population averaged almost twice as much of their genome is in ROH than other North African populations, 230 Kb versus 120 Kb respectively (Figure S3). The pattern of ROH and pairwise IBD in the Tunisian Berbers is likely the result of endogamy due to geographic isolation or cultural marriage preferences.

That's why they perform so weirdly, relating always to themselves almost before any other affinity. This fact makes them a poor and mostly uninformative population. 

Different sampling strategy, somewhat different results

As I say, the main difference between my sample strategy and Henn's (and the result produced) is in Tropical Africa: I used Ethiopians, Mandenka and Fulani; Henn used also Fulani and then also West and East Africans but different ones. I found apparent Mandinka (West African) admixture in NW Africa (and almost no East African/Ethiopian one), Henn found apparent Luhya (East African) admixture instead (and almost no West African one).

I don't know yet how these two apparent different findings may conciliate but the difference of findings is in itself interesting, outlining the strategy of future research. 

Something that is quite obvious as Henn uses such a broad Tropical African sample is that many of the components discerned are just one for each Tropical African population. This is interesting, underlining the immense genetic diversity of Africa, but not very informative in regard to North Africans. 

That (and the fact that I went down to K=11 - and even K=12 but this one was uninformative) is probably the reason why I, with a smaller peripheral sample, could detect what I believe that is a very old layer of North African specificity. 

So the sampling strategy (both sample choice and number of individuals in each sample), as well as the K-depth reached can affect the results of these analysis of the population genetic structure. There is almost always a different approach that can produce complementary information as result. 

Back to Africa but when?

But overall the results are very similar: the bulk of North African genetic affinity is with West Eurasia and not so much Africa as such. That is the most obvious result and indicates that the Out-of-Africa migration had an important backflow which affected several parts of Africa but very specially the North. 

Nothing unexpected, at least for me. But it really hits a blow to those who, quite lightly, associate Y-DNA and overall ancestry: if there is Y-DNA and mtDNA contradiction, as is the case in North Africa, where most of the patrilineages are African but most of the matrilineages are of Eurasian origin, in most cases the mtDNA is right and the Y-DNA is nothing but a varnish. 

The main exceptions seem to be areas of sustained male inflow across generations, notably some parts of Latin America. But this kind of sustained industrialized migration pattern is unlikely to have ever existed in prehistory or even pre-Modern history anywhere. 

Anyhow, interestingly, the authors make an interesting exercise to find out estimate times of Eurasian arrival. The result is forewarned with reasonable precautions:

Since this model neglects migration, we expect our results to form a lower bound on the population divergence time, as similar levels of population divergence would require a longer separation in the presence of migration.

So at least this old:

Fig. 3 (edited to correct a color typo) - click to expand

Although these divergence time estimates may not be precise, as they do not adequately model ancient migration, they do suggest that the population divergence between the ancestral Maghrebi population and neighboring Mediterranean populations occurred at least 12,000 ya and indeed more likely predated even the Last Glacial Maximum.

It is interesting anyhow that the Fst distance to Europe are lower than to Arabia and that the window for a possible migration from Europe can well fit with the Oranian genesis c. 22,000 years ago, which I am pretty sure that is related with Iberian Gravetto-Solutrean: Oranian was back in the day called Iberomaurusian for a reason and, regardless of revisionisms, the Oranian dates for the West are quite older than those of the East - never mind that at least 25% of North African mtDNA (and maybe 10% of Y-DNA) is of European (and most likely Iberian) derivation and that European affinity remains apparent, distinct and important (specially in Algeria and North Morocco) even after North African specific components have become obvious and dominant.

So the old theory of migration from Iberia c. 22,000 years ago (maybe with some backmigration northwards as well) is not any colonial construct but something most probable, as indicate both archaeological and genetic data very consistently.

Less clear is whether there was a previous West Eurasian flow c. 40,000 years ago with the Dabban industries (so far only known in Libya, although unmistakably "Aurignacoid" in character). Genetically the main support for this first Eurasian backflow is mtDNA U6 (derived from Eurasian U), whose origin is probably in Morocco, where most of the basal diversity accumulates (and then around it, in Canary Islands and Iberia). 

