July 2, 2014

Altitude-adaption in Tibetans is "Denisovan-like"

It seems that archaic humans left a small but critical legacy among us:

Emilia Huerta Sánchez et al., Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 2014. Pay per viewLINK [doi:10.1038/nature13408] 
Abstract

As modern humans migrated out of Africa, they encountered many new environmental conditions, including greater temperature extremes, different pathogens and higher altitudes. These diverse environments are likely to have acted as agents of natural selection and to have led to local adaptations. One of the most celebrated examples in humans is the adaptation of Tibetans to the hypoxic environment of the high-altitude Tibetan plateau1, 2, 3. A hypoxia pathway gene, EPAS1, was previously identified as having the most extreme signature of positive selection in Tibetans4, 5, 6, 7, 8, 9, 10, and was shown to be associated with differences in haemoglobin concentration at high altitude. Re-sequencing the region around EPAS1 in 40 Tibetan and 40 Han individuals, we find that this gene has a highly unusual haplotype structure that can only be convincingly explained by introgression of DNA from Denisovan or Denisovan-related individuals into humans. Scanning a larger set of worldwide populations, we find that the selected haplotype is only found in Denisovans and in Tibetans, and at very low frequency among Han Chinese. Furthermore, the length of the haplotype, and the fact that it is not found in any other populations, makes it unlikely that the haplotype sharing between Tibetans and Denisovans was caused by incomplete ancestral lineage sorting rather than introgression. Our findings illustrate that admixture with other hominin species has provided genetic variation that helped humans to adapt to new environments.


Figure 3: A haplotype network based on the number of pairwise differences between the 40 most common haplotypes.
The haplotypes were defined from all the SNPs present in the combined 1000 Genomes and Tibetan samples: 515 SNPs in total within the 32.7-kb EPAS1 region. The Denisovan haplotypes were added to the set of the common haplotypes. The R software package pegas23 was used to generate the figure, using pairwise differences as distances. Each pie chart represents one unique haplotype, labelled with Roman numerals, and the radius of the pie chart is proportional to the log2(number of chromosomes with that haplotype) plus a minimum size so that it is easier to see the Denisovan haplotype. The sections in the pie provide the breakdown of the haplotype representation amongst populations. The width of the edges is proportional to the number of pairwise differences between the joined haplotypes; the thinnest edge represents a difference of one mutation. The legend shows all the possible haplotypes among these populations. The numbers (1, 9, 35 and 40) next to an edge (the line connecting two haplotypes) in the bottom right are the number of pairwise differences between the corresponding haplotypes. We added an edge afterwards between the Tibetan haplotype XXXIII and its closest non-Denisovan haplotype (XXI) to indicate its divergence from the other modern human groups. Extended Data Fig. 5a contains all the pairwise differences between the haplotypes presented in this figure. ASW, African Americans from the south western United States; CEU, Utah residents with northern and western European ancestry; GBR, British; FIN, Finnish; JPT, Japanese; LWK, Luhya; CHS, southern Han Chinese; CHB, Han Chinese from Beijing; MXL, Mexican; PUR, Puerto Rican; CLM, Colombian; TSI, Toscani; YRI, Yoruban. Where there is only one line within a pie chart, this indicates that only one population contains the haplotype.


See also this entry on Neanderthal introgression being subject to positive and negative selection.

Sino-Basque is not for real

Unmistakable evidence: beret-wearing Chinese!
(humorously borrowed from Zubia-Qiao blog,
which is about real Basque-China relations)
Linguistic speculation haunts us and today I stumbled on this paper, which has an interesting introduction but ends up claiming the extremely unlikely Sino-Caucasian family (including Basque and what-not):

Murray Gell-Mann, Ilia Peiros & George Starostin, Distant Language Relationships: The Current Perspective. Available at academia.eduLINK

I admit I have been skeptic of the Sino-Caucasian hypothesis since I tried once to learn some Chinese and was surprised of how little this language actually resembles Basque. Probably a random African or Australian language is not more different than Chinese is to Basque, or so I thought without having performed until now any formal test of the hypothesis.

There are a lot of reasons: the general skepticism of most linguists but also the lack of any apparent archaeological or meaningful genetic relationship since maybe 60 Ka ago (or, if Sino-Tibetan is related to Amerind and other Native American languages, since c. 45 Ka ago at the latest).

