Most Africans do not have significant Eurasian admixture

This is major news: the authors of the study on the ancient East African genome of Mota have recanted their conclusions. In a correction note echoed by Nature they say:

Erratum'to'Gallego'Llorente'et'al.'2015'

The results presented in the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent“ were affected by a bioinformatics error. A script necessary to convert the input produced by samtools v0.1.19 to be compatible with PLINK was not run when merging the ancient genome, Mota, with the contemporary populations SNP panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with Neanderthals and Denisovans was not affected). When those positions were included, 255,922 SNP out of 256,540 from the contemporary reference panel could be called in Mota. The conclusion of a large migration into East Africa from Western Eurasia, and more precisely from a source genetically close to the early Neolithic farmers, is not affected. However, the geographic extent of the genetic impact of this migration was overestimated: the Western Eurasian backflow mostly affected East Africa and only a few SubUSaharan populations; the Yoruba and Mbuti do not show higher levels of Western Eurasian ancestry compared to Mota.

We thank Pontus Skoglund and David Reich for letting us know about this problem.

This makes much better sense admittedly. I strongly appreciate the willingness of Gallego, Jones et al. for publicly amending their wrong as quickly as possible. It's said that erring is human but correcting is only for the wise.

First African ancient nuclear DNA

Major update (Feb 12 2016): the authors have publicly corrected their conclusions: the alleged Eurasian admixture in Yoruba and Mbuti does not exist. See HERE for further details.

Mota cave

Whatever we may think of the conclusions (see below), this study is a most important breakthrough because it shows that ancient DNA can be obtained from remains preserved in hostile (hot) conditions, removing the technical barriers for research in these areas, which make up most of the inhabited world. The method, which relies in the vault-like conditions of the inner petrous earbone, was demonstrated earlier this year by Pinhasi et al. (open access) and is in itself a technical revolution in ancient DNA research.

M. Gallego Llorente, E.R. Jones et al., Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. Science 2015. Pay per view → LINK [doi:10.1126/science.aad2879]

Supplementary materials are free (as usual) and most information seems to be there anyhow.

Abstract

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.

Massive and late European Neolithic-like migration into Africa, even into the Bushmen, Pygmy and Hadza hunter-gatherers?! Well, that's the thesis and the authors seem to have some reasons to believe it. However I am a bit skeptic to say the least. 

The logic behind Llorente & Jones' conclusions is that, when replacing the "non-admixed African" baseline from the usual reference populations such as the Yoruba (a major SW Nigerian population) and Mbuti (Eastern Pygmies from the Ituri jungle of NE Congo) to this newly sequenced paleo-Ethiopian genome from Mota cave, all Africans appear more similar to West Eurasians, particularly to the reference ancient farmer "Stuttgart" (LBK) or his closest modern relatives: Sardinians. 

However this is untrue for some of the populations from the same region as Mota: most Ethiopian populations actually show a slight but significant decrease in their putative Eurasian ancestry (table S5). This is very intriguing, as is the main thesis of the study, and I have the impression that at least part of that appearance of European-like admixture may be explained by ancient internal African structure rather than true immigration. This possibility is not addressed in the study, so we will have to wait for counter-studies, be them professional or amateur. It would not be the first case where a pioneer study "finds" things that become less clear as new research is done, I am thinking of course on stuff like the problematic "ANE" component of Lazaridis 2014 or the extreme "Indoeuropean admixture" conclusions of Haak & Lazaridis 2015, which are much milder and clinal in other comparable studies.

So let's keep calm and wait for more data or improved analyses.

Fig. S6. The proportion of West Eurasian ancestry in modern eastern African populations. λYoruba,Druze (using Yoruba as the non-admixed reference and Druze as the source), estimated for individuals belonging to a number of Ethiopian populations.

Affinities

Mota seems to be most akin to modern Ari people of SW Ethiopia, who speak an Omotic language. He is also rather similar to the Sandawe of Southern Tanzania, who speak a distinct click language. These similitudes underline the importance that "tribal" nations have, among other reasons, for deciphering the ancient African demographic landscape.  

Fig. S5. PCA showing the relationship between Mota and contemporary Ethiopian populations. Components were loaded on contemporary Ethiopian populations using ~480k SNPs, with Mota projected on these dimensions.

His mtDNA haplogroup is L3x2a (table S3), described by Behar 2008 in Ethiopia and the Arabian peninsula (but most likely original from The Horn) and his Y-DNA one is E1b1 (table S4), a major African haplogroup, most likely original from the same Upper Nile region, with some offshoots in West Eurasia.

He did not carry any known allele for lactase persistance (table S13) but he was homozygous for three alleles that seem to confer altitude adaptation (resistance to hypoxia, table S14). 

He had brown eyes and dark or black hair, skin color determination was inconclusive (the matter is still ill-understood) but he did not carry any European alleles associated with lighter pigmentation, so most likely he was black (or, with more chromatic descriptive precision, brown).

Neanderthal admixture testing

This seems to be the detail that most strongly supports the thesis of the study: Mota is even less akin to Neanderthals than modern Africans. From article S11:

The two African genomes, Yoruba and Mbuti, also have slightly positive D values, indicating that they are slightly more similar to Neanderthal than Mota is. This result is likely driven by the West Eurasian component found in modern Africans.

However when we look at the raw data (table S9), we can see that, while the Yoruba Neanderthal admixture estimate is slightly larger than the error margin, the Mbuti one is markedly smaller, so we can still consider the latter to be effectively zero or at the very least negligible. 

