Out of Egypt or Out of Ethiopia?

I am skeptical that once you remove non-African ancestry from Egyptians (even if you were able to do so perfectly), what you are left with is indigenous Northeastern Africans, the direct descendants of people who left Africa tens of thousands of years ago.

For one thing, Egypt has not only experienced gene flow from Europe and the Middle East, but also from elsewhere in Africa, more recently because of enslaved black Africans.

For another, even if you perfectly identified and removed both Eurasian and African non-native influences on the Egyptian population, you're left with some kind of indigenous northeastern African. But, did such a population with long-term continuity exist in Egypt since Out-of-Africa? The Eurasian experience (where ancient DNA falsifies continuity left and right even in a 1/10th of the OOA time scale) makes me doubt this. The Nile may have facilitated gene flow in a north-south direction, and the relatively recent emergence of the Sahara desert may very well have pumped populations into Egypt.


AJHG DOI: http://dx.doi.org/10.1016/j.ajhg.2015.04.019

Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians

Luca Pagani et al.

The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt.

Link

An archaeological scenario for Out of Arabia

Jeffrey Rose and Anthony Marks have a preprint in which he details an archaeological scenario for the emergence of the Emiran (arguably the best candidate for the ur-Upper Paleolithic at the moment) from Arabian progenitors who themselves had Northeast African Nubian Levallois progenitors. I proposed Out of Arabia a few years ago and followed research suggestive of such a trajectory of modern humans in various posts under the Out of Arabia label.

In a nutshell, it seems to me that the 50kya OoAfrica model is wrong, falsified by (i) the dating of Neandertal adixture (which precedes it and could only have happened outside of Africa), (ii) the dating of human mtDNA and NRY trees in numerous papers that show a split that precedes 50kya. This in itself proves that the Upper Paleolithic (which is attested in the post-50kya period and rapidly spreads across Eurasia in a genetic Big Bang of expansion leading to the full disappearance of Neandertals by ~40kya) must have local Eurasian origins rather than being an import from Africa.

If UP is not linked to the Out-of-Africa event, then two questions arise: (i) how did the UP arise in Eurasia, and (ii) when did the Out-of-Africa event take place? The increasing adoption of a "slow mutation rate", the discovery of a potential ~100kya layer of ancestry separating Europeans from East Asians, and, on the archaeology side, the proliferation of evidence against the "coastal migration route" all hint in OoAfrica taking place much earlier than the UP revolution in answer to question (ii).  Indeed, one of the few stumbling blocks of a much earlier Out-of-Africa (the date of L3~70kya) may actually be falling, if it turns out that African L3 is nested within Eurasian M+N and not vice versa. The new preprint by Rose snf Marks helps answer question (i) by proposing an archaeological scenario that derives the UP of the Levant from the MP of Arabia.

From the paper:

In sum, the tool assemblages of the early Emiran include a combination of both classic UP tool types and MP Levallois points; it cannot be accurately characterized as fully UP, rather, an amalgamation of MP and UP forms. Viewed solely within a Levantine context, the technological and typological patterning of the early Emiran might suggest it derived from local innovation without significant external demographic input. 

... 

So, with no clear cut antecedents in the Levant, do the three Emiran technological traits that have no deep Levantine ancestry (i.e., bidirectional core preparation, the use of cresting, and the presence of lateral modification on Levallois points), have  demonstrable origins elsewhere? Conversely, do those deeply rooted Levantine characteristics of the Emiran (i.e., elongated Levallois point production and UP tool  manufacture) have comparable analogues in adjacent areas? 

...  

Given these technological and typological considerations, we find no direct relationship between any northeast African MIS 5 industry and the early Emiran. The African data do suggest that the Emiran preferential bidirectional Levallois point production strategy ultimately arose in northeast Africa during late MIS 6. This reduction strategy became increasingly widespread during MIS 5, where it spread as far south as the Ethiopian Rift and east into the Arabian Peninsula. This wide distribution suggests extensive cultural contact, either direct or indirect, along the Nile Valley and across the Red Sea during the Last Interglacial, when climatic conditions were optimal. 

...  

By MIS 5.3 (~ 100 ka), perhaps, even as early as the Last Interglacial, the African Nubian Complex was widespread in Arabia, from the Yemeni Hadramawt to the eastern edge of the Nejd Plateau in southern Oman. Additional manifestations of this technocomplex have been found in the Rub' al Khali, central Saudi Arabia, and the Al Jawf basin of northern Saudi Arabia, less than 300 km southeast of ‘Ain Difla. Given the Nilotic origin of the Nubian Complex, its presence in Arabia may be firmly understood as a huntergatherer range expansion out of northeast Africa.  

...  

The techno-typological patterns we have observed point to an origin of the Emiran that was neither wholly rooted in the Levant nor the result of a complete demographic replacement from groups expanding out of Africa; rather, the Emiran combines elements of the Nubian Levallois system with typological elements from the southern Levantine Mousterian. This scenario envisions a zone stretching across the interface of northwestern Arabia and the southern Levant, where the territories of Levantine and Arabian huntergatherer populations overlapped during MIS 5. Bilateral exchange over time resulted in the incorporation of an Afro-Arabian core reduction strategy with a Levantine toolmaking tradition that extends back to the Early Mousterian. 

...  

