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

Arabian origin of the Upper Paleolithic in the Levant

This is a very useful review of research on the origin of the Upper Paleolithic (Emiran) in the Levant, arguing against a recent (c. 50kya ) African origin and in favor of an Arabian one. The argument is mainly archaeological, although it is informed by genetic evidence. From the chapter:

After a century of research, the origins of the Levantine UP still remain an enigma. At this point, at least one thing is clear: the Emiran has no African progenitor. As such, there is a disconnect between the archaeological database and the Replacement paradigm, which necessitates that the earliest Levantine Upper Paleolithic must have come fully developed from northeast Africa. The Replacement model should have been a parsimonious prism through which to view the transition from the MP to the UP in the Levant. It was not.

The recent acceptance of: (i) a slower autosomal mutation rate, and (ii) evidence for interbreeding with Neandertals largely predating the c. 50kya mark, and (iii) coalescence of Eurasian mtDNA haplogroup N well before that time, have all but killed, in my opinion the idea of a 50kya spread of modern humans from Africa. Modern humans must have lived in Eurasia much earlier than that time, and what remains is to figure out how much earlier.

A century of research into the origins of the Upper Palaeolithic in the Levant

Anthony E. Marks and Jeffrey I. Rose

Link

Middle Paleolithic and Neolithic occupations around Mundafan palaeolake (Crassard et al. 2013)

From the paper:

Survey in the Mundafan palaeolake basin revealed, for the first time, Middle Palaeolithic occupations. Recovery of Middle Palaeolithic assemblages corresponds with recent environmental and geoarchaeological studies that indicate at least three lacustrine wet phases in MIS 5 [23]. The main diagnostic lithic technology observed is the preferential Levallois reduction method, which is also present at the Jubbah palaeolake during MIS 5 (JQ-1, JSM-1 and JKF-1 sites: [21], [22]) and at the Jebel Faya rock shelter at the transition between MIS 6–5e (Assemblage C: [6]). This technology is absent in MIS 3 in southwest Yemen (SD1, SD2 and AS1 sites: [8], [9]). Earlier dating for preferential Levallois in Arabia, in MIS 7, is possible, but still insufficiently represented owing to small sample size at the Jubbah palaeolake (JQ-1: [22]). Other preferential Levallois methods have been observed in Dhofar, including in the Nubian Complex, dated to at least ca. 106 ka [7], in Hadramawt and the southern fringe of the Rub’ al-Khali, Oman [10], and in central Saudi Arabia at Al-Kharj [75]. Nubian Complex technology has not yet been identified at Mundafan. We associate the Levallois component in Mundafan with the wet pluvials of MIS 5, most probably during the wetter events of MIS 5e (ca. 125 ka), MIS 5c (ca. 100 ka) and MIS 5a (80 ka), when conditions were more favorable for hominin dispersals. The Middle Palaeolithic evidence thus provides empirical support for Rosenberg and colleagues assertion [23] that the dispersal of hominins into the Rub’ al-Khali occurred during ameliorated periods, and perhaps supports their claim for the expansion of Homo sapiens into this marginal environment.

PLoS ONE 8(7): e69665. doi:10.1371/journal.pone.0069665

Middle Palaeolithic and Neolithic Occupations around Mundafan Palaeolake, Saudi Arabia: Implications for Climate Change and Human Dispersals

Rémy Crassard et al.

The Arabian Peninsula is a key region for understanding climate change and human occupation history in a marginal environment. The Mundafan palaeolake is situated in southern Saudi Arabia, in the Rub’ al-Khali (the ‘Empty Quarter’), the world’s largest sand desert. Here we report the first discoveries of Middle Palaeolithic and Neolithic archaeological sites in association with the palaeolake. We associate the human occupations with new geochronological data, and suggest the archaeological sites date to the wet periods of Marine Isotope Stage 5 and the Early Holocene. The archaeological sites indicate that humans repeatedly penetrated the ameliorated environments of the Rub’ al-Khali. The sites probably represent short-term occupations, with the Neolithic sites focused on hunting, as indicated by points and weaponry. Middle Palaeolithic assemblages at Mundafan support a lacustrine adaptive focus in Arabia. Provenancing of obsidian artifacts indicates that Neolithic groups at Mundafan had a wide wandering range, with transport of artifacts from distant sources.

Link

Nubian complex site from central Arabia (Crassard & Hilbert 2013)

From the paper:

The palaeoclimatic record of Arabia indicates that three distinct wet phases occurred during MIS 5 [109]. The first of these wet phases occurred between 130 and 125 kya (MIS 5e) and precedes the presence of Nubian technology in Arabia. The two following wet phases, positioned around 100 kya (MIS 5c) and between 80 to 75 kya (MIS 5a) may be viewed as possible windows for the Nubian expansion into and across Arabia (Figure 11).