This is potentially contradictory with the alleged 6-7% West Eurasian admixture that the study claims for Mbuti (table S5), which would be almost the same as that of Yorubas (7-8%), so I think that there is something not properly pondered and that, while Yorubas may have some (very minor?) West Eurasian admixture, the case for the Mbuti is very much suspect of false positive caused by confounding factors, such as ill understood ancient African diversity. 

Most strange is the case of Khoisan populations. While two of them (Nama and Khomani) do seem to have clear Eurasian admixture, as they stick up well above the average, several others (Xun, Juhoansi or GuiGhanaKgal) are very low when using Yoruba as reference and the tiny bit can be attributed to the pull effect caused by the mere fact that Yoruba and Khoisan are very different populations, which diverged (at least in the essentials) even before the Out-of-Africa migration took place. I strongly suspect that this confounding factor is also at play when comparing with Mota and even more strongly so, because Mota quite obviously lacks the later intra-African partial homogenization tendency caused by migrations such as the Nilotic or Bantu ones. 

Fig. S7. Maps showing the proportion of West Eurasian ancestry in African populations. The proportion of West Eurasian ancestry calculated using either (A), Druze. λMota,Druze, or (B), LBK, λMota,LBK, as a source, and Mota as the non-admixed African reference in both cases.

Early European farmers or...?

Sure, among the tested populations, Sardinians are the best apparent matches for the source of the alleged Eurasian admixture in Africa (tables S6 and S7). But next in line are Belorussians and Lithuanians, what is a bit perplexing, because in the European analyses these are two completely opposite poles along the PC1. Basques and Russians however are surprisingly bad matches, with French, Italian, Spaniards, etc. being in between. 

Among ancient populations, Stuttgart (LBK) appears as a good match when using a Yoruba reference but not so good when using a Mbuti one. Inversely, Lochsbour (Epi-Magdalenian) looks a very bad match when using Yoruba but a bit better when using Mbuti. As Mbuti seem still to be a more clear outgroup than Yoruba, I think that table S7 holds preference over S6. 

Hence I'd rather discard that the source of the apparent Eurasian admixture is LBK-like. However Sardinians (or a similar ancient population) are a better candidate. But what about Belorussians and Lithuanians, whose scores are also very high? Perplexing.

So basically I have all kind of doubts and I look forward to further research that may clarify them.

Sudan and South Sudan autosomal genetics

Quantity over quality series.

Begoña Dobon et al., The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape. Nature - Scientific Reports 2015. Open access → LINK [doi:10.1038/srep09996]

Abstract

East Africa is a strategic region to study human genetic diversity due to the presence of ethnically, linguistically, and geographically diverse populations. Here, we provide new insight into the genetic history of populations living in the Sudanese region of East Africa by analysing nine ethnic groups belonging to three African linguistic families: Niger-Kordofanian, Nilo-Saharan and Afro-Asiatic. A total of 500 individuals were genotyped for 200,000 single-nucleotide polymorphisms. Principal component analysis, clustering analysis using ADMIXTURE, FST statistics, and the three-population test were used to investigate the underlying genetic structure and ancestry of the different ethno-linguistic groups. Our analyses revealed a genetic component for Sudanese Nilo-Saharan speaking groups (Darfurians and part of Nuba populations) related to Nilotes of South Sudan, but not to other Sudanese populations or other sub-Saharan populations. Populations inhabiting the North of the region showed close genetic affinities with North Africa, with a component that could be remnant of North Africans before the migrations of Arabs from Arabia. In addition, we found very low genetic distances between populations in genes important for anti-malarial and anti-bacterial host defence, suggesting similar selective pressures on these genes and stressing the importance of considering functional pathways to understand the evolutionary history of populations.

Figure 3: ADMIXTURE results for the 14 populations.

Ancient inter-continental admixture in the Horn of Africa

A new and quite interesting study finds strong support for Upper Paleolithic (~ LSA) Eurasian inflows into the Horn of Africa and confirms that most of the populations of that region are in essence an ancient mix of West Eurasian and African ancestries.

Jason A. Hodgson et al., Early Back-to-Africa Migration into the Horn of Africa. PLoS Genetics 2014. Open access → LINK [doi:10.1371/journal.pgen.1004393]

Abstract

Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new data with published genome-wide genetic data from the HOA and a broad selection of surrounding populations. We used multidimensional scaling and ADMIXTURE methods in an exploratory data analysis to develop hypotheses on admixture and population structure in HOA populations. These analyses suggested that there might be distinct, differentiated African and non-African ancestries in the HOA. After partitioning the SNP data into African and non-African origin chromosome segments, we found support for a distinct African (Ethiopic) ancestry and a distinct non-African (Ethio-Somali) ancestry in HOA populations. The African Ethiopic ancestry is tightly restricted to HOA populations and likely represents an autochthonous HOA population. The non-African ancestry in the HOA, which is primarily attributed to a novel Ethio-Somali inferred ancestry component, is significantly differentiated from all neighboring non-African ancestries in North Africa, the Levant, and Arabia. The Ethio-Somali ancestry is found in all admixed HOA ethnic groups, shows little inter-individual variance within these ethnic groups, is estimated to have diverged from all other non-African ancestries by at least 23 ka, and does not carry the unique Arabian lactase persistence allele that arose about 4 ka. Taking into account published mitochondrial, Y chromosome, paleoclimate, and archaeological data, we find that the time of the Ethio-Somali back-to-Africa migration is most likely pre-agricultural.