African Nubian Complex toolmakers, at least, were modern humans. AMH specimens have been documented in North Africa from 150 ka onward (Smith et al., 2007; Hublin and McPherron, 2012), while no other species has yet been found there. An AMH child burial was excavated from an extraction pit associated with Activity Phase III at Taramsa Hill 1 (Vermeersch et al., 1998; Van Peer et al., 2010), with a terminus post quem of ca. 70 ka. Given the technological similarity of the Classic Dhofar Nubian and the Late Nubian Complex of the Middle Nile Valley in Egypt, as well as the fact that there is no evidence for prior MP human occupation in southern Oman, it is reasonable to associate the distribution of Nubian Complex sites with a population of AMHs spread across northeast Africa and the Arabian Peninsula. The presence of Nubian Levallois technology in southern Arabia and the Horn of Africa (Clark, 1954; Kurashina, 1978; Clark, 1988; Beyin, 2013), as well as northern Arabia and in the Red Sea hills of Egypt, suggests that early human groups traveled to and from Africa via both the Arabian and Levantine Corridors.

It is unfortunate that Arabia is so poor (to wholly deficient?) in ancient human remains from this critical period. Nonetheless, it makes sense that if modern humans were present in Northeast Africa in association with Nubian Complex tools, they would be the ones who carried them to Arabia. The presence of AMH in the Levant (associated with Mousterian tools) was often dismissed until recently as the Out-of-Africa that failed, partly because the Shkul/Qafzeh hominins were the only pre-UP modern humans in Eurasia (making their extinction plausible) and partly because of the widespread view that Out-of-Africa happened ~70-50kya (which by definition would imply that the Mount Carmel hominins weren't the Out-of-Africa.

However, if AMH were also present in Arabia during the MP it is much more difficult to argue for extinction of Eurasian modern humans and later replacement by a "late" Out-of-Africa event: this would imply that both the Levantine and Arabian humans would disappear. Moreover, the genetics no longer requires a late Out-of-Africa event and the UP is no longer plausibly concurrent with the OoAfrica event. In short, a quite simple explanation is that one group of AMH (from Arabia) mixed with another group of AMH (from the Levant) and the UP arose in this population. The latter group (from the Levant) lived in proximity to Neandertals and thus the evidence for Neandertal admixture in non-Africans is easily explained (no need to invoke unattested Neandertals admixing with "coastal route" migrating humans).

"Out of Arabia" and the Middle-Upper Palaeolithic transition in the southern Levant 

Jeffrey I. Rose, Anthony E. Marks

Beginning some 50 thousand years ago, a technological transition spread across the Near East and into Eurasia, in the most general terms characterized by a shift from preferential, prepared core reduction systems to the serial production of elongated points via opposed platform cores. The earliest known occurrence of such a technological shift is the Emiran Industry, whose earliest manifestations are found in the southern Levant. The cultural and demographic source(s) of this industry, however, remain unresolved. Looking to archaeogenetic research, the emerging picture indicates a major dispersal of our species out of Africa between 100 and 50 thousand years ago. Ancient DNA evidence points to low levels of admixture between Neanderthal and these pioneering modern human populations, which some suggest occurred in the Near East between 60 and 40 thousand years ago. These propositions underscore the significance of the Emiran and beg a reassessment of its origins. In this paper, we ask whether the Emiran was a local development, a cultural/demographic replacement, or the fusion of indigenous and exogenous lithic traditions. Our analysis considers the techno-typological features of the early Emiran in relation to late Middle Palaeolithic and contemporaneous assemblages from adjacent territories in Northeast Africa and the Arabian Peninsula, in order to identify overlapping cultural features and potential antecedents. Parsimonious with the archaeogenetic scenario of admixture, the Emiran seems to represent a fusion of local southern Levantine Mousterian typological elements with the Afro-Arabian Nubian Levallois reduction strategy. We conclude that the Emiran is primarily rooted in the Early Nubian Complex of the Nile Valley, which spread into the Arabian Peninsula during the Last Interglacial and developed at the interface of these two contextual areas between 100 and 50 thousand years ago.

Link

Recent origin of North African populations

This makes sense since North Africans are so close (phenotypically) to West Eurasians that it makes sense that they cannot have been isolated from them for very long, i.e., since Out-of-Africa.

PLoS ONE 8(11): e80293. doi:10.1371/journal.pone.0080293

Genome-Wide and Paternal Diversity Reveal a Recent Origin of Human Populations in North Africa

Karima Fadhlaoui-Zid, Marc Haber et al.

The geostrategic location of North Africa as a crossroad between three continents and as a stepping-stone outside Africa has evoked anthropological and genetic interest in this region. Numerous studies have described the genetic landscape of the human population in North Africa employing paternal, maternal, and biparental molecular markers. However, information from these markers which have different inheritance patterns has been mostly assessed independently, resulting in an incomplete description of the region. In this study, we analyze uniparental and genome-wide markers examining similarities or contrasts in the results and consequently provide a comprehensive description of the evolutionary history of North Africa populations. Our results show that both males and females in North Africa underwent a similar admixture history with slight differences in the proportions of admixture components. Consequently, genome-wide diversity show similar patterns with admixture tests suggesting North Africans are a mixture of ancestral populations related to current Africans and Eurasians with more affinity towards the out-of-Africa populations than to sub-Saharan Africans. We estimate from the paternal lineages that most North Africans emerged ~15,000 years ago during the last glacial warming and that population splits started after the desiccation of the Sahara. Although most North Africans share a common admixture history, the Tunisian Berbers show long periods of genetic isolation and appear to have diverged from surrounding populations without subsequent mixture. On the other hand, continuous gene flow from the Middle East made Egyptians genetically closer to Eurasians than to other North Africans. We show that genetic diversity of today's North Africans mostly captures patterns from migrations post Last Glacial Maximum and therefore may be insufficient to inform on the initial population of the region during the Middle Paleolithic period.