PLoS ONE 8(7): e69221. doi:10.1371/journal.pone.0069221

A Nubian Complex Site from Central Arabia: Implications for Levallois Taxonomy and Human Dispersals during the Upper Pleistocene

Rémy Crassard, Yamandú Hieronymus Hilbert

Archaeological survey undertaken in central Saudi Arabia has revealed 29 surface sites attributed to the Arabian Middle Paleolithic based on the presence of Levallois blank production methods. Technological analyses on cores retrieved from Al-Kharj 22 have revealed specific reduction modalities used to produce flakes with predetermined shapes. The identified modalities, which are anchored within the greater Levallois concept of core convexity preparation and exploitation, correspond with those utilized during the Middle Stone Age Nubian Complex of northeast Africa and southern Arabia. The discovery of Nubian technology at the Al-Kharj 22 site represents the first appearance of this blank production method in central Arabia. Here we demonstrate how a rigorous use of technological and taxonomic analysis may enable intra-regional comparisons across the Arabian Peninsula. The discovery of Al-Kharj 22 increases the complexity of the Arabian Middle Paleolithic archaeological record and suggests new dynamics of population movements between the southern and central regions of the Peninsula. This study also addresses the dichotomy within Nubian core typology (Types 1 and 2), which was originally defined for African assemblages.

Link

Lakes in SE Arabia ~60 thousand years ago

From the paper:

From the current archaeological evidence, it seems that after MIS 5, the different lithic traditions within Arabia develop along separate trajectories, with no indication of additional input from Africa. Recent genetic evidence (Fernandes et al., 2012) also indicates that the relict distribution of minor haplogroups N1, N2 and X, reflects an ancient ancestry of these groups within the Arabian Peninsula which, the authors conclude, then spread from the Gulf region toward the Near East and Europe between 55 and 24 ka. The potential occurrence of increased humidity within the Arabian interior during MIS 3 would, therefore, have been instrumental in determining the success and trajectory of the autochthonous development of early human communities within the region at this time. Although Rosenberg et al. (2012) may be correct in their description of Arabia between ca. 75 and 10.5 ka as a natural barrier for human dispersal, it is possible that indigenous inhabitants may have persisted in environmental refugia around Arabia, such as the Gulf Oasis (e.g. Rose, 2010). The occurrence of a pluvial phase during the early stages of MIS 3, therefore, may have facilitated a range expansion of early humans previously contained within such refugia. To address these important issues, we present a multiproxy record of an early MIS 3 wet phase from a palaeolake sequence within the continental interior of SE Arabia.

Quaternary International Available online 22 February 2013

An early MIS 3 pluvial phase in Southeast Arabia: Climatic and archaeological implications

Ash Parton et al.

Climatic changes in Arabia are of critical importance to our understanding of both monsoon variability and the dispersal of anatomically modern humans (AMH) out of Africa. The timing of dispersal is associated with the occurrence of pluvial periods during Marine Isotope Stage (MIS) 5 (ca. 130–74 ka), after which arid conditions between ca. 74 and 10.5 ka are thought to have restricted further migration and range expansion within the Arabian interior. Whilst a number of records indicate that this phase of aridity was punctuated by an increase in monsoon strength during MIS 3, uncertainties regarding the precision of terrestrial records and suitability of marine archives as records of precipitation, mean that the occurrence of this pluvial remains debated. Here we present evidence from a series of relict lake deposits within southeastern Arabia, which formed at the onset of MIS 3 (ca. 61–58 ka). At this time, the incursion of monsoon rainfall into the Arabian interior activated a network of channels associated with an alluvial fan system along the western flanks of the Hajar Mountains, leading to lake formation. Multiproxy evidence indicates that precipitation increases intermittently recharged fluvial systems within the region, leading to lake expansion in distal fan zones. Conversely, decreased precipitation led to reduced channel flow, lake contraction and a shift to saline conditions. These findings are in contrast to the many other palaeoclimatic records from Arabia, which suggest that during MIS 3, the latitudinal position of the monsoon was substantially further south and did not penetrate the peninsula. Additionally, the occurrence of increased rainfall at this time challenges the notion that the climate of Arabia following MIS 5 was too harsh to permit the further range expansion of indigenous communities.

Link

The case for earlier Out-of-Africa (Boivin et al. 2013)

An informative review critical of the ~60kya coastal-Out-of-Africa hypothesis. On the left, the authors' estimate of the distribution of hominin groups during MIS5.