It is not impossible that the lineage might have arrived, still as undefined U*, via Europe, however the structure of the autosomal DNA, as illustrated in this study or in my exercise from December, evidences that the North African specific components (excepted the "Aterian" one) are most akin to West Eurasia (by much). So there was probably a first migration from West Asia c. 40 Ka. ago and then an Iberian layer overlapped. 

This paper also suggests more recent migrations from Tropical Africa, although I am unsure if I can take their timeline conclusions at face value, specially regarding the East African component, that I imagine quite older (they suggest, table 1, just 25 generations ago, what I find most hard to believe for such a notable impact).

I would personally conclude that the North African genetic composition appears to be made up of:

1. A deep, quite diluted, 'Aterian' layer
2. A dominant North African specific layer of mostly West Eurasian roots
3. An Iberian or European layer (Oranian)
4. Maybe an East African (Capsian) layer (needs clarification but agrees with Y-DNA)
5. Maybe a lesser Arab layer and also maybe some recent Tropical African input

Caught in the act: lactose intolerant and lactose tolerant populations together but mostly unmixed in Chalcolithic Upper Ebro

There is a new paper on ancient DNA from the southernmost Basque Country that has found the oldest known lactose tolerance alleles in prehistoric Europe:

Theo S. Plantiga et al., Low prevalence of lactase persistence in Neolithic South-West Europe. European Journal of Human Genetics 2012. Pay per view.

Context

The samples studied are the same (in part) as those from Izagirre and de la Rúa 1999, specifically 19 individuals from San Juan Ante Porta Latinam (Araba) and 7 from Longar  (Navarre). In spite of both sites being inside Euskal Herria (Basque Country) as usually acknowledged, the are both very close to Logroño, capital of La Rioja autonomous region. I mention because this area of the Upper Ebro is at least somewhat distinct from the higher reaches of the core Basque Country and may not be representative of ancient (proto-)Basque genetics but rather of Ebro Valley populations.

It is easy to appreciate in genetic research as that of Adams 2008, that Aragon (I presume representative of the overall Ebro Valley) is markedly distinct from sub-Pyrenean neighbors like Basque Country or Catalonia, holding a much larger apportion of presumably Neolithic haplogroups of Transmediterranean origin (surely E, G, J and T, as well as maybe most of I), being more similar in this to Valencia, Ibiza or Western Iberia.

Paleo- and Epipaleolithic Basque Country

Similarly the Ebro Valley is a region of very early Neolithic settlement in which often no pre-Neolithic habitation is known to have existed. However the data I know for the Basque part of the Upper Ebro basin (X. Peñalver 1996), suggests an Epipaleolithic (epi-Magdalenian) settlement of most of Araba (but not the Ebro banks as such) and only the highland parts of Navarre (right). 

It is therefore only in the Neolithic and later on in the Chalcolithic (term used sometimes loosely to indicate the late part of the Neolithic, when social complexity increases, regardless of the presence of copper, gold or silver), when the Upper Ebro, including that within conventional Basque borders is colonized. 

These colonists may or not have been of aboriginal (proto-Basque) stock. In fact anthropometric estimates emphasize the presence of Gracile Mediterranean types in devastated La Hoya town, contrasting with the native Pyrenean type of apparent Paleolithic stock.

Chalcolithic and Early Bronze sites

Whatever the case, it is clear that the Upper Ebro valley is not the core of the Basque Country, located further north, but a border area which may have been colonized partly by people of exotic origins upon the arrival of Neolithic. Of course all this is open for discussion and further analysis of the available data. 

[See also: Wikipedia: Basque Prehistory].

Findings

Luckily several readers have sent me copies of the paper (you people are awesome, thanks), and even some ideas on what is most interesting (not always the most obvious).

The findings are detailed in table 3:

The most important finding is also the most obvious: the lactose tolerance allele (or more specifically rs4988235 in its T variant, as there are others less famous such alleles) is found at the oldest known site in Europe and that is (in spite of all my previous caveats) in the Basque Country. 

There is a similar aged site in Götland, Sweden (Mälstrom 2010), but the apportions are even lower (1/19 alleles or 1/10 persons had the CT combo). All other older of contemporary sites in Central Europe or nearby Occitania have yielded negative for what is nowadays a dominant allele in Western and Northern Europe. However there are many blanks: for example no Neolithic (never mind Paleolithic) British or Atlantic French or Portuguese samples have ever been tested for. In fact no Basque samples other than these either... so the question marks are still many.