But the hypothesis continues to have some currency and today I finally decided to test it following the Swadesh-100 method suggested in the paper. The result:

Sino-Tibetan/Basque/English Swadesh-100 comparison (open office ODT format, similar to Excel - if anyone has a problem, please ask and I will upload an Excel version of it). 

Conclusion: Basque is not more related to Sino-Tibetan (either Mandarin or Burmese) than English is. If anything, the opposite is true, although the low level of plausible cognates for both languages (5-7%) seems merely stochastic noise, or maybe in some case wanderworts. Of course, the exact number of similar words (possible cognates) depends on one's permisivity but the pattern is so similar for the three possible pairings that, if there is any relationship at all, it must include English and therefore Indoeuropean.

Check it yourself, of course.

June 29, 2014

Pan-Homo split: 11-17 million years ago

Chimpanzee mutation rate is largely determined by fathers' age and, overall, implies a Pan-Homo divergence rate of ~13 million years (95% CI: 11-17 Ma), about double than usually assumed by conservative scholastic inertia.

Oliver Venn et al., Strong male bias drives germline mutation in chimpanzees. Science 2014. Pay per viewLINK [doi:10.1126/science.344.6189.1272]

cc Matthew Hoelscher
The focus of this study are the important differences between patrilineal and matrilineal mutation rate depending on the father's age among chimpanzees, notably more biased than among humans. However the resulting estimate for Pan-Homo divergence is not less important because it radically challenges the usual assumptions of 5-7 Ma, repeated once and again in molecular clock estimates, which are based on studies that are already quite obsolete.

In the studied captive population of Western chimpanzees 30 out of 35 mutations happened in the paternal lineage, and these increase with the father's age. No effect could be attributed to maternal age or familiar peculiarities.

Interestingly most of these patrilineal mutations happen near the telomeres, an effect not seen in female line mutations.

Owing to this gender bias, the mutation rate of the X chromosome among chimpanzees is 74% that of autosomal DNA (in humans: 85%). 

The gender bias in mutation rate and its differential with humans is attributed to differences in mating systems among great apes, with chimpanzees having the greatest competition among males, what is reflected in testicle size. They predict that gorillas (who experience less competition between males) will show less patrilineal mutation rate bias than humans and chimpanzees.

This is probably the more synthetic paragraph from the study:
Under a model in which the mutation rate increases linearly with parental age, the rate of neutral substitution is the ratio of the average number of mutations inherited per generation to the average parental age. We predict the neutral substitution rate to be ~0.46 × 10−9 per base pair (bp) per year in chimpanzees, compared to estimates in humans of ~0.51 × 10−9 bp−1 year−1 (9). These results are consistent with near-identical levels of lineage-specific sequence divergence (12) but surprising given the differences in paternal age effect. In the intersection of the autosomal genome accessible in this study and regions where human and chimpanzee genomes can be aligned with high confidence, the rate is slightly lower (0.45 × 10−9 bp−1 year−1) and the level of divergence is 1.2% (13), implying an average time to the most common ancestor of 13 million years, assuming uniformity of the mutation rate over this time (95% ETPI 11 to 17 million years; table S11).


13 million years of the hominid line

This is not at all the first study to highlight the extreme dubiousness of the usual scholastic assumptions regarding the Pan-Homo divergence, which taint so many genetic studies, turning their chronological estimates totally worthless.

In 2010, Wilkinson et al. estimated a Pan-Homo divergence rate of 8-10 Ma. In 2012 Langergraber et al. recalibrated previous studies getting a Pan-Homo divergence bracket of 6.78-13.45 Ma (fig.2), while the divergence from Gorilla would be significantly older: 8.31-20.0.

Fig. 1 from Langergraber 2012. Legend: Diagram illustrating the branching pattern and timing of the splits between humans, chimpanzees, bonobos, western gorillas, and eastern gorillas. The paler shading indicates the range of split times inferred in this study. Cartoon skulls indicate approximate age of the indicated fossil remains, but do not imply that these fossils were necessarily on those ancestral lineages or that entire crania actually exist for these forms.


A key fossil affecting this controversy is Sahelanthropus tchadiensis (Toumaï), which has been recently confirmed to be in the human line on several hardly questionable traits and is dated to c. 7 Ma.