From the paper:

Another under-appreciated issue is the anomalous nature of the genetic evidence for a rapid spread of modern humans from Africa to Asia. Echoing the fossil date anomaly, the mtDNA branch lengths for sampled populations are longest for those which are farthest east, in Near Oceania, and shortest in the Asian areas that would have been encountered first (Merriwether et al., 2005; Oppenheimer, 2009). The real problem, however, is that the variation in branch lengths suggests that a single genotype engaged in the expansion actually existed for 30 ka, which does not support a rapid expansion. The anomaly can be explained by what we call an an ‘M buffer’ effect (see Supplementary material A) which implies that the branch ages we observe are considerable underestimates of the time of arrival of the genotype to these areas. Such anomalously long-lived genotypes have been directly observed through ancient DNA in species such as the Iberian lynx (Dalen et al., 2011).

and:

We have focused here on the possibility that the modern human exit recorded by fossil evidence in the Levant in MIS 5 does not represent a failed dispersal, and that in fact our species was not only in the Levant but also the Arabian peninsula during this marine isotope stage, and spread to India before the Toba eruption at 74 ka (Petraglia et al., 2007). Another valid hypothesis we do not explore here is that H. sapiens was able to leave Africa in MIS 6 via a grassland corridor (Frumkin et al., 2011; see also Scally and Durbin, 2012). Yet another is that our species dispersed out of Africa shortly after its first appearance c. 195 ka, in MIS 7 (Dennell and Roebroeks, 2005: 1102). One other possibility is that there were several, separate dispersals of our species out of Africa (Dennell and Petraglia, 2012). At the same time, we acknowledge that major demographic changes occurred in MIS 4 and MIS 3, perhaps explaining the relatively young mtDNA coalescence age in living populations. The increasing evidence for complexity as well as the clear patterns of bias for all records, whether archaeological, fossil or genetic, suggests the need for an open mind to multiple scenarios for Out of Africa, as well as for more rather than less complex models of H. sapiens dispersal across Eurasia.

Quaternary International doi:10.1016/j.quaint.2013.01.008

Human Dispersal Across Diverse Environments of Asia during the Upper Pleistocene

Nicole Boivin et al.

The initial out of Africa dispersal of H. sapiens, which saw anatomically modern humans reach the Levant in Marine Isotope Stage 5, is generally regarded as a ‘failed dispersal’. Fossil, archaeological and genetic findings are seen to converge around a consensus view that a single population of H. sapiens exited Africa sometime around 60 thousand years ago (ka), and rapidly reached Australia by following a coastal dispersal corridor. We challenge the notion that current evidence supports this straightforward model. We argue that the fossil and archaeological records are too incomplete, the coastal route too problematic, and recent genomic evidence too incompatible for researchers not to remain fully open to other hypotheses. We specifically explore the possibility of a sustained exit by anatomically modern humans, drawing in particular upon palaeoenvironmental data across southern Asia to demonstrate its feasibility. Current archaeological, genetic and fossil data are not incompatible with the model presented, and appear to increasingly favour a more complex out of Africa scenario involving multiple exits, varying terrestrial routes, a sub-divided African source population, slower progress to Australia, and a degree of interbreeding with archaic varieties of Homo.

Link

Who inhabited the Jubbah lake in the Nefud Desert during the Middle Paleolithic?

Many readers may have heard of the Nefud Desert while watching Lawrence of Arabia (was that filmed on location?). It is hard to imagine that desolate landscape as being instrumental in the tale of human origins, but it may very well have been. A new paper describes Middle Paleolithic settlement evidence from the Jubbah Palaeolake, especially during MIS stages 7 and 5.

Arabia is a very interesting case for a variety of reasons: It has to be implicated one way or another in the tale of human origins and dispersals: it lies in the natural route Out-of-Africa, and in the intermediate space between the early modern human remains from Ethiopia, the later modern humans from the Levant, as well as the disputed late Neandertals of West Asia.

Unfortunately, current climatic conditions, as well as past episodes desiccation have resulted in substantial population; if anyone wanted to find out what the people who lived there during the Middle Paleolithic were like, he will find little continuity between them and the current inhabitants. The lack of genetic evidence is, unfortunately also accompanied by a general lack of anthropological evidence. Industries with links to Africa or the Levant are devoid of associated remains. But, the paper produces a hopeful note:

Yet, recent support for an MIS 5 expansion of Homo sapiens comes from archaeological finds of characteristic Middle Palaeolithic technologies in Arabia in MIS 5e–c [19]–[20] and nuclear genomic estimates which indicate that the split between Africans and non-Africans occurred as early as 130 to 90 ka [41], consistent with fossil finds of Homo sapiens in the Levant [52], [53] and at the time of possible interbreeding of Homo sapiens and Neanderthals [54]. These controversies indicate the need to recover hominin fossils in Arabia, which is feasible given the identification of Pleistocene mammalian fauna in a nearby lake basin of the Nefud [24], [55].

In the absence of genes or bones, we can only make inferences based on stones, which may not have a direct correspondence with populations. While Figure 17 from the paper (left) shows a clear differentiation of India vis a vis. the west, relationships in the Near East and Africa are not as clear cut; Skhul resembles North Africa (Haua Fteah and Aterian) and it would be tempting to associate them with Homo sapiens. But, Horn of Africa MSA  -where the earliest anatomically modern humans were found- is linked to El Wad, Tabun C, and Jebel Qattar/Katefeh, the latter two sites being the ones from the Nefud.