The study makes three different formal admixture tests (f3, Adler and D-stat), as well as a Rolloff simulation, in order to confirm these findings. This part is quite technical and therefore I am not going to discuss it further. Feel free to explore the extensive supplemental materials. 

I will instead stop on what I know better, which is ADMIXTURE and FST distances, which are more visually amenable and ultimately tell the same story. 

Figure 2. Population structure of Horn of Africa populations in a broad context.
ADMIXTURE analysis reveals both well-established and novel ancestry components in HOA populations. We used a cross-validation procedure to estimate the best value for the parameter for the number of assigned ancestral populations (K) and found that values from 9 to 14 had the lowest and similar cross-validation errors (Figure S2). (A) The differences in inferred ancestry from K = 9–14 are most pronounced in the HOA for K = 10–12, where two ancestry components that are largely restricted to the HOA appear (the dark purple and dark green components). (B) Surface interpolation of the geographic distribution of eight inferred ancestry components that are relatively unchanging and common to the ADMIXTURE results from K = 10–12. (C) Individual ancestry estimation for HOA populations (with language groups indicated) and surface plots of the changing distributions of the Nilo-Saharan (light blue) and Arabian (brown) ancestry components for K = 10–12. At K = 11, a new HOA-specific ancestry component that we call Ethiopic appears (dark purple) and at K = 12 a second new ancestry component that we call Ethio-Somali (dark green) appears with its highest frequencies in the HOA.

Above we have the original presentation of ADMIXTURE results for K=10-12. It must be said that the cross validation score is lowest (optimal) for K=12 but that this value is only slightly smaller than those for K=9-14, which make a plateau (fig. S2). 

Therefore their use of K=10 and K=11 is justified, particularly because it is also interesting to turn off the old amalgamation reflected in the Ethiopic (Ari, Woloytta) and Ethio-Somali (Cushitic, Ethiopian Semitic) components, and that is done by using K=10 instead of the optimal K=12.

This issue is best perceived in the FST distances table (within text S1), which I include here with some convenient annotations:

The red-orange colored frames (as well as the red notes on the components) in the table above were added by me to better illustrate the meaning of these FST values:

• The red frames capture two groups of components with very low differences (<50): West Asia-Europe and West-East Africa.
• The dark orange frames indicate other two groups with quite low distances (<70): South-Central Asian and the West Eurasian core.
• The lighter orange frames indicate large clusters of middling distances (<125) of continental nature: Eurasian and African. 
• Intercontinental FST scores are systematically larger, for example European-West African is 176, while European East African ("Nilo-Saharan") is 172, only slightly smaller. 

K=12

It is quite apparent that there are three components that overflow these continental boundaries:

• The so-called Mahgrebi (North African) has some extra affinity with the Ethiopic (Omotic) component, and vice versa. These two components fall otherwise within my approximative continental boxes but they still show lower scores for all the other components of the other "box". This is consistent with their nature as Afro-Eurasian admixed components, each with its own proportions.
• The Ethio-Somali (Cushitic?) component is actually more intermediate than the previous ones: although its strongest affiliation is towards Eurasia and particularly with the North African and Arabian components, it also shows strong affinity with the core African components (East and West African, i.e. Nilo-Saharan and Niger-Congo). This is consistent with the other evidence in this study that reveals it as an ancient Afro-Asian mix.

I must mention here that some of the labels used by the authors are not at all the ones I would have chosen and this is particularly true re. the Nilo-Saharan (light blue) component, which peaks among the Sandawe (Aboriginal East Africans from Southern Tanzania, speaking a click language), the Anuak (Nilo-Saharan Ethiopians) and the Gumuz (other Ethiopians of quite dubious Nilo-Saharan linguistic affiliation). Hence I prefer to call it East African or East African 1. 

The authors conclude with the following remarks (emphasis mine):

We find that most of the non-African ancestry in the HOA can be assigned to a distinct non-African origin Ethio-Somali ancestry component, which is found at its highest frequencies in Cushitic and Semitic speaking HOA populations (Table 2, Figure 2). In addition to verifying that most HOA populations have substantial non-African ancestry, which is not controversial [11]–[14], [16], we argue that the non-African origin Ethio-Somali ancestry in the HOA is most likely pre-agricultural. In combination with the genomic evidence for a pre-agricultural back-to-Africa migration into North Africa [43], [61] and inference of pre-agricultural migrations in and out-of-Africa from mitochondrial and Y chromosome data [13], [32]–[37], [47], [99]–[102], these results contribute to a growing body of evidence for migrations of human populations in and out of Africa throughout prehistory [5]–[7] and suggests that human hunter-gatherer populations were much more dynamic than commonly assumed.

We close with a provisional linguistic hypothesis. The proto-Afro-Asiatic speakers are thought to have lived either in the area of the Levant or in east/northeast Africa [8], [107], [108]. Proponents of the Levantine origin of Afro-Asiatic tie the dispersal and differentiation of this language group to the development of agriculture in the Levant beginning around 12 ka [8], [109], [110]. In the African-origins model, the original diversification of the Afro-Asiatic languages is pre-agricultural, with the source population living in the central Nile valley, the African Red Sea hills, or the HOA [108], [111]. In this model, later diversification and expansion within particular Afro-Asiatic language groups may be associated with agricultural expansions and transmissions, but the deep diversification of the group is pre-agricultural. We hypothesize that a population with substantial Ethio-Somali ancestry could be the proto-Afro-Asiatic speakers. A later migration of a subset of this population back to the Levant before 6 ka would account for a Levantine origin of the Semitic languages [18] and the relatively even distribution of around 7% Ethio-Somali ancestry in all sampled Levantine populations (Table S6). Later migration from Arabia into the HOA beginning around 3 ka would explain the origin of the Ethiosemitic languages at this time [18], the presence of greater Arabian and Eurasian ancestry in the Semitic speaking populations of the HOA (Table 2, S6), and ROLLOFF/ALDER estimates of admixture in HOA populations between 1–5 ka (Table 1).