Link

A chronology of ancient Egypt

PNAS doi: 10.1098/rspa.2013.0395
An absolute chronology for early Egypt using radiocarbon dating and Bayesian statistical modelling

Michael Dee et al.

The Egyptian state was formed prior to the existence of verifiable historical records. Conventional dates for its formation are based on the relative ordering of artefacts. This approach is no longer considered sufficient for cogent historical analysis. Here, we produce an absolute chronology for Early Egypt by combining radiocarbon and archaeological evidence within a Bayesian paradigm. Our data cover the full trajectory of Egyptian state formation and indicate that the process occurred more rapidly than previously thought. We provide a timeline for the First Dynasty of Egypt of generational-scale resolution that concurs with prevailing archaeological analysis and produce a chronometric date for the foundation of Egypt that distinguishes between historical estimates.

Link

Stable isotopes and Nubian/Egyptian relationships

Wikipedia on Tombos site:

Tombos in an archaeological site in Northern Sudan. The village of Tombos was located at the third cataract of the Nile, not far from Kerma near the present Karmah. An important granite quarry was located here in the Pharaonic era. Its stone was used mostly to build statues and buildings between the river delta and the southern regions of the kingdom. A statue to the Pharaoh Taharqa, abandoned for over 2700 years, contains inscriptions. About 3000 years ago, there were pyramids dedicated to ten noble Egyptians. 

In 2000, several discoveries were made by the archaeologist, Professor Stuart Tyson Smith of the University of California, Santa Barbara. Smith and his team discovered the remains of a pyramid more than 3,500 years old, and the buried remains of an Egyptian colonial administrator named Siamun and his wife, Wernu. The two mummies were intact, and were buried with Ushabti figurines, a boomerang, and painted Mycenaean terracotta.[1] The burial chamber includes a series of rooms, some plundered by thieves, while others were undisturbed in whole or in part. Also, an epigraphic survey by the British Museum uncovered pharaonic rock-inscriptions.[2]

Might be interesting to look at DNA from remains from the Tombos site, both the ones mentioned in Wikipedia and the likely Egyptian immigrants mentioned in the following article.


Am J Phys Anthropol DOI: 10.1002/ajpa.22235

Strontium isotope (87Sr/86Sr) variability in the Nile Valley: Identifying residential mobility during ancient Egyptian and Nubian sociopolitical changes in the New Kingdom and Napatan periods

Michele R. Buzon, Antonio Simonetti

As a successful technique for identifying residential mobility in other areas, this study investigates the feasibility of using 87Sr/86Sr analysis to track the movements of the ancient peoples of Egypt and Nubia in the Nile Valley, who interacted via trade, warfare, and political occupations over millennia. Dental enamel from faunal remains is used to examine variability in strontium sources in seven regional sites; human enamel samples are analyzed from eight Nile Valley sites in order to trace human movements. The faunal samples show a wide range of 87Sr/86Sr values demonstrating that some animals were raised in a variety of locales. The results of the human samples reveal overlap in 87Sr/86Sr values between Egyptian and Nubian sites; however, Egyptian 87Sr/86Sr values (mean/median [0.70777], sd [0.00027]) are statistically higher than the Nubian 87Sr/86Sr values (mean [0.70762], median [0.70757], sd [0.00036], suggesting that it is possible to identify if immigrant Egyptians were present at Nubian sites. Samples examined from the site of Tombos provide important information regarding the sociopolitical activities during the New Kingdom and Napatan periods. Based on a newly established local 87Sr/86Sr range, human values, and bioarchaeological evidence, this study confirms the preliminary idea that immigrants, likely from Egypt, were present during the Egyptian New Kingdom occupation of Nubia. In the subsequent Napatan period when Nubia ruled Egypt as the 25th Dynasty, 87Sr/86Sr values are statistically different from the New Kingdom component and indicate that only locals were present at Tombos during this developmental time. 

Link

Y chromosome of Ramesses III

From the paper:

Genetic kinship analyses revealed identical haplotypes in both mummies (table 1⇓); using the Whit Athey’s haplogroup predictor, we determined the Y chromosomal haplogroup E1b1a.

Ethiohelix has more.
Added in my compendium of ancient Y chromosome studies.

BMJ 2012; 345 doi: http://dx.doi.org/10.1136/bmj.e8268

Revisiting the harem conspiracy and death of Ramesses III: anthropological, forensic, radiological, and genetic study

Abstract

Objective To investigate the true character of the harem conspiracy described in the Judicial Papyrus of Turin and determine whether Ramesses III was indeed killed.

Design Anthropological, forensic, radiological, and genetic study of the mummies of Ramesses III and unknown man E, found together and taken from the 20th dynasty of ancient Egypt (circa 1190-1070 BC).

Results Computed tomography scans revealed a deep cut in Ramesses III’s throat, probably made by a sharp knife. During the mummification process, a Horus eye amulet was inserted in the wound for healing purposes, and the neck was covered by a collar of thick linen layers. Forensic examination of unknown man E showed compressed skin folds around his neck and a thoracic inflation. Unknown man E also had an unusual mummification procedure. According to genetic analyses, both mummies had identical haplotypes of the Y chromosome and a common male lineage.