A related debate is whether primates in general are much older than usually claimed and lived already in the Jurassic, something suggested by the already mentioned Wilkinson study and also by Heads 2010. Here a major issue is that mainline conservative estimates would have the ancestors of New World monkeys swimming (island hoping) to South America, something that those monkeys (and most other primates) simply will not do. The radiation of primates to South America and possibly also Madagascar is much better explained if these animals could just tree-hop, rather than island-hop to their destinations. However this would demand a radical revision of the usual age estimate for vertebrate radiation, what so far lacks fossil support (but lack of evidence is not evidence of lack, you know: fossil ages can only be taken as terminus ante quem dates and not absolute direct references).

But this is a side question, what really matters to us is that our ancestors split from the chimpanzee line c. 13 Ma (according to this study) and not after 8 Ma in any case (weighting all the evidence). This not just renders most "molecular clock" estimates useless and effectively false (wrong, erroneous, inadequate, misleading, junk, pseudoscientific...) but also help us to rethink our ancestral history in the African savannas since long before we became humans (Homo sp.)

Looking for some ecological context clues, I found this 1996 study by Jean Maley, which shows that Africa was largely humid in the early Miocene (smectite: evidence of water) but that it became increasingly arid towards the middle Miocene (kaolinite: evidence of sand). Up to this key ecological change of the Middle Miocene, the rainforest extended all the way to Egypt and East Africa. This kind of ecology allows for the common ancestor of African great apes to have arrived and first diverged in a jungle-dominated ecology and, later, for the speciation event leading to humans (bipedalism) to have happened as this once widespread jungle became scarcer, yielding to deserts and savanna.

Sahelanthropus (from fossilized.org)
It just makes all sense that the evolution of bipedalism was coincident with the vanishing of that originally widespread jungle environment whose dating is of approx. 13 Ma ago. However it must be said that the consolidation of the Sahara only happened much later, c. 7 Ma ago, already approaching the Pliocene.

Regardless of the exact split-time, a big question I have on hominid evolution is how on Earth did our small-brained and small-toothed precursors like Toumaï survive in the open savannas and grasslands without fire nor weapons. Even if they resorted to trees (isolated or in patches) for refuge, there were already felines of the saber-toothed family roaming in Africa and these big cats were no doubt be able  to climb on trees and in some cases they have been shown to predate on australopithecines. How could our precursors in the hominin line be able to face this menace without the advantage of speed (as ruminants have) or good defenses? Were their strong forelimbs, together with team action enough to confront the threat of predators? Did they use primitive weapons such as branches and stone throwing?

June 21, 2014

Claim of 13 Ma Pan-Homo split

[Update (Jun 29): new entry on this issue available].

[Update: the origin of this news is Venn 2014 but I could not find the mention of the 13 Ma split initially, as it was not something they underlined at all. I will write something as soon as possible. Thanks to all the people who helped my confused mind].

Live Science reports this week that the divergence of the human and chimpanzee lines may be as old as 13 million years. This is the oldest range of what Langergraber 2012 suggested (8-13 Ma in Fig.1, although in text they wrote "6.8-11.6 Ma") and older than the Wilkinson 2010 estimates (8-10 Ma), and would totally break all the usual "molecular clocks" so extremely abused in human genetics because it is double of the usual scholastic mindless parroting (5-7 Ma, which are necessarily too recent because they do not allow for Sahelanthropus' evolution and not even for bonobo evolution under the protection of the mighty Congo river).

Sadly the article includes no reference to the source, not even the name of the scientists involved, and I could not find it any reference online. For a moment I thought it could be another new study on gender bias in chimpanzee mutation rate (Venn et al. 2014 (ppv)) but after getting a copy it does not seem to have any direct relation.

So I would appreciate if someone can give me a lead on where this claim may come from.

Atapuerca skulls show "intermediate" features

H. heidelbergensis from Atapuerca
Cranium 5 "Miguelón"
(CC by José Manuel Benito)
This has been in the news all around this week with various emphasis, but probably the most important highlight is that, according to Atapuerca researchers, Homo heidelbergensis may well be a diffuse category with varied degrees of affinity to their Neanderthal successors.