Tabun is associated with Neandertals, although that attribution, like most everything in palaeoanthropology is controversial.So, it might be possible that the Jubbah was occupied by Neandertals too, and this might make this population a prime candidate for the signal of Neandertal admixture carried by non-Africans.

At present, there seem to be two candidates for the modern human Out-of-Africa: Skhul (Levant; linked to Northwest Africa here) and the Nubian technocomplex of (south Arabia; linked to Northeast Africa). I don't have a clear picture of how it may have all played out; it would certainly be wonderful if it were possible to extract DNA from, say, Skhul/Qafzeh modern humans or the Levantine Neandertals, because that would definitely show how (i) the former may either be related to later Eurasians, or may be a failed experiment as hitherto supposed, and (ii) the latter might be a source of Neandertal DNA in non-Africans, or indeed something much closer to modern humans as their morphological intermediacy might suggest.

PLoS ONE 7(11): e49840. doi:10.1371/journal.pone.0049840

Hominin Dispersal into the Nefud Desert and Middle Palaeolithic Settlement along the Jubbah Palaeolake, Northern Arabia

Michael D. Petraglia et al.

The Arabian Peninsula is a key region for understanding hominin dispersals and the effect of climate change on prehistoric demography, although little information on these topics is presently available owing to the poor preservation of archaeological sites in this desert environment. Here, we describe the discovery of three stratified and buried archaeological sites in the Nefud Desert, which includes the oldest dated occupation for the region. The stone tool assemblages are identified as a Middle Palaeolithic industry that includes Levallois manufacturing methods and the production of tools on flakes. Hominin occupations correspond with humid periods, particularly Marine Isotope Stages 7 and 5 of the Late Pleistocene. The Middle Palaeolithic occupations were situated along the Jubbah palaeolake-shores, in a grassland setting with some trees. Populations procured different raw materials across the lake region to manufacture stone tools, using the implements to process plants and animals. To reach the Jubbah palaeolake, Middle Palaeolithic populations travelled into the ameliorated Nefud Desert interior, possibly gaining access from multiple directions, either using routes from the north and west (the Levant and the Sinai), the north (the Mesopotamian plains and the Euphrates basin), or the east (the Persian Gulf). The Jubbah stone tool assemblages have their own suite of technological characters, but have types reminiscent of both African Middle Stone Age and Levantine Middle Palaeolithic industries. Comparative inter-regional analysis of core technology indicates morphological similarities with the Levantine Tabun C assemblage, associated with human fossils controversially identified as either Neanderthals or Homo sapiens.

Link

Nubian Complex reduction strategies in Dhofar, southern Oman (Usik et al. 2012)

From the paper:

If there was no Nubian Complex occupation in Egypt during the MIS 5de5b hiatus, from where did the Egyptian Late Nubian, dating no earlier than MIS 5a, come? Did it spread north from Sudan or was there an expansion of Arabian Nubian Complex toolmakers back into Africa? Certainly, the striking similarities between the Classic Dhofar Nubian and Egyptian Late Nubian, as compared with the Sudanese Late Nubian, might indicate such a scenario. Again, greater chronological resolution in African and Arabian Nubian assemblages is required to answer these questions.   

It seems overly simplistic to expect the expansion of Nubian Complex toolmakers into Arabia was a single migration or event; rather, it was more likely a process of recurring bidirectional movements across the Red Sea linked to consecutive phytogeographic range expansions and contractions. At the same time, the presence of technologically distinct, non-Nubian industries elsewhere in Arabia from MIS 5a to MIS 3 indicates separate, autochthonous culture groups and/or input from other adjacent regions (Marks, 2009; Armitage et al., 2011; Petraglia et al., 2011; Delagnes et al., 2012). In the case of the Wadi Surdud stratified assemblages in Yemen, dated tow60e40 ka BP (Delagnes et al., 2012), and Jebel Faya successive assemblages B and A, bracketed within MIS 3 (Armitage et al., 2011), both archaeological sequences are thought to be the products of local lithic traditions. Clearly, Late Pleistocene demography in Arabia was far more complex than one population emanating from a single source area.   

For now, it is clear that the Afro-Arabian Nubian Complex exhibits a robust archaeological signature on both sides of the Red Sea, in terms of site density, distribution, and long-term technological variability, always based on the core principal of opposed platform exploitation. This is likely the result of populations who were well and truly established in their respective regions for an extended period of time. Perhaps we have made too much of tracking routes of expansion and the timing of sea crossings into Arabia. The Red Sea may be more of a barrier for scholars today than it ever was for humans in the Middle Stone Age. 

Related comment (my emphasis):

Nubian technology has been found in association with a modern human child within occupation Phase 3 at the site of Taramsa 1 in Egypt. Science would suggest they're modern. Unless, of course, one is willing to propose an entirely new species that occupied NE Africa 100,000 years ago? 