Conclusions This study suggests that Ramesses III was murdered during the harem conspiracy by the cutting of his throat. Unknown man E is a possible candidate as Ramesses III’s son Pentawere.

Link

Instantaneous vs. continuous admixture dynamics (Jin et al. 2012)

A new paper in AJHG discusses the distribution of chromosomal segments of distinct ancestry (CSDAs) under three different models of admixture dynamics (left). In the hybrid isolation (HI) model, admixture is instantaneous and results in a hybrid population that evolves with drift and recombination only. In the gradual admixture (GA) model, the hybrid population continues to receive admixture from the unadmixed parental populations. Finally, in the continuous gene flow model (CGF), one of the populations becomes admixed while the other continues to exist unadmixed and to contribute to the admixed one.

In practical terms, the HI model results in the diminution of CSDA length due to recombination over time, and at "present" there is a paucity of long CSDAs. In the GA model there are more long CSDAs for both populations, while in the CGF model there is an asymmetry in the CSDAs donated by Pop1 and Pop2, with those from the "donor" population being longer (because fresh "long" segments are added in every generation).

The conclusions of the paper regarding some particular admixture cases are also interesting. For African Americans:

Although the actual population admixture of African Americans might be more complex than what our simulation suggested, the CGF1 model setting at 14 generations was found to be reasonably  epresentative, capturing the main pattern of the population admixture dynamics.

The CGF1 model has Africans as recipients and Europeans as donors. This makes sense, since African Americans are descended from slaves who were transported to the New World, with the slave trade ending centuries ago, hence there was mostly no replenishment of the AA population with fresh African-origin individuals. On the other hand, European Americans, both due to social dynamics and their numerical majority continued to exist as a distinct population that contributed to the AA population.

I should mention that according to HAPMIX, the admixture time was 7 generations, with is close to the 6 +/- 1 generations inferred by rolloff analysis by Moorjani et al. So, in this case this admixture time appears to be an "average" of a continuing process of admixture that began 14 generations ago.

Onto Mexicans:

In short, the GA model at 24 generations fit the empirical data best among all these simulated scenarios, as indicated by the distribution of EMDs.

Again, this makes sense, because in Mexico there continued to exist unadmixed populations of Europeans and Amerindians that contributed to the Mestizo population of the country.

On the African admixture in Mozabites:

Comparing the empirical distribution of CSDAs with that simulated, we found that the Mozabite admixture process essentially fit the HI model with 100 generations since admixture. There was an almost complete absence of recent gene flow from European populations to the Mozabite gene pool (Figure 6A). For the Sub-Saharan African ancestral component, there were more long CSDAs at the tail of empirical distribution than those in the HI model, which confirmed that recent gene flow from African populations had contributed to the Mozabite gene pool (Figure 6B). 

Again, this makes sense: Berber groups were not replenished from other Caucasoid sources, so their original admixture with native Africans resulted in a blend that persisted largely unaffected by "Europeans", but did find occasion of admixture with Sub-Saharans. Hence, the asymmetry in the presence of long "European" vs. "Sub-Saharan" segments.

A similar pattern was evident for Bedouin, Palestinians, and Druze:

Analyses of European ancestral component in Bedouin and Palestinian populations also showed that the empirical distributions essentially fit the HI model for both populations (Figures 6C and 6E). Although the empirical CSDA distribution of Sub-Saharan African ancestral component also fit the HI model  best, both distributions showed a long tail at the right compared with those under the HI model, indicating that recent gene flow from Sub-Saharan Africans also contributed to the two admixed populations (Figures 6D and 6F). ... For Druze, their European component of ancestry fit the HI model very well. However, their African ancestral component contained much shorter CSDAs than those of simulated (Figure S14), which might indicate that previous studies had underestimated the admixture time of Druze. In addition, populations receiving recent gene flow from their parental populations showed higher variation of individual ancestral proportions than those who did not (Figure S13).

The Druze have well-known Egyptian connections, and they may have largely avoided Sub-Saharan African admixture during the Islamic period, principally because of its avoidance of proselytism. Hence, their African admixture may stem from Egyptian adherents who were themselves a product of much earlier Caucasoid/Sub-Saharan admixture during the course of pre-Islamic Egypt.


The American Journal of Human Genetics, 25 October 2012 doi:10.1016/j.ajhg.2012.09.008

Exploring Population Admixture Dynamics via Empirical and Simulated Genome-Wide Distribution of Ancestral Chromosomal Segments

Wenfei Jin et al

Abstract

The processes of genetic admixture determine the haplotype structure and linkage disequilibrium patterns of the admixed population, which is important for medical and evolutionary studies. However, most previous studies do not consider the inherent complexity of admixture processes. Here we proposed two approaches to explore population admixture dynamics, and we demonstrated, by analyzing genome-wide empirical and simulated data, that the approach based on the distribution of chromosomal segments of distinct ancestry (CSDAs) was more powerful than that based on the distribution of individual ancestry proportions. Analysis of 1,890 African Americans showed that a continuous gene flow model, in which the African American population continuously received gene flow from European populations over about 14 generations, best explained the admixture dynamics of African Americans among several putative models. Interestingly, we observed that some African Americans had much more European ancestry than the simulated samples, indicating substructures of local ancestries in African Americans that could have been caused by individuals from some particular lineages having repeatedly admixed with people of European ancestry. In contrast, the admixture dynamics of Mexicans could be explained by a gradual admixture model in which the Mexican population continuously received gene flow from both European and Amerindian populations over about 24 generations. Our results also indicated that recent gene flows from Sub-Saharan Africans have contributed to the gene pool of Middle Eastern populations such as Mozabite, Bedouin, and Palestinian. In summary, this study not only provides approaches to explore population admixture dynamics, but also advances our understanding on population history of African Americans, Mexicans, and Middle Eastern populations.