The second finding is that the apportions are low, even if it is enough for lactose tolerance to kick in that a single T allele exists (classical Mendelian dominance), only 31% and 14% of the people sampled were lactose tolerant, meaning that (most probably) non-processed milk was rare in their diet. This is contradictory with the idea that the allele became common thanks to positive selection, after all these people had been herding livestock of various types for 2000-2500 years already (just in situ, i.e. not counting their likely ancestors in Italy, the Balcans or West Asia: add other 3000 or 4000 years maybe) and yet most were lactose intolerant (apparently). 

This is something that the authors also find surprising, pondering that maybe its frequency levels may have risen more recently just because of cultural pressure. What?! Drinking milk became fashionable and you were stoned to death if you found it nasty? Hard to believe, honestly, and if you did not die from not drinking milk, there is no (or extremely low) selective pressure we can take seriously.

Two populations?

But the most striking finding, not even mentioned by the authors is the following: there are almost no heterozygous individuals in these samples: with two exceptions in the San Juan APL  sample, people fall either to the CC (lactose intolerant) or the TT genotype. The percentage of heterozygous is much lower than that of the allele itself (11% vs. 26% in SJAPL and 0% vs. 14% in Longar).

I don't know how can you explain this but for me it is crying two populations that are still at the early stages of blending: one almost homogenously TT and the other almost homogenously CC. 

Otherwise, if the admixture process would be advanced, there would be more heterozygous (CT) individuals than TT homozygous ones. 

Which can be these two populations? Hard to say for sure but my natural intuition, knowing what I know about Basque Prehistory, is that the CC population would be made up of colonists of Mediterranean stock (possibly trans-Mediterranean: Balcanic, Italian or West Asian, as suggested by recent studies of mitochondrial DNA from Epicardial sites) who were quite obviously lacking the T allele altogether even if they were the ones to have the goats, sheep and cows initially.

These peoples left a legacy in the Ebro Valley and elsewhere in Iberia and Europe but they ultimately must have failed to become fully dominant and today their ancestry seems to be just a fraction of modern Western Europeans, seldom looking dominant even in the patrilineages. 

The TT population must therefore be some other. Which one? In this context I can only think of the local aborigines rooted in the Paleolithic cultures of the area and described by anthropometric usages as of Pyrenean stock (I think Heraus would say Dinaromorphic Atlanto-Mediterranean but that's too long - incidentally he just posted on the phenotypes of Arabako Errioxa). 

So this brings me to my fallback theory: the lactose tolerance allele is a mere fluke which became fixated randomly in pre-Neolithic populations just because (or maybe, speculatively, related to motherly lactation practices), eventually showing an unexpected use in drinking milk and eating desserts, what was nice for the development of Basque cuisine but mostly unrelated to survival. 

Being able to enjoy rice pudding (as I'm doing right now) is probably the most clear advantage of the T allele

See also: Leherensuge: Actual lactase persistance more common than genes predict.

Update (Jan 19): a scanned paper by Belén Márquez et al., describes in detail the burials of SJAPL and Longar, both looking rather militarized (mostly adult males, abundance of arrow points and arrow injuries...)

'Denisovan' admixture may actually be from H. erectus

H. erectus (fem.) reconstruction

Neanderfollia mentions today[cat] a new paper published at the moment only at arXiv that re-analyzes the data from Reich 2010 and related papers and concludes that the Denisovan admixture may well be original from Homo erectus, and not even individuals closely related to the Denisova cave specimens after all.

Peter J. Waddell, Jorge Ramos, and Xi Tan. Homo denisova, Correspondence Spectral Analysis, Finite Sites Reticulate Hierarchical Coalescent Models and the Ron Jeremy Hypothesis. Pre-publishing at arXiv (2012, freely accessible). 

This article shows how to fit reticulate finite and infinite sites sequence spectra to aligned data from five modern human genomes (San, Yoruba, French, Han and Papuan) plus two archaic humans (Denisovan and Neanderthal), to better infer demographic parameters. These include interbreeding between distinct lineages. Major improvements in the fit of the sequence spectrum are made with successively more complicated models. Findings include some evidence of a male biased gene flow from the Denisova lineage to Papuan ancestors and possibly even more archaic gene flow. It is unclear if there is evidence for more than one Neanderthal interbreeding, as the evidence suggesting this largely disappears when a finite sites model is fitted.