Nubian technology has now been identified in central Arabia (article in press by Crassard and Hilbert) and seems to be spread across central and eastern Yemen as well. The Mudayyan Industry, published in Usik et al. 2012, falls sometime after the Nubian occupation of Dhofar and is clearly derived from Nubian Levallois technology. Moreover, this particular technology governed by bidirectional recurrent Levallois blank production is interpreted as the transition from Middle Palaeolithic Levallois to Upper Palaeolithic blade reduction as exemplified at Initial Upper Palaeolithic sites in the Levant such as Boker Tachtit and Ain Difla. Essentially, the Nubians in Arabia have provided the technological missing link for the MP-UP transition in the Levant. 

So, Nubians entered Arabia sometime between 130 - 100 ka and appear to have subsequently expanded northward during the early MIS 3 wet phase that would have facilitated north-south demographic exchange throughout the Peninsula. As for the Out of Arabia expansion eastward, this is still anyone's guess. We can be sure it wasn't related to Nubian Complex toolmakers.

Quaternary International doi:dx.doi.org/10.1016/j.quaint.2012.08.2111

Nubian Complex reduction strategies in Dhofar, southern Oman

Vitaly I. Usik et al.

Between 2010 and 2012, the Dhofar Archaeological Project has located and mapped 260 Nubian Complex occurrences across Dhofar, southern Oman. Many of these lithic assemblages are technologically homologous to the Late Nubian Industry found in Africa, while others may represent a local industry derived from classic Nubian Levallois technology. The purpose of this paper is to describe the various reduction strategies encountered at a sample of Nubian Complex sites from Dhofar, to explore inter-assemblage variability, and, ultimately, to begin to articulate technological units within the “Dhofar Nubian Tradition.” To achieve this aim, we have developed an analytical scheme with which to describe variability among Nubian Levallois reduction strategies. From our analysis, we are able to discern at least two distinct industries within a regional lithic tradition. Demographic implications of the enduring Dhofar Nubian Tradition are considered in light of new evidence found throughout the Arabian Peninsula.

Link

ESHE 2012 abstracts

Some abstracts of interest from the European Society for the study of Human Evolution 2012 meeting (pdf). To avoid making this too long, I will just post the titles and the most relevant quotes. You can read the abstracts in the linked pdf for authors names and more information.

Neandertal and Denisovan Genomes from the Altai 

Susanna Sawyer  et al.

In 2010 a draft genome sequence was determined from a small finger bone found in Denisova Cave in southern Siberia. Its analysis revealed that it derives from an individual who belonged to a population related to, but distinct from, Neandertals. A molar has also been described from Denisova Cave and has shown to carry an mtDNA genome closely related to that of the finger bone.  We have recently determined the DNA sequence of the Denisova genome to a quality similar to present-day human genomes. We have also retrieved a complete mitochondrial genome and nuclear DNA sequences from an additional molar found in Denisova Cave. Furthermore, we have determined a high-quality nuclear genome from a pedal phalanx found in Denisova Cave in 2010. We show that the pedal phalanx derived from a Neandertal and thus that Neandertals as well as Denisovans have been present in the cave. We will discuss the genetic history of Denisovans as well as Neandertals in light of these new genome sequences. 

The discovery of a Neandertal genome from Denisova cave is certainly interesting. I have previously commented that:

If Vindija and Denisova, two caves less than 5,000km apart were home to people more divergent from each other than any two humans are today, it's strange to think that only "modern humans" inhabited Africa at the same time.

Now, it appears that Neandertals and Denisovans were present (when?) not only 5Mm apart, but literally on the same spot. Much later, during the Neolithic we see very differentiated humans co-existing in Europe. And, we get archaic hominins in Africa long after the appearance of anatomically modern humans there. I think the evidence is looking good for my hypothesis that regional human populations have recently gotten more similar over time through extensive admixture between divergent hominin groups, rather than that they became more dissimilar over time  through tree-like divergence.

On the same topic, here is more evidence for Neandertal presence in the Altai:

A Neanderthal mandible fragment from Chagyrskaya Cave (Altai Mountains, Russian Federation)

Both the mandible and the dentition preserve numerous derived Neanderthal traits: among else a posteriorly placed mandibular foramen, an oblique mylohyoid line, an asymmetrical P4 and continuous mid-trigonid crests on the M1 and M2. ... Ongoing ancient DNA analyses of the hominin remains from Chagyrskaya cave and absolute dates for the site will hopefully help to clarify the origin of the Altai Neanderthals, and their relationship with the Denisovans.