Link

Back to (North) Africa (Henn et al. 2012)

A great new paper has just appeared, presenting new data, new conclusions about African prehistory, and new methodologies. I'll have to read it before I comment on it, but since it's open access you can read it for yourselves.

UPDATE I:


The new data are publicly available here, with information about samples here.
The new PCADMIX software is also available.

PLoS Genet 8(1): e1002397. doi:10.1371/journal.pgen.1002397 

Genomic Ancestry of North Africans Supports Back-to-Africa Migrations 

Brenna Henn et al.

 North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.

Link

Activity patterns of Garamantes

A different paper on cranial nonmetric traits from the same team and on the same population (Garamantes).

From the current paper:

The study of the activity patterns of the Garamantes, a population that flourished at Central Sahara approximately 3,000 years ago, offers some interesting insights on the levels of stress imposed by a sedentary life in a hyper-arid environment. The population showed low bilateral asymmetry, possibly due to limited task specialization. Moreover, the Garamantes exhibited low sexual dimorphism in the upper limbs, which is consistent to the pattern found in agricultural populations and implies that the engagement of males in warfare  and construction works was not particularly intense. In the lower limbs, males were stronger in TA possibly as a result of their involvement in herding and mobility on the uneven terrain of Fezzan. Finally, the Garamantes did not appear systematically more robust than other North African populations occupying less harsh environments, indicating that life in the Sahara did not require particularly strenuous daily activities.

AJPA DOI: 10.1002/ajpa.21597

Activity patterns in the Sahara Desert: An interpretation based on cross-sectional geometric properties

Efthymia Nikita et al.

The Garamantian civilization flourished in modern Fezzan, Libya, between 900 BC and 500 AD, during which the aridification of the Sahara was well established. Study of the archaeological remains suggests a population successful at coping with a harsh environment of high and fluctuating temperatures and reduced water and food resources. This study explores the activity patterns of the Garamantes by means of cross-sectional geometric properties. Long bone diaphyseal shape and rigidity are compared between the Garamantes and populations from Egypt and Sudan, namely from the sites of Kerma, el-Badari, and Jebel Moya, to determine whether the Garamantian daily activities were more strenuous than those of other North African populations. Moreover, sexual dimorphism and bilateral asymmetry are assessed at an intra- and inter-population level. The inter-population comparisons showed the Garamantes not to be more robust than the comparative populations, suggesting that the daily Garamantian activities necessary for survival in the Sahara Desert did not generally impose greater loads than those of other North African populations. Sexual dimorphism and bilateral asymmetry in almost all geometric properties of the long limbs were comparatively low among the Garamantes. Only the lower limbs were significantly stronger among males than females, possibly due to higher levels of mobility associated with herding. The lack of systematic bilateral asymmetry in cross-sectional geometric properties may relate to the involvement of the population in bilaterally intensive activities or the lack of regular repetition of unilateral activities.

Link

Forensic analysis of King Tut and his relatives

DNA Tribes has released an analysis, based on 8 forensic autosomal STR markers, of the "Amarna Pharaohs". The analysis is based on data from Ancestry and Pathology in King Tutankhamun's Family.

The results of the DNA Tribes analysis can be seen below:

They seem to indicate that there is something definitely "African" about this collection of mummies. I have previously used PopAffiliator and STRUCTURE with CODIS markers. The results of that analysis suggest that even this small number of markers is sufficient to place a sample in a continental group with high accuracy, but insufficient to estimate levels of admixture. There is a new version of PopAffiliator, which, unfortunately, does not allow for incomplete data entry, and hence cannot be used to verify the results of the DNA Tribes analysis.

The DNA Tribes results are interesting, but may hinge upon a few marker values that are more prevalent in Africa than in Eurasia. Also, it is not clear which population(s) make up the "North African" group. It would be interesting to extract full genome sequences from Egyptian mummies in order to properly place them in the global genetic landscape.

Pictorial evidence in Egyptian art, as well as the statements of classical Greco-Roman authors strongly suggest that the ancient Egyptians occupied an intermediate position in the phenotypic continuum between Near Eastern and "Ethiopian" people. It is also clear that there was variation within ancient Egypt itself: geographic, temporal, and even perhaps social aspects of this variation may have existed. But these qualitative observations are no substitute for the harder type of evidence that can be provided by authentic ancient DNA.

Hopefully, the debate on the genetic identity of the ancient Egyptians can proceed on the basis of new data, although I am not holding my breath that this will happen anytime soon, both because of the fluid state of politics in Egypt itself, the existence of various fringe theories outside of Egypt, and, the rather controversial state of mummy DNA analysis itself.

Cranial nonmetric traits of Garamantes

Am J Phys Anthropol DOI: 10.1002/ajpa.21645


Sahara: Barrier or corridor? Nonmetric cranial traits and biological affinities of North African late holocene populations

Efthymia Nikita et al.