The paper needs some style revision but is otherwise very interesting, even if it's largely an exercise of statistical analysis, often resulting somewhat arid.

Some excerpts:

(...) one of the most surprising features of the planner NeighborNet model is that it does not reverse the positions of Neanderthal and Denisova, so that Papuan could have a unique split with the Denisovan (as Reich et al. 2010 suggest the Papuan lineage received ~5% of its genes from that lineage). As we will see later, the apparent reason for this would seem to be that the distance from Denisova to Chimp is more strongly underestimated than that from Denisova to Papuan. The underestimation of the Denisova to Chimp distance could be due to Denisova harboring some very archaic alleles, or it could be sequencing error.

(...)

The decrease in frequency of the DP pattern on X, particularly when compared to the NP pattern (which is near autosomal average frequency on X) suggests the possibility of asymmetric gene flow in this introgression event. If so, it would seem that this might be most readily explained by greater survival and reproduction of the offspring of Denisova males impregnating the modern human female ancestors of Papuans rather than the other way around.

(...)

Note the high frequency of the DNP pattern, which may be due to the Denisovan relatives that mixed not being closely related to the Denisovan sampled.

(...)

It seems tempting then to think that a model of three independent out of Africa lineages, with three independent mixings with the same population of Neanderthals (plus the independent Denisovan mixing event), would fit markedly better than the present model.

This last bit I find hard to believe, notably because we know of no Neanderthals ever existing in East Asia. In addition it would be a very odd coincidence that all three arrived to the approximate same amount of Neandrthal admixture. It seems much more likely that these smaller differences have been fixated as the three populations diverged in the Greater Eurasian expansion, after the OoA initial migration, when they probably incorporated the Neanderthal ancestry. (My two cents anyhow).

In any case, their conclusions follow:

Discussion

Overall, the fitting shows that a hierarchical structured coalescent model with at least two introgression events between archaic humans and out of Africa Moderns leads to a substantial increase in fit. Overall fit however, is still far far worse than could be expected. It seems that to improve the fit a number of factors may come into play. Firstly, there are too many private NH, NF and NP [Neanderthal-Han, -French and -Papuan] patterns. Secondly, the latter of these, NP, seems markedly less than the former two. Thirdly, there may be too many sequencing/alignment errors in the present data to confidently move towards refining so many parameters and the overall fit. The marked improvement in fit when a finite sites model is employed is consistent with this. One model that may do a better job of describing the data with fewer parameters is independent mixing of Neanderthal genes with Han and French, but to a nearly identical total degree. Also, lesser mixing of Neanderthal genes into Papuan, made up for by a larger proportion of archaic alleles in Papuans coming from the mixing with an archaic that is only slightly closer to Denisova than to Neanderthal. This would in turn suggest that the mixing with Neanderthals was not purely right out of Africa and it was not a single event. Instead, there may have been opportunity for European ancestors to pick up Neanderthal alleles, in the unknown part of Eurasia they existed in prior to moving into Europe, ditto and independently for the ancestors of the East Asians, while Papuan ancestors moved fairly rapidly through the zone of classical Neanderthals and picked up most of their archaic genes in the Indonesian region. The form of this ancestral population may have been about equally related to Neanderthals and Denisovans, but may also have had an appreciable proportion of even earlier (e.g., Homo erectus genes) in its genome. This last point comes up in a number of analyses including the resampled NeighborNet and the finite sites model, but confirmation is difficult as the rate of sequencing / assembly error could be having a similar effect.

For background in this blog and its antecessor Leherensuge (from oldest to most recent):

• Neanderthal gene flow found in modern humans (on Green 2010)
• Exploring the Neanderthal admixture episode (version 1)
• Denisova hominins, Neanderthals, Melanesians and so on... (on Reich 2010)
• Explaining 'Denisovan' and also 'Neanderthal' admixture: the simplest scenario (where I first hypothesize that H. erectus and also maybe a relative of Neanderthals like the Hathnora hominin, could be the actual culprits).
• Is X-DNA lineage Neanderthal?
• Denisovan admixture widespread beyond Wallace Line, non-existent elsewhere - but then:
• Minimal Denisovan admixture in SE Asians.