K=12 detail for a fraction of the Horn of Africa and distribution of the four main components

Technological revolution in African Acheulean some 800,000 years ago

Well, maybe the title is a bit of a hype but something like that seems to be the most relevant finding on the Acheulean of Konso (SNPP region, Ethiopia): that the technique stood the same for a million years and then, some 800,000 years ago, became more refined in which was apparently one of the first technological leaps of archaic Humankind. Specifically it is the edges of the handaxes (the archetypal Acheulean finding, which may have been more a knife of sorts than a true axe) which became more refined and apt for its cutting purpose.

Yoyas Beyene et al., The characteristics and chronology of the earliest Acheulean at Konso, Ethiopia. PNAS 2013. Open access → LINK [doi:10.1073/pnas.1221285110]

Abstract

The Acheulean technological tradition, characterized by a large (>10 cm) flake-based component, represents a significant technological advance over the Oldowan. Although stone tool assemblages attributed to the Acheulean have been reported from as early as circa 1.6–1.75 Ma, the characteristics of these earliest occurrences and comparisons with later assemblages have not been reported in detail. Here, we provide a newly established chronometric calibration for the Acheulean assemblages of the Konso Formation, southern Ethiopia, which span the time period ∼1.75 to <1.0 Ma. The earliest Konso Acheulean is chronologically indistinguishable from the assemblage recently published as the world’s earliest with an age of ∼1.75 Ma at Kokiselei, west of Lake Turkana, Kenya. This Konso assemblage is characterized by a combination of large picks and crude bifaces/unifaces made predominantly on large flake blanks. An increase in the number of flake scars was observed within the Konso Formation handaxe assemblages through time, but this was less so with picks. The Konso evidence suggests that both picks and handaxes were essential components of the Acheulean from its initial stages and that the two probably differed in function. The temporal refinement seen, especially in the handaxe forms at Konso, implies enhanced function through time, perhaps in processing carcasses with long and stable cutting edges. The documentation of the earliest Acheulean at ∼1.75 Ma in both northern Kenya and southern Ethiopia suggests that behavioral novelties were being established in a regional scale at that time, paralleling the emergence of Homo erectus-like hominid morphology.

Fig. 4. Handaxe refinement through time. Upper, dorsal; Lower, ventral.
From left to right, two each are shown from KGA6-A1 (∼1.75 Ma), KGA4-A2 (∼1.6 Ma), KGA12-A1 (∼1.25 Ma), and KGA20 (∼0.85 Ma). In each pair of handaxes from the respective sites, near-unifacial (left) and more extensively bifacial (right) examples are shown (except with the KGA20 handaxes, which are both well worked bifacially).

I am a bit intrigued by the all-covering work style of the last handaxes, which remind somewhat to the later MSA technology, which belongs already to Homo sapiens. Our species may have also evolved in that very area of the Nile Basin, with the oldest specimen known being from nearby Omo River.

Of course that there are hundreds of thousands of years in between and of course that the peculiar orography of the Rift Valley is susceptible of offering archaeological findings from old much more easily than other areas but still...

Other sources: Pileta, NBC News.



Update: much more than just the edges but a whole technological paradigm change:

I was not really appreciating the whole extent of the technological revolution implicit in these changes. I just took note (reading too fast, too many things to do) of the edge refinement but Va_Highlander has correctly called my attention on that it was a much more ample and complex change in the whole technology of stone flaking and not just the edges, maybe even a whole jump in our mental capacities:

In contradistinction to the >1.2-Ma assemblages, the younger ∼0.85-Ma Konso Acheulean is characterized by considerably refined handaxes. Some of these handaxes are refined to the extent that they would qualify as approaching “three-dimensional symmetry” (i.e., symmetric not only in plan view but also in cross-section form) (Fig. 4 and Fig. S2). Some suggest that manufacturing 3D symmetric tools is possible only with advanced mental imaging capacities and that such tools might have emerged in association with advanced spatial and navigational cognition, perhaps related to an enhanced mode of hunting adaptation. It has been pointed out that purposeful thinning of large bifacial tools is technologically difficult, even in modern human ethnographic settings. In modern humans, acquisition and transmission of such skills occur within a complex social context that enables sustained motivation during long-term (>5 y) practice and learning.
 
In light of the above information, it is of interest that our metric analysis shows that there may be a fundamental difference between the handaxe technologies of >1.2 and ∼0.85 Ma. Whereas refinement of handaxe shape did occur from ∼1.6 to ∼1.2 Ma, this refinement did not result in tool thinning and advanced 3D symmetry.

Ethiopian haploid genetics

Ethio Helix mentioned yesterday a doctoral thesis on Ethiopian haploid DNA:

Christopher Andrew Plaster, Variation in Y chromosome, mitochondrial DNA and labels of identity within Ethiopia. The Center of Genetic Anthropology, University College of London, 2012 (doctoral thesis) ··> LINK (PDF).