The Garamantes flourished in southwestern Libya, in the core of the Sahara Desert ∼3,000 years ago and largely controlled trans-Saharan trade. Their biological affinities to other North African populations, including the Egyptian, Algerian, Tunisian and Sudanese, roughly contemporary to them, are examined by means of cranial nonmetric traits using the Mean Measure of Divergence and Mahalanobis D2 distance. The aim is to shed light on the extent to which the Sahara Desert inhibited extensive population movements and gene flow. Our results show that the Garamantes possess distant affinities to their neighbors. This relationship may be due to the Central Sahara forming a barrier among groups, despite the archaeological evidence for extended networks of contact. The role of the Sahara as a barrier is further corroborated by the significant correlation between the Mahalanobis D2 distance and geographic distance between the Garamantes and the other populations under study. In contrast, no clear pattern was observed when all North African populations were examined, indicating that there was no uniform gene flow in the region.

Link

Oldest North African rock art

Antiquity Volume: 85 Number: 330 Page: 1184–1193

First evidence of Pleistocene rock art in North Africa: securing the age of the Qurta petroglyphs (Egypt) through OSL dating

Dirk Huyge et al

Long doubted, the existence of Pleistocene rock art in North Africa is here proven through the dating of petroglyph panels displaying aurochs and other animals at Qurta in the Upper Egyptian Nile Valley. The method used was optically stimulated luminescence (OSL) applied to deposits of wind-blown sediment covering the images. This gave a minimum age of ~15 000 calendar years making the rock engravings at Qurta the oldest so far found in North Africa.

Link

iGENEA's King Tut claims

iGENEA is a Swiss ancestry analysis company which I had deservedly mocked a couple of years ago because of its ridiculous claims. In my experience, commercial ancestry analysis outfits are often plagued by either of two problems:

1. They offer too little value, such as a breakdown of an individual into the categories of "Europe", "Asia", and "Africa".
2. They pretend to offer too much value, such as the ability to connect one's Y-chromosome with Old Testament priests, numerous ancient "tribes", or to break down one's genome to a very fine detail that is not commensurate with the power of the DNA evidence they collect (e.g., with the CODIS markers)
   

iGENEA is a great example of #2.

Now, they have done it again, pretending to be able to link men with a particular R1b1a2 haplotype with King Tut. Note that the Y-chromosome of King Tut has never been published, and speculation about it is based on some screencaps from a Discovery Channel documentary that may or may not belong to the Pharaoh:

iGENEA was able to reconstruct the Y-DNA profile of Tutankhamun, his father Akhenaten and his grandfather Amenhotep III with the help of a recording of the Discovery Channel. The astonishing result:

Indeed, the whole business of mummy DNA is highly suspect, as Jo Marchant has covered quite comprehensively in Nature News; see also King Tut's DNA in doubt.

The original paper in the JAMA was remarkable for its non-publishing of crucial data necessary to validate the claims within it. This is yet another argument against the flawed peer-review system whose main objective, it seems, is to take in money for journals and dole out prestige to authors, and not to do actual science.

Personally, I'm against most regulation of personal genetics products, unless there is a clear and present medical danger arising from their use: I don't trust government bureaucrats and paternalistic know-it-all scientists to tell us what deserves to be marketed and what does not.

On the other hand, the absence of regulation makes the community's responsibility to speak out against bad products all the more important: such products can only be identified if there is an active and broad group of informed individuals willing to put out the relevant facts out there, and let potential customers decide for themselves.

mtDNA discontinuity in the Nile Valley

From the paper:

The distribution of subsets of haplogroups U6 and M1 also suggests the presence of a discontinuity between Libya and Egypt, separating western North Africa from eastern North Africa. Even if both haplogroups are thought to have been carried by a back-to-Africa migration from the Near East, significant increased U6 frequencies have been detected in the West compared to the East. The network of all U6 sequences found in the database presents two nodes with star-like shape, U6a* and U6a1. In a similar way, M1a1 is the node with starlike topology in haplogroup M1, and the node where most of the eastern sequences are found. Time estimates of these nodes are 13.5 +/- 3.7, 13.0 +/- 5.7, and 13.1 +/- 7.0 kya for haplogroups U6a*, U6a1, and M1a1 respectively. The most plausible explanation of the frequency distribution of M1a, U6, and M1b1 lineages, their coalescence age estimates, and the star-like shape would be an early split in the back to Africa migration followed by a period of stability and a period of expansion. The split would have produced two different migration waves, one westward, represented by U6 and possibly M1b1 in lower frequencies, and the other southward, represented by M1a.

Am J Phys Anthropol DOI: 10.1002/ajpa.21472

Mitochondrial DNA structure in North Africa reveals a genetic discontinuity in the Nile Valley

Karima Fadhlaoui-Zid et al.