An hypothesis for the phylogenetic position of Homo floresiensis

Our cladistic analysis places H. floresiensis unequivocally as part of a clade with H. habilis

Who are you calling ”modern”? An assessment of the dental morphology and metrics of Homo sapiens

Although dental reduction has long been cited as a derived feature of H. sapiens, our data indicate this claim may be no longer tenable ... the single metrical assessment that groups all H. sapiens (early, Upper Paleolithic and recent) apart from other taxa is the ratio between mandibular:maxillary crown areas.  the results of our study are important for assessing recent claims of great antiquity for H. sapiens outside of Africa

Neanderthal in Malthusian demographic trap

It can be hypothesized that the demography of the Neanderthal metapopulation, living under conditions where extreme environmental instability with short periods was the norm, was primarily stagnant,

with frequent bottlenecks and episodes of decline.

 A New Framework for the Upper Paleolithic of Eastern Europe

The results of field and laboratory research during the past decade require a new classificatory framework for the Upper Paleolithic in Eastern Europe. It is now apparent that people making artifacts assigned to the Ahmarian industry occupied both the southern and northern slopes of the Caucasus Mountains (i.e., Ortvale Klde, Layer 4d; Mezmaiskaya Cave, Layer 1C). Their sites probably indicate a separate movement of anatomically modern humans (AMH) from the Near East directly into Eastern Europe, establishing an independent line of development during the earlier Upper Paleolithic that parallels the Proto-Aurignacian and Aurignacian sequence in Western and Central Europe. this East European industry is most fully represented at the Kostenki-Borshchevo sites on the Don River before 40,000 cal BP (e.g., Kostenki 14, Layer IVb). It is followed by a closely related industry, also characterized by bladelet production, that is dated to the interval between 40,000 and 30,000 cal BP in Crimea and the East European Plain. The proposed new framework reflects recognition of these distinctive East European entities and of two environmental events that had significant impacts on human settlement in Eastern Europe: (1) the Campanian Ignimbrite (CI) volcanic eruption (40,000 cal BP); and (2) the Last Glacial Maximum (LGM) ( 25,000 cal BP). It has been suggested that the early Upper Paleolithic (EUP) industry present in Eastern Europe before 40,000 cal BP should be labeled an eastern variant of the contemporaneous Proto-Aurignacian of Mediterranean Europe. However, given the separate movement of people from the Near East via the Caucasus Mountains, and independent development of the East European EUP, this industry is more appropriately termed “Proto-Gravettian.” The younger bladelet industry, which includes assemblages at Buran-Kaya III (Layer 6-1), Mira (Layer II/2), Kostenki 8 (Layer II), and probably Shlyakh (Layers 4C, 6), may be termed “Early Gravettian” to distinguish it from the classic Gravettian industry that dates to less than 30,000 cal BP (e.g., Avdeevo, Zaraisk).The upper temporal boundary of the Proto-Gravettian corresponds to the CI eruption (40,000 cal BP), while the classic Gravettian of the East European Plain appears to have been effectively terminated by the LGM ( 25,000 cal BP). Several sites that date to the 40,000–30,000 cal BP interval (e.g., Kostenki 1, Layer III) contain elements that suggest a connection with the Aurignacian technocomplex of Western-Central Europe. These assemblages may be placed into the category of “Eastern Aurignacian,” which reflects differences in content with the West and Central European sites. The apparent spread of this industry into Eastern Europe from Central Europe may be related to the impact of the CI eruption on portions of the East European Plain. 

 Conflicting dates for the Late Aterian

First at the huge Ifri n’Ammar sites, TL dates have indicated 80,000 years for the Late Middle Palaeolithic/Aterian levels. Our new C14 dates yield 35,000 BP for exactly the same levels. At the “grotte des Contrebandiers”, formerly dated at 28,000 BP by Debenath and his team, is now dated at 100,000 years by new TL dates. As starting points, this kind of methodological contradiction should be confronted, understood and resolved.

 The Rio Secco Cave in the North Adriatic Region, Italy. A new context for investigating the Neanderthal demise and the settllement of Anatomically Modern Humans

A sequence of several thin layers dated to 46.0–42.1ky Cal BP represents the final Mousterian.

The Dhofar Nubian Tradition: an enduring Middle Stone Age technocomplex in southern Arabia

Between 2010 and 2012, the Dhofar Archaeological Project has located and mapped 260 Nubian Complex occurrences across the Nejd Plateau of southern Oman. Diagnostic Nubian artifacts werefound cemented in fluvial sediments at the site of Aybut Al Auwal in Dhofar, with two OSL dates around 106 ka BP; hence, roughly contemporaneous with the African Nubian Complex (Rose et al. 2011). Many of these lithic assemblages, such as that from Aybut al Auwal, are technologically homologous to the Late Nubian Industry found in northeast Africa, sensu stricto, while others may represent local facies of the greater “Afro-Arabian Nubian Technocomplex.” This presentation describes the various reduction strategies encountered at a sample of Nubian Complex sites from Oman, explores inter-assemblage variability, and begins to articulate technological units within the “Dhofar Nubian Tradition.” To achieve this aim, we have developed an analytical scheme with which to describe technological variability among Nubian Levallois reduction strategies in both Africa and Arabia. Our analysis indicates at least two distinct Nubian industries. The first, which we refer to as the “Classic Dhofar Nubian,” is virtually identical to Late Nubian Industry from the Lower Nile Valley and Red Sea Hills in Egypt. Thee subsequent group of assemblages in Dhofar, called the “Mudayyan,” exhibits a technological shift toward diminutive Nubian Levallois cores and that, recurrent bidirectional cores with opposed, faceted striking platforms. We interpret this evidence to indicate an enduring, local Nubian tradition in Dhofar that is ultimately rooted in the African Nubian Complex. 