The study deals with the anthropology, ethnology and linguistics of the African state, and especially with the haploid genetics (although more in detail with the Y-DNA side of the matter than with mtDNA). It is very much worth reading for anyone interested on the anthropology and population genetics of Africa and in particular the Horn region.

Personally I find most interesting the fact that there seem to be some correlations between Y-DNA and mtDNA. The author mentions that there is such correlation in diversity but it seems apparent that there is some more than just that, as should be obvious for example in the following graphs:

Population codes are:

• AF Afar (Cushitic, Afar region: 2)
• AM Amhara (Semitic, Amhara region: 3)
• AN Anuak (Nilotic, Gambela: 6)
• ML Maale (Omotic, SPNN region: 10)
• OR Oromo (Cushitic, Oromia: 8)

What I have in mind is, first of all, that those populations who have the most Eurasian (F-derived) Y-DNA lineages also have the most Eurasian (N, M) mtDNA ones. However there is noticeably greater apportion of mtDNA from Eurasia than Y-DNA - and most of that excess corresponds to mtDNA M (all of it M1).

In a simplistic scenario in which one or several waves from Eurasia would be the only element to consider, we would expect similar apportions for male and female lineages or even noticeably more immigrant Y-DNA. This is not the case and therefore it is perplexing.

After some thoughts on the matter I realized that the situation is similar, mutatis mutandi, to the one of North Africa. This probably means that the cause of both anomalies can well be the same: a relatively recent (Epipaleolithic?) expansion of Afroasiatic-speaking peoples with mostly African male lineages (typically E1b1b-M215). But notice that in North Africa also J1 (ultimately from West Asia) appears to be also important in the Afroasiatic phenomenon, as it is in the Horn (and certainly in West Asia), making the situation even more complex for interpretation.

In this regard it is worth mentioning that haplotype networks from this study show that while the Amhara and Oromo J1 is intermingled and diverse, the Afar J1 forms a very tight cluster, strongly suggestive of an ancient founder effect.

Another such apparent correlation could be Y-DNA E1 and E1b1a7 with specific subclades (?) of mtDNA L0/L1 (probably L0) and L2. At least the apportions are almost identical among the Anuak (but not among other groups, hence why I suggest specific subclades to be determined).

It is a pity that no more fine detail was achieved with mtDNA, especially the more purely African part of it, i.e. L(xM,N). Much better detail is provided instead for the once-backmigrant M and N derived lineages (table 5.9), from which I highlight the following (only >5% shown):

• All M is M1 (overall: 10%, AM 17%, OR 13%, AF 9%, ML 6%)
• R0(xHV) reaches 11% among the Amhara (all R0: 15%)
• N1 reaches 7% among the Afar
• U(xK) reaches 6% among the Afar (all U: 9%)
• K reaches 6% among the Maale (all U: 9%)
• The Anuak seem the most purely African population among this selection with only 3% of M1 and 0% N. 

I would seem that even the Omotic, the most remote Afroasiatic branch according to linguists (some even consider it a distinct family), have some Eurasiatic genetic influence. However I'd say that this influence is at least largely pre-Neolithic and has been subject to deep reshaping by internal African dynamics as suggested above. Still Neolithic and even maybe post-Neolithic layers of West Eurasian deposition are also apparent in the structure - always in my understanding.

Update: 

Ethio Helix has updated with extra information not included in the thesis.  Notable is a graph with much greater detail on the Y-DNA haplogroup distribution.

The E1* block is now split between a number of E1b1b subclades and some important dose of E1b1c, which is the dominant lineage among the Maale (and hence maybe among other Omotic peoples). Among the E1b1b sublineages, the Afar are relatively dominated by E1b1b1e, while the Maale have an important bloc of E1b1b1c1 and the Oromo appear dominated by E1b1b1a1b.

The B bloc is also split in several subclades, all them only relevant among the Anuak (most of it B2a and most B2a within B2a1a.

It is also quite notable that some J(xJ1,J2) has been found among the Maale. For reference on this rare paragroup, I'll mention that another niche of J* is the nearby island of Socotra (74%, probably a verly local founder effect and specific lineage to be described) and there is also some J* reported among peninsular Arabs, some Turks, Greeks, Jews and a few others - but otherwise most Y-DNA J either belongs to J1 or J2.

Latest genetic news (links)

Anthropological and genetic news have been piling up in this strike journey. I'm not sure if I will be able to address all as they may deserve so I'm listing them here in very quick review.

My apologies because I meant that the "links" format would be over but if people overseas (and in some cases also in Europe) insist on working in the general strike journey and publishing things all around, all I can do is this (or risking not even doing anything at all).

Chimpanzee enterotype variation is just like ours. 

Even if our genomes have diverged the microscopic environments we host in our guts are almost exactly the same, with three different types depending exclusively on diet.

Andrew H. Moeller et al., Chimpanzees and humans harbour compositionally similar gut enterotypes. Nature Communications, 2012. Pay per view ··> LINK [doi:10.1038/ncomms2159]

Abstract

Microbes inhabiting the human gastrointestinal tract tend to adopt one of three characteristic community structures, called ‘enterotypes’, each of which is overrepresented by a distinct set of bacterial genera. Here we report that the gut microbiotae of chimpanzees also assort into enterotypes and that these chimpanzee enterotypes are compositionally analogous to those of humans. Through the analysis of longitudinal samples, we show that the microbial signatures of the enterotypes are stable over time, but that individual hosts switch between enterotypes over periods longer than a year. These results support the hypothesis that enterotypic variation was present in populations of great apes before the divergence of humans and chimpanzees.