Human population movements in North Africa have been mostly restricted to an east-west direction due to the geographical barriers imposed by the Sahara Desert and the Mediterranean Sea. Although these barriers have not completely impeded human migrations, genetic studies have shown that an east-west genetic gradient exists. However, the lack of genetic information of certain geographical areas and the focus of some studies in parts of the North African landscape have limited the global view of the genetic pool of North African populations. To provide a global view of the North African genetic landscape and population structure, we have analyzed ∼2,300 North African mitochondrial DNA lineages (including 269 new sequences from Libya, in the first mtDNA study of the general Libyan population). Our results show a clinal distribution of certain haplogroups, some of them more frequent in Western (H, HV0, L1b, L3b, U6) or Eastern populations (L0a, R0a, N1b, I, J) that might be the result of human migrations from the Middle East, sub-Saharan Africa, and Europe. Despite this clinal pattern, a genetic discontinuity is found in the Libyan/Egyptian border, suggesting a differential gene flow in the Nile River Valley. Finally, frequency of the post-LGM subclades H1 and H3 is predominant in Libya within the H sequences, highlighting the magnitude of the LGM expansion in North Africa.

Link

King Tutunkhamun's DNA in doubt

Royal rumpus over King Tutankhamun's ancestry

Can we be sure which mummy was the daddy? When a state-of-the-art DNA analysis of Tutankhamun and other ancient Egyptian royals was published last year, its authors hailed it as "the final word" on the pharaoh's family tree. But others are now voicing doubts.

The analysis of 11 royal mummies dating from around 1300 BC was carried out by an Egyptian team led by Egypt's chief archaeologist Zahi Hawass. The project was overseen by two foreign consultants, Albert Zink of the EURAC Institute for Mummies and the Iceman in Bolzano, Italy, and Carsten Pusch of the University of Tübingen, Germany.

The researchers used the DNA data to construct a family tree of Tutankhamun and his immediate relatives. The study, published last February in the Journal of the American Medical Association (vol 303, p 638), concluded that Tutankhamun's father was the pharaoh Akhenaten, that his parents were brother and sister, and that two mummified foetuses found in Tutankhamun's tomb were probably his stillborn daughters – conclusions that have since become received wisdom.

But many geneticists complain that the team used inappropriate analysis techniques. Far from being definitive, the study is "not seen as rigorous or convincing", says Eline Lorenzen of the Center for GeoGenetics at the Natural History Museum in Copenhagen, Denmark. "Many of us in the DNA community are surprised that this has been published."

...

To judge the quality of the team's results, Lorenzen and others are asking for access to raw data not included in the Journal of the American Medical Association paper – but Zink is reluctant to oblige, fearing the data would spark "a lot of arguing" over technicalities.

However, Zink, Pusch and colleagues insist that they will soon be able to put any doubts to rest. They say they have also extracted the mtDNA that Lorenzen and others consider necessary for rigorous genetic analysis and are still working on the data. They hope to publish the results this year.

But the critics are still advising caution. "When working with samples that are so well-known, it is important to convince readers that you have the right data," says Lorenzen. "I am not convinced."

This is the paper they are referring to (Ancestry and Pathology in King Tutankhamun's Family, Zahi Hawass et al., JAMA. 2010;303(7):638-647. doi: 10.1001/jama.2010.121)

I don't understand what is the problem with "arguing over technicalities". That's the whole point of releasing as much data as possible, to make it easier for others to evaluate your conclusions. I don't understand why a scientist would want data to be hidden: perhaps it might make sense for nuclear scientists or virus experts to keep some data hidden, but why would Tut's DNA be hidden?

People who liked at Tut's alleged Y-STR values from screencaps have concluded that he belonged to haplogroup R1b; as this is a rare haplogroup in Egypt, and frequent in Europe, it has sparked debate about his origins. If the Y-STR values are legit, an alternative explanation is that the ancient DNA is not authentic but represents a European contaminant. In any case, I hope that as much data as possible about the case is released, so that everyone can make an informed assessment.

Ancient DNA provides clues to donkey domestication

Proceedings of the Royal Society B doi: 10.1098/rspb.2010.0708

Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication

Birgitta Kimura et al.

Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass.

Link

Radiocarbon based chronology for ancient Egypt (Ramsey et al. 2010)

Science Vol. 328. no. 5985, pp. 1554 - 1557
DOI: 10.1126/science.1189395

Radiocarbon-Based Chronology for Dynastic Egypt

Christopher Bronk Ramsey et al.

The historical chronologies for dynastic Egypt are based on reign lengths inferred from written and archaeological evidence. These floating chronologies are linked to the absolute calendar by a few ancient astronomical observations, which remain a source of debate. We used 211 radiocarbon measurements made on samples from short-lived plants, together with a Bayesian model incorporating historical information on reign lengths, to produce a chronology for dynastic Egypt. A small offset (19 radiocarbon years older) in radiocarbon levels in the Nile Valley is probably a growing-season effect. Our radiocarbon data indicate that the New Kingdom started between 1570 and 1544 B.C.E., and the reign of Djoser in the Old Kingdom started between 2691 and 2625 B.C.E.; both cases are earlier than some previous historical estimates.

Link

Cambyses' army found in Egypt

VANISHED PERSIAN ARMY SAID FOUND IN DESERT

Bones, jewelry and weapons found in Egyptian desert may be the remains of Cambyses' army that vanished 2,500 years ago.

The remains of a mighty Persian army said to have drowned in the sands of the western Egyptian desert 2,500 years ago might have been finally located, solving one of archaeology's biggest outstanding mysteries, according to Italian researchers.

Bronze weapons, a silver bracelet, an earring and hundreds of human bones found in the vast desolate wilderness of the Sahara desert have raised hopes of finally finding the lost army of Persian King Cambyses II. The 50,000 warriors were said to be buried by a cataclysmic sandstorm in 525 B.C.