From Late Mousterian to Evolved Aurignacian: New evidence for the Middle-to-Upper Paleolithic transition in Mediterranean Spain

Combined, the evidence from CA and FDM indicates that, in chronostratigraphic terms, the Middle-to-Upper Paleolithic transition in Murcia consists of the replacement of a Late Mousterian by an Evolved Aurignacian and occurred some time during the 38th millennium cal BP

Pre-Neolithic dispersals into Arabia

The harsh climate of Arabia, periodically interrupted by more "green" periods has probably meant that the population living there has occasionally been driven out as climate deteriorated, with new populations moving in as climate improved. In more recent times, technological invention (e.g., the camel, the deep water well, or even more recently the discovery of oil) has allowed people to subsist in the desert a little more "comfortably."

One interesting question is whether the current Arabian population derives entirely from early Levantine Neolithic peoples, or also from people who had ventured there prior to it. A new paper in AJPA suggests that living Arabians are not entirely the descendants of Neolithic peoples, but also preserve signals of pre-Neolithic input from the Near East, by studying the mtDNA haplogroup R2 (see map on left for its current distribution).

From the paper:

It is noteworthy, however, that these pre-Neolithic sites do not bear any technological traits analogous to Terminal Pleistocene (Epipalaeolithic) assemblages found in the Near East. The only germane possibility of a connection between Arabia and the Near East during this period comes from the Faw Well site at the western edge of the Rub’ Al Khali (Edens, 2001). Although undated, the Faw Well lithic assemblage bears a close resemblance to the Late Ahmarian of the Levant (20–17 ka). Perhaps it was this, or a subsequent pulse from the Levant, that provided the demographic input expressed by the genetic lineages documented in this article.   

The results from the three analyzed southern Arabian clades do not support population continuity from the first occupants more than 50 ka ago (Fernandes et al., 2012) but do suggest some continuity across the Pleistocene- Holocene boundary. Our analysis indicates that the observed population expansion 13–12 ka is probably the result of genetic input from the Near East a few thousand years before the (debated) arrival of the PPNB culture in Arabia. If, however, there was a population expansion southward through Arabia some 13–12 ka, we have not yet found its archaeological signatures. Both regions exhibit stone tool technologies with some overlapping features, so it is warranted to suppose that we may one day locate a firm link between southern Arabia and the Near East sometime during the Late Pleistocene. Given the vast amount of unexplored territory in Arabia and paucity of archaeological sites with numerical ages, future investigations (both archaeogenetical and archaeological) throughout the Peninsula will undoubtedly serve to shed more light on this question. 

American Journal of Physical Anthropology DOI: 10.1002/ajpa.22131

Pleistocene-Holocene boundary in Southern Arabia from the perspective of human mtDNA variation

Abdulrahim Al-Abri et al.

It is now known that several population movements have taken place at different times throughout southern Arabian prehistory. One of the principal questions under debate is if the Early Holocene peopling of southern Arabia was mainly due to input from the Levant during the Pre-Pottery Neolithic B, to the expansion of an autochthonous population, or some combination of these demographic processes. Since previous genetic studies have not been able to include all parts of southern Arabia, we have helped fill this lacuna by collecting new population datasets from Oman (Dhofar) and Yemen (Al-Mahra and Bab el-Mandab). We identified several new haplotypes belonging to haplogroup R2 and generated its whole genome mtDNA tree with age estimates undertaken by different methods. R2, together with other considerably frequent southern Arabian mtDNA haplogroups (R0a, HV1, summing up more than 20% of the South Arabian gene pool) were used to infer the past effective population size through Bayesian skyline plots. These data indicate that the southern Arabian population underwent a large expansion already some 12 ka. A founder analysis of these haplogroups shows that this expansion is largely attributed to demographic input from the Near East. These results support thus the spread of a population coming from the north, but at a significantly earlier date than presently considered by archaeologists. Our data suggest that some of the mtDNA lineages found in southern Arabia have persisted in the region since the end of the Last Ice Age.

Link

Population structure in Qatar

The recent publication of Omberg et al. (2012) has reminded me of the data of Henn et al. (2012) on Qatar which I don't believe I've used yet. I used the K12b calculator on ~20,000 SNPs that are common between it and the Affymetrix chip used.