A more detailed review can be found at John Hawks' Weblog.

Fig. 1 (a) Left chimpanzee enterotypes, right human ones

High altitude adaptions in Ethiopia

Research on Ethiopian genetic nuances with a Basque name as lead researcher:

Gorka Alkorta Aranburu et al., The genetic architecture of adaptations (sic) to high altitude in Ethiopia. Pre-pub at arXiv, 2012. Freely accessible ··> LINK [ref. code: arXiv:1211.3053 [q-bio.PE]]

Abstract

Although hypoxia is a major stress on physiological processes, several human populations have survived for millennia at high altitudes, suggesting that they have adapted to hypoxic conditions. This hypothesis was recently corroborated by studies of Tibetan highlanders, which showed that polymorphisms in candidate genes show signatures of natural selection as well as well-replicated association signals for variation in hemoglobin levels. We extended genomic analysis to two Ethiopian ethnic groups: Amhara and Oromo. For each ethnic group, we sampled low and high altitude residents, thus allowing genetic and phenotypic comparisons across altitudes and across ethnic groups. Genome-wide SNP genotype data were collected in these samples by using Illumina arrays. We find that variants associated with hemoglobin variation among Tibetans or other variants at the same loci do not influence the trait in Ethiopians. However, in the Amhara, SNP rs10803083 is associated with hemoglobin levels at genome-wide levels of significance. No significant genotype association was observed for oxygen saturation levels in either ethnic group. Approaches based on allele frequency divergence did not detect outliers in candidate hypoxia genes, but the most differentiated variants between high- and lowlanders have a clear role in pathogen defense. Interestingly, a significant excess of allele frequency divergence was consistently detected for genes involved in cell cycle control, DNA damage and repair, thus pointing to new pathways for high altitude adaptations. Finally, a comparison of CpG methylation levels between high- and lowlanders found several significant signals at individual genes in the Oromo. 

H/t: Haldane's Sieve. 

An extensive review can be found at Ethio Helix (where else?)

Pig and boar genomes and evolutionary history

Martien A.M. Groenen et al., Analyses of pig genomes provide insight into porcine demography and evolution. Nature 2012. Open access ··> LINK [doi:10.1038/nature11622]

Abstract

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

Fig. 3 - reconstructed/estimated demographic history of boars

Less obvious strategies in long term evolutionary co-adaption

Interesting read on how competition can cause the formation of deep evolutionary valleys or gorges from which it is most difficult to exit and are therefore evolutionarily stable.

Eric Chastain et al., Defensive complexity and the phylogenetic conservation of immune control. Pre-pub at arXiv, 2012. Freely accessible ··> LINK [ref code: arXiv:1211.2878 [q-bio.PE]]

Abstract

One strategy for winning a coevolutionary struggle is to evolve rapidly. Most of the literature on host-pathogen coevolution focuses on this phenomenon, and looks for consequent evidence of coevolutionary arms races. An alternative strategy, less often considered in the literature, is to deter rapid evolutionary change by the opponent. To study how this can be done, we construct an evolutionary game between a controller that must process information, and an adversary that can tamper with this information processing. In this game, a species can foil its antagonist by processing information in a way that is hard for the antagonist to manipulate. We show that the structure of the information processing system induces a fitness landscape on which the adversary population evolves. Complex processing logic can carve long, deep fitness valleys that slow adaptive evolution in the adversary population. We suggest that this type of defensive complexity on the part of the vertebrate adaptive immune system may be an important element of coevolutionary dynamics between pathogens and their vertebrate hosts. Furthermore, we cite evidence that the immune control logic is phylogenetically conserved in mammalian lineages. Thus our model of defensive complexity suggests a new hypothesis for the lower rates of evolution for immune control logic compared to other immune structures. 

H/t: Haldane's Sieve.

Genetics and psychology in relation to heroin use and abuse

Ting Li et al., Pathways to Age of Onset of Heroin Use: A Structural Model Approach Exploring the Relationship of the COMT Gene, Impulsivity and Childhood Trauma. PLoS ONE, 2012. Open access ··> LINK [doi:10.1371/journal.pone.0048735] 

Abstract

Background

The interaction of the association of dopamine genes, impulsivity and childhood trauma with substance abuse remains unclear.

Objectives

To clarify the impacts and the interactions of the Catechol -O-methyltransferase (COMT) gene, impulsivity and childhood trauma on the age of onset of heroin use among heroin dependent patients in China.

Methods

202 male and 248 female inpatients who meet DSM-IV criteria of heroin dependence were enrolled. Impulsivity and childhood trauma were measured using BIS-11 (Barratt Impulsiveness Scale-11) and ETISR-SF (Early Trauma Inventory Self Report-Short Form). The single nucleotide polymorphism (SNP) rs737866 on the COMT gene-which has previously been associated with heroin abuse, was genotyped using a DNA sequence detection system. Structural equations model was used to assess the interaction paths between these factors and the age of onset of heroin use.

Principal Findings

Chi-square test indicated the individuals with TT allele have earlier age of onset of heroin use than those with CT or CC allele. In the correlation analysis, the severity of childhood trauma was positively correlated to impulsive score, but both of them were negatively related to the age of onset of heroin use. In structure equation model, both the COMT gene and childhood trauma had impacts on the age of onset of heroin use directly or via impulsive personality.