"We have found the first archaeological evidence of a story reported by the Greek historian Herodotus," Dario Del Bufalo, a member of the expedition from the University of Lecce, told Discovery News.

According to Herodotus (484-425 B.C.), Cambyses, the son of Cyrus the Great, sent 50,000 soldiers from Thebes to attack the Oasis of Siwa and destroy the oracle at the Temple of Amun after the priests there refused to legitimize his claim to Egypt.

After walking for seven days in the desert, the army got to an "oasis," which historians believe was El-Kharga. After they left, they were never seen again.

"A wind arose from the south, strong and deadly, bringing with it vast columns of whirling sand, which entirely covered up the troops and caused them wholly to disappear," wrote Herodotus.

A century after Herodotus wrote his account, Alexander the Great made his own pilgrimage to the oracle of Amun, and in 332 B.C. he won the oracle's confirmation that he was the divine son of Zeus, the Greek god equated with Amun.

Video on the Lost Army of Cambyses. Another video.

UPDATE: Rogue Classicism is skeptical.

Coastal-inland differences in Y chromosomes of the Levant

More on this after I get a hold of and digest the information in the paper.

Just a quick comment, based only on the abstract, that the Levantine populations should be studied in a European context as well, as they have been influenced by prehistoric populations from the Aegean, Greeks, Romans, medieval Crusaders, or Ottomans of various origins.

UPDATE: The paper has several supplementary figures and tables.

In Figure S1 we see the biallelic markers used in this study, and their representation in the various populations. It is a chronic problem with studies of this sort to undertype samples; there are phylogeographically informative markers within haplogroups G, L, E1b1b, and J2 for example, which would have added important information about the specific affinities of these haplogroups in the studied populations.


Inspit of these deficiencies, we may still make some useful observations. For example, IE-speaking Iranians have largely the same haplogroups as Arabs, but a much higher representation of haplogroup J2 compared to J1. The converse is true for all Arabs except the Lebanese. But, we do know, that even in Lebanon itself, Muslims have a higher J1/J2 ratio than Christians, and Islam was the main vehicle of Arabization in the region. The Christians are descended from the pre-Arab Byzantine Greco-Aramaic populations (with an addition of Western European Y-chromosomes in some Christian communities, which would not have substantially upset the J1/J2 balance).

It is fairly clear to me that in the Middle East, Greek and Iranian-settled regions have a higher J2/J1 ratio than regions with solid Semitic or NE Caucasian populations where J1 predominates.

UPDATE II (Aug 27):

The paper reports a near zero frequency of haplogroup J1 in Tunisia and Morocco, after an earlier study by the same authors. However, a different study (Onofri et al.) on Moroccan and Tunisian Y chromosomes report 20 and 35% respectively, which is in agreement with an earlier study on North African Y-chromosomes (Arredi et al.) The discrepancy in the J1 frequency seems too large to have arisen by chance given the sample sizes, and it would be interesting to see how it may have arisen.

Annals of Human Genetics doi:10.1111/j.1469-1809.2009.00538.x

Geographical Structure of the Y-chromosomal Genetic Landscape of the Levant: A coastal-inland contrast

Mirvat El-Sibai et al.

Abstract

We have examined the male-specific phylogeography of the Levant and its surroundings by analyzing Y-chromosomal haplogroup distributions using 5874 samples (885 new) from 23 countries. The diversity within some of these haplogroups was also examined. The Levantine populations showed clustering in SNP and STR analyses when considered against a broad Middle-East and North African background. However, we also found a coastal-inland, east-west pattern of diversity and frequency distribution in several haplogroups within the small region of the Levant. Since estimates of effective population size are similar in the two regions, this strong pattern is likely to have arisen mainly from differential migrations, with different lineages introduced from the east and west.

Link

Y chromosomes and mtDNA in Egyptian West Desert

Notice that all Y-chromosomes belong to either E-subclades or to J1. I would definitely not equate J1 with the Neolithic in this case; it is more likely to be due to historical movements of Semitic/Arabic populations into Egypt. The complete absence of J2 is noteworthy and resembles Arabian peninsula populations where the J2/J1 ratio reaches its minimum.

American Journal of Physical Anthropology doi:10.1002/ajpa.21078

Near Eastern Neolithic genetic input in a small oasis of the Egyptian Western Desert

Martina Kujanová et al.

Abstract

The Egyptian Western Desert lies on an important geographic intersection between Africa and Asia. Genetic diversity of this region has been shaped, in part, by climatic changes in the Late Pleistocene and Holocene epochs marked by oscillating humid and arid periods. We present here a whole genome analysis of mitochondrial DNA (mtDNA) and high-resolution molecular analysis of nonrecombining Y-chromosomal (NRY) gene pools of a demographically small but autochthonous population from the Egyptian Western Desert oasis el-Hayez. Notwithstanding signs of expected genetic drift, we still found clear genetic evidence of a strong Near Eastern input that can be dated into the Neolithic. This is revealed by high frequencies and high internal variability of several mtDNA lineages from haplogroup T. The whole genome sequencing strategy and molecular dating allowed us to detect the accumulation of local mtDNA diversity to 5,138 ± 3,633 YBP. Similarly, theY-chromosome gene pool reveals high frequencies of the Near Eastern J1 and the North African E1b1b1b lineages, both generally known to have expanded within North Africa during the Neolithic. These results provide another piece of evidence of the relatively young population history of North Africa.

Link