J.L. Arsuaga et al., Neandertal roots: Cranial and chronological evidence from Sima de los Huesos. Science 2014. Pay per viewLINK [doi:10.1126/science.1253958]


Months ago, it was found that Atapuerca's H. heidelbergensis and the Denisova hominins formed a single mitochondrial DNA clade to the exclusion of Neanderthals and us. However Arsuaga et al. find that facial traits in the hominins of Sima de los Huesos seem to be already much closer to those of Neanderthals than to the local precursors. Instead other cranial traits such as brain size do not seem to change yet. 

There seems to be some uncertain speculation by the researchers on what this partial "neanderthalization" process in Atapuerca hominins could signify. 
"We think based on the morphology that the Sima people were part of the Neanderthal clade," Arsuaga said, "although not necessarily direct ancestors to the classic Neanderthals."

This, I guess, could indicate some sort of convergent evolution or be caused by some Neanderthal admixture on the male side.
 
Another important finding is that, contrasting with the similitude of the various specimens from Sima de los Huesos ("Chasm of the Bones", a key subsite of Atapuerca), other contemporary European specimens look quite different, suggesting that H. heidelbergensis was a quite diverse human species.

The study includes seven new specimens, as well as ten other previously reported ones.

Atlas of Inuit trails

An anthropological and geographical resource that may be of interest:


The atlas seems so far mostly limited to Nunavut and other parts of Northern Canada.

From the Introduction:
The Atlas provides a synoptic view (although certainly incomplete) of Inuit mobility and occupancy of Arctic waters, coasts and lands, including its icescapes, as documented in written historical records (maps of trails and place names). 

The documents that form the foundation of this Atlas consist of both published and unpublished accounts of Inuit engagement with cartography during the 19th and 20th centuries. All documents are held in public libraries or archives. The focus of the Atlas in this initial project is on material from the Eastern and Central Canadian Arctic. It is hoped that the Atlas can be further developed in subsequent phases to present material of other Inuit groups such as the Inupiat, Inuvialuit, and peoples of Nunatsiavut (Labrador) and Nunavik. 

Delineations of trails and place names play a critical role in documenting the Inuit spatial narratives about their homelands. To show where these trails lead and connect to other trails, the historical records used in making this Atlas are being relationally linked, referenced geospatially, and displayed on a base map.


Partial image of the atlas

June 15, 2014

Mexico's Native American diversity

Interesting study on Mexico's Native American diversity:

Andrés Moreno Estrada et al., The genetics of Mexico recapitulates Native American substructure and affects biomedical traits. Science 2014. Freely available with registrationLINK [doi:10.1126/science.1251688]
Abstract

Mexico harbors great cultural and ethnic diversity, yet fine-scale patterns of human genome-wide variation from this region remain largely uncharacterized. We studied genomic variation within Mexico from over 1000 individuals representing 20 indigenous and 11 mestizo populations. We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation. Some groups were as differentiated as Europeans are from East Asians. Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country. Furthermore, two independently phenotyped cohorts of Mexicans and Mexican Americans showed a significant association between subcontinental ancestry and lung function. Thus, accounting for fine-scale ancestry patterns is critical for medical and population genetic studies within Mexico, in Mexican-descent populations, and likely in many other populations worldwide.

Fig. 1-D
First of all it has to be highlighted that the sentence "some groups were as differentiated as Europeans are from East Asians" is a bit misleading. It refers to the raw FST parameter (Fixation Index) which in these cases is caused by extreme drift, product of isolation and small number endogamy.

Otherwise the Seris (Comcaac), who are the only population affected by the claim, are clearly derived not only from the same root as the rest of Native Americans but more specifically from the ancestor population of the Tarahumaras (Rarámuri), as fig.1-D reflects (right). 

The Seris are a small population of coastal Sonora who add up to less than one thousand people and have remained proudly distinct, not only from the colonial population but also from other fellow Native Americans. In spite of this long extreme isolation that makes the appear "as differentiated as Europeans are from East Asians", it is apparent that they must derive from the Uto-Aztecan populations of NW Mexico (and maybe also across the border). 

K=9 (fig. 2-B-part)
Other very isolated and heavily drifted populations are the Lacandon and Tojolabal Mayas. Again, in spite of their radical isolation, they seem related to other Mayas by origin. In these cases their languages are recognized as members of the Maya family, while the Seri language is considered an isolate. 

Actually the extreme FST scores only apply between these extremely drifted populations: FST{Seri-Lacandon}=0.136, FST{Seri-Tojolabal}=0.121. 