Conclusions

Our findings indicated that the COMT gene, impulsive personality traits and childhood trauma experience were interacted to impact the age of onset of heroin use, which play a critical role in the development of heroin dependence. The impact of environmental factor was greater than the COMT gene in the development of heroin dependence.

The Nubian techno-complex of Dhofar: yet another evidence for an early migration out-of-Africa via Arabia

Jeffrey Rose and colleagues gift us with a beautifully written and delightfully detailed open access study on a culture of the Middle Paleolithic of Arabia: the Nubian techno-complex of Dhofar: 

Jeffrey I. Rose et al., The Nubian Complex of Dhofar, Oman: An African Middle Stone Age Industry in Southern Arabia. PLoS ONE 2011. Open access.

I strongly recommend reading this paper in full: it really deserves your attention.

The Nubian Complex: extension and origins

The Nubian techno-complex is a facies of the pan-African Middle Stone Age macro-culture (MSA for short), which is roughly equivalent in timeline to the Middle Paleolithic of Europe (and, as techno-culture, to Mousterian in this other context). A facies that is mostly concentrated in North Sudan and Upper Egypt (with the occasional Ethiopian site) and, now we get to know, in Dhofar (Oman).

Fig. 1 Nubian Complex occurrences

In Africa:

Late Nubian Complex assemblages have been found in stratigraphic succession overlying early Nubian Complex horizons at Sodmein Cave [11] and Taramsa Hill 1 [21] in Egypt; in both cases separated by a chronological hiatus. The early Nubian Complex roughly corresponds to early MIS 5, while numerical ages for the late Nubian Complex in northeast Africa fall in the latter half of MIS 5.

In Arabia:

For the time being, the apparent distribution of Nubian Levallois technology in Arabia is limited to the Nejd plateau and, perhaps, Hadramaut valley (Fig. 1). Archaeological surveys in central/northern Oman have not produced any evidence of Nubian Complex occupation [66], [68], nor have Nubian Complex occurrences yet been found in eastern [22], [69]–[71], central, or northern Arabia [72]–[74].

Fig. 10 Dhofar Nubian Complex' points

Note that the authors' concept of Nedj plateau does not correspond with that of Wikipedia, as they are obviously talking of the sites in highland Dhofar and not anywhere in Saudi Arabia (see map below).

The authors express their expectation that eventually other sites will be found within drainage systems along the western coast and hinterlands of central Arabia, linking Nubia with South Arabia. However it is also possible, I'd say, that the actual link is via the Horn of Africa, specially as Arabia has been quite extensively combed in recent years.

The Nubian techno-complex in Sudan appears to have evolved locally:

Taking into account its distinct, regionally-specific characteristics, Marks [2] notes that the Nubian Complex has no exogenous source and, therefore, probably derives from a local Nilotic tradition rooted in the late Middle Pleistocene (~200–128 ka). This supposition is supported by the early Nubian Complex assemblage at Sai Island, northern Sudan, which overlies a Lupemban occupation layer dated to between ~180 and 150 ka.

The oldest known Lupemban culture is dated to c. 300 Ka ago in Kenya and Tanzania.

The authors reject the presence of Nubian Complex tools claimed in the past for the Levant (Levantine Mousterian) and Persian Gulf (Jebel Barakah).

Previously to this work:

The first hint of the Nubian Complex extending into southern Arabia was documented by Inizan and Ortlieb [31], who illustrate three cores from Wadi Muqqah in western Hadramaut, Yemen, with Nubian Type 1 and Type 2 technological features. More recently, Crassard [32] presents a handful of Levallois point cores exhibiting Nubian Type 1 preparation from Wadi Wa'shah, central Hadramaut, Yemen.

Time frame and ecology: the wet MIS 5

The chronological reference of Marine Isotope Stage 5, time frame of  the Nubian Complex, corresponds to a warm period between c. 130 and 74 thousand years ago, and corresponds very roughly with the Abbassia Pluvial, when the arid region of the Sahara and Arabia was quite more welcoming. 

Fig. 3 Dhofar ecological zones and place names mentioned in text.

MIS 5 is divided in the following substages (figures are Ka ago and may vary a bit depending on source):

• MIS 5a - 84-74 (wet)
• MIS 5b - 92-84 (?)
• MIS 5c - 105-92 (wet)
• MIS 5d - 115-105 (?)
• MIS 5e - 130-115 (very wet and warm: Eemian interglacial)

MIS 5 was followed by MIS 4, a cold and dry period triggered by the Toba caldera explosion (supervolcano).

In what regards to Dhofar:

... the monsoon increased in intensity during three intervals within MIS 5. Among these humid episodes, the last interglacial (sub-stage 5e; 128–120 ka) appears to represent the most significant wet phase within the entire Late Pleistocene, with rainfall surpassing all subsequent pluvials [42], [43]. Later, less substantial humid episodes associated with sub-stages 5c (110–100 ka) and 5a (90–74 ka) are also attested to in the palaeoenvironmental record. Uncertainties remain concerning the extent to which the climate deteriorated in the intervening sub-stages 5d (120–110 ka) and 5b (100–90 ka).

The increased humidity provided water security to all the region and is also correlated with plant and animal migration from Africa, what the authors think should almost forcibly make humans participant in this overall biological outpouring. 

Out of Africa: the alternative routes

Dhofar mountains in monsoon season

The authors discard the Levantine route because of the techno-cultural isolation of the Shkul-Qafzeh group.

They acknowledge the conceptual debt to population genetics for unveiling the probable Arabian route Out of Africa, with particular mention to Behar 2008, who points to the possibility (that I have re-elaborated myself on my own means but on his data) of mtDNA L3'4'6 (and I'd say also L0) having left very indicative remnants in Arabia Peninsula. However they make unnecessary conceptual contortions in order to adapt archaeological knowledge to the molecular clock pseudo-science when it must be the other way around, if anything. No need.

In any case, and this is very important, they describe two different cultural groups in interglacial Arabia:

... we surmise that at least two technologically (hence culturally) differentiated groups were present at this time: Nubian Levallois in southern Arabia and centripetal preferential Levallois with bifacial tools in northern/eastern Arabia.

They also suggest that, after the arid MIS 4 parenthesis, South Arabia experienced another mildly wet period with the MIS 3 (since c. 60 Ka ago), which would have enabled:

... north-south demographic exchange between ~60–50 ka. South Arabian populations may have spread to the north at this time, taking with them a Nubian-derived Levallois technology based on elongated point production struck from bidirectional Levallois cores, which is notably the hallmark of the Middle-Upper Palaeolithic transition in the Levant [105], [106].

But the whole Persian Gulf and Arabian Sea area, not to mention East Asia, remains to be fit in (archaeologically speaking) if we are to understand this period's colonization of West Asia from the East (according to the genetic data).

See also:

In this blog:

• Some key archaeological papers on the 'coastal route' (on Fields 2007, Bailey 2009 and Rose 2010)
• Coastal route through Arabia 130,000 years ago confirmed? (on Armitage 2011)
• Middle Paleolithic of Nefud (Arabia) (on Petraglia 2011)
• The various options for the migration out of Africa (a review of all the former)

In external sites:

• R.C. Walter 2000, Early human occupation of the Red Sea coast of Eritrea during the last interglacial (Nature - ppv)
• P. van Peer 2003, The Early to Middle Stone Age Transition and the Emergence of Modern Human Behaviour at site 8-B-11, Sai Island, Sudan (PDF)
• Ghanim Wahida 2009, A Middle Paleolithic Assemblage from Jebel Barakah, Coastal Abu Dhabi Emirate (PDF)
• M. Petraglia 2010, Out of Africa: new hypothesis and evidence for the dispersal of Homo sapiens along the Indian Ocean rim (scribd)

Update (Jan 11): I have received a copy of a related paper dealing with the relations of Hadramaut tools in the context of global Levallois technique. It is however too technical and inconclusive for me to discuss separately. Yet I do not see it being published anywhere online (PPV or open source or whatever), so I am just uploading it online (for a year) so you can download and read it yourself:

Rémy Crassard and Céline Thiébaut, Levallois points production from eastern Yemen and some comparisons with assemblages from East-Africa, Europe and the Levant.

Many interesting short news

Partly because of the arrival of the Archaeo News bulletin but also because of mere randomness, it seems to me, a lot of more or less interesting news items are accumulating. In most cases I lack the information to deal with them in any greater depth but are still interesting to read about:


Genetics

Study suggests that the populations leading to modern Africans and Non-Africans did keep mixing for some 40,000 years before a Non-Africans suffered a severe bottleneck and became truly separated. This period of early divergence with interaction could have begun c. 120,000 or 100,000 years ago and would have ended c. 80-60 Ka ago. It could add support to the idea that Toba explosion caused a bottleneck. I'd like to write more about this but I have no access to the paper. -> Science Daily, -> Nature (PPV).

Inheritable epigenetics confirmed: may explain how living beings of all sorts adapt to changing conditions without need to alter their genetic backbone (DNA). -> Science Daily.


Human evolution

Chimpanzee brains do not shrink with age. Unlike humans, chimpanzee do not suffer the array of symptoms we loosely call senility, this may be therefore a hidden cost of having such large brains and living for so long. -> Science News.



Archaeology

Heacham burial

Magdalenian Age erotic art found in Bavaria (Germany). The unusual rock art was found near Bamberg and are believed to be c. 12,000 years old. It seems that the natural shapes in thecave may have inspired the ancient artists. -> news.com.au (no images provided).

Epipaleolithic open air cemetery found in Somerset (England). It is dated to c. 10,000 years ago. -> BBC.

England: Sheffield 6000 BCE: people lived continuously at nearby Whirlow Hall Farm since the Epipaleolithic and into the Iron Age. -> The Star. 

5000 years-old skeleton unearthed in Aosta Valley (Italy). The woman has been nicknamed Lady of Introd and was more or less contemporary of Ötzi the iceman, found frozen in Tyrol years ago. -> Archaeo News.

Tall el-Hammam pottery

And more England findings: burial of two women with amber beads found in Yorkshire, near Heacham, and dated to c. 2500 BCE (late Neolithic by British chronology, Chalcolithic by pan-European standards). -> EDP24.

Egyptian Old Kingdom may have succumbed to drought, suggests geological survey at Lake Tana (Ethiopia) at the source of the Blue Nile (the main contributor to the Nile in volume and the responsible of seasonal floods). -> PhysOrg.

Bronze and Iron Age city unearthed in Jordan, NE of the Dead Sea (near modern Kafrein, just across the Jordan river from Jerico). -> Tall el-Hammam (dig site), -> Popular Archaeology.