This reference is interesting because it explains how subcontinental levels of differentiation can happen in relatively short time if the founder populations are small and isolated for some 20 Ka. It is a warning call against reaching to too many conclusions based only on populations with a long history of isolation.

Otherwise the Seri FST scores are high but more normal: 0.087 to 0.096.  See table S-4 for further details. 

The tree is interesting also because it suggest a main division separating the Nahuas from the rest of the Uto-Aztecan meta-population (Saris included). The Nahuas, who approximately correspond to the the ancient Aztecs, are actually divided in several groups, which seem rather akin to their immediate neighbors and not so much among them or their linguistic relatives. 

This implies that, as the ancestors of the Nahuas migrated southwards, they assimilated so many locales that they largely lost their distinctiveness. In the ADMIXTURE graph to the left, we see that they do keep a variably small fraction of Uto-Aztecan affinity (not just them, also the Purepecha and Totonac, whose languages are distinct). 

Otherwise Mexican Natives have two main components at K=9: the main Mexican one (blue) and the Maya one (orange). The Maya division is also apparent in the tree. 

However it must be mentioned that the ADMIXTURE run available in the supp. materials (fig. S-10) reaches down to K=20, showing further differentiation between the various Mesoamerican populations dominated by the blue components at K=9. 

For comparison, in the European segment only the Basque component shows up as distinct in all those runs (since K=10). So we are talking about a fairly diverse population compared with European relative homogeneity.

Sequence of further components or distinctions showing at depths greater than K=9:
  • K=12: Tarahumara
  • K=14: Nahua-Purepecha-Totonac
  • K=15: Tepehuan
  • K=16: Purepecha + Jalisco-Nahua
  • K=18: Triqui
  • K=20 Totonac



Mestizo ancestries

An issue worth mentioning, particularly in relation to the so far unconfirmed but quite plausible Canarian origin of a large share of the "European" ancestry in the Caribbean region, is that the European ancestry of Mexicans seems essentially Iberian, as shown in fig. S-14:


I am anyhow awaiting for a sensible geneticist to address this question properly. When dealing with Mexicans and other Latin American populations of complex colonial ancestry, it seems quite apparent that so diverse European samples are in excess and that instead a North African control is surely missing instead.

A more regionalized approach to Iberian ancestry could also be interesting.

Regarding the Native American share of the ancestry, a finding of this study is that there is important regional variation: Yucatan and Campeche Mexicans have clearly strong Maya ancestry, while in Sonora it is something more like Tarahumara and in the core of Mexico it seems Nahua-like or from other "central" populations like the Zapotec or Totonac. See fig. 2A for details.

There is also very minor Tropical African ancestry across the board, somewhat more relevant in Guerrero and Veracruz, states which historically hosted the main port cities of New Spain and still have some small Afrodescendant populations.

June 14, 2014

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 accessLINK [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

June 11, 2014

China and Mexico go open access

In China the Academy of Science has made compulsory to deposit research in open access publications 12 months after the original publication in a pay per view one. In Mexico new legislation will affect in the same way to all studies partly financed by public funds. 

Via BMC newsletter.


June 9, 2014

The oldest know rope and spoon

Noticias de Prehistoria-Prehistoria al Día[es] mentions this week two quite impressive archaeological findings that illustrate the richness of the lives of our remote ancestors.

Ardales petrified rope
A petrified rope (right) was found in the cave of Ardales (Andalusia). The rope now transformed into stone by the same mechanism that forms stalactites was apparently tended to allow access to a remote section of the cave rich in rock art. 

Other findings are several fixed lamps created by the breaking of stalagmites, as well as several portable lamps found earlier in the research. In these lamps marrow or wax was burned. 

The rope has been indirectly dated to c. 30 Ka BP, what in Southern Iberia would still be the Aurignacian period.

Evidences of ropes of slightly more recent age are also known from Moravia (Gravettian) thanks to patterns left on their famous terracotta figurines.

The other not less spectacular finding comes from Russia, where an ivory spoon was found in Avdeevo cave, near Kursk. It belongs to the Gravettian period and is dated c. 23-22 Ka BP. 

The same site also provided a beautiful spatula almost identical to another one previously found in Kostenki, as well as other materials including a "Venus" figurine.

These findings illustrate the wealth of creativity displayed by the Paleolithic hunter-gatherers, not so different from ours after all.

Avdeevo ivory spoon