Below is the population portrait of the Qatari population:

Obviously this isn't a homogeneous population. In order to figure out which ancestral groups are present there, I ran MCLUST over the admixture proportions, which resulted in individuals assigned to five different clusters. Here are the average admixture proportions of these five clusters:

On the basis of the above, I conclude that there are several different groups represented in the Qatari population. I have absolutely no knowledge about the Qatari population, so it would be interesting to see if readers find correspondences between these and known social divisions in Qatar.

For example, I could wager that #5 which is a "Southwest Asian"+"Caucasus" mix represents a pure Arabian group with little outside influences. #1 and #2 are also Arab-like but with various degrees of admixture. #3 appears to include substantial African descendants and #4 a clear Iranian signal due to the high "Gedrosia" component. Of interest is that the "African" group #3 also scores high in the "South Asian" component.

SupportMix

This sounds amazing, hopefully I can give it a try before not too long. Software link.

BMC Genetics 2012, 13:49 doi:10.1186/1471-2156-13-49

Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations

Larsson Omberg et al.

Abstract (provisional)

Background

Populations of the Arabian Peninsula have a complex genetic structure that reflects waves of migrations including the earliest human migrations from Africa and eastern Asia, migrations along ancient civilization trading routes and colonization history of recent centuries. 1

Results

Here, we present a study of genome-wide admixture in this region, using 156 genotyped individuals from Qatar, a country located at the crossroads of these migration patterns. Since haplotypes of these individuals could have originated from many different populations across the world, we have developed a machine learning method "SupportMix" to infer loci-specific genomic ancestry when simultaneously analyzing many possible ancestral populations. Simulations show that SupportMix is not only more accurate than other popular admixture discovery tools but is the first admixture inference method that can efficiently scale for simultaneous analysis of 50-100 putative ancestral populations while being independent of prior demographic information.

Conclusions

By simultaneously using the 55 world populations from the Human Genome Diversity Panel, SupportMix was able to extract the fine-scale ancestry of the Qatar population, providing many new observations concerning the ancestry of the region. For example, as well as recapitulating the three major sub-populations in Qatar, composed of mainly Arabic, Persian, and African ancestry, SupportMix additionally identifies the specific ancestry of the Persian group to populations sampled in Greater Persia rather than from China and the ancestry of the African group to sub-Saharan origin and not Southern African Bantu origin as previously thought.

Link

Discovery at al-Magar

An excellent piece by Peter Harrigan on the newly discovered Neolithic site of Saudi Arabia.

AAPA 2012 abstracts (part 1)

Here are some interesting abstracts from the 81st Annual Meeting of the American Association of Physical Anthropologists.


Maternal marks of admixture in Cape Coloreds of South Africa.
KRISTINE G. BEATY1, DELISA L. PHILLIPS1, MACIEJ HENNEBERG2 and MICHAEL H. CRAWFORD1.

Previous studies of genetic diversity have suggested that the Cape Coloureds of South Africa are a highly admixed population with genetic roots from indigenous African groups including Khoisans, and the later arrival of Bantu speaking Xhosa farmers. Further genetic contributions came during European colonization of South Africa, which added to the inclusion of largely male European markers to the gene pool. Slaves from Indonesia, Malaysia, Madagascar and India are also thought to have contributed to the genetic makeup of this ethnic group. This study examines the maternal contribution of each of these groups to the genetic diversity of the Cape Coloreds through sequencing of the hypervariable region I of the mitochondrial DNA and through restriction fragment length polymorphism.
A total of 123 individuals were examined for this study. High frequencies of haplogroups L1 and L2 were found at 81.3 percent in this group (100 of the 123 individuals), which indicates that this group has a large African contribution to its mitochondrial makeup. Restrictions of the major European haplogroups identified nine individuals, 7.3 percent of the sample, belonged to haplogroups I and J. Five individuals (4.1 percent of the sample) belonged to the superhaplogroup M, indicating that Asian slaves did contribute to the maternal gene pool. The majority of maternal lineages in this Cape Coloured sample are African in origin, with some European influence and a small contribution from Asian maternal lineages.

Ancient DNA reveals the population origin of the Eastern Xinjiang.
SHIZHU GAO2, HONGJIE LI1, CHUNXIANG LI1 and HUI ZHOU1,3.

Connecting with the Turpan Basin, the Eurasia steppe and the Gansu Corridor, the Eastern region of Xinjiang has played a significant role in the history of human migration, cultural developments, and communications between the East and the West. The population origin, migration and integration of this region have attracted extensive interest among scientists.
In order to research the population origin and movement of the Eastern Xinjiang, genetic polymorphisms studies of the Hami population were conducted. The Hami site is located in the East of Tian-Moutain in Xinjiang, dating back to the Bronze-early Iron Age. Archaeological studies showed that the culture of the Hami site possessed features from both the East and the West. Ancient mtDNA analysis showed that A, C, D, F, G, Z and M7 of the Eastern maternal lines, and W, U2e, U4, and U5aof the Western maternal lines were identified. Tajimas’D test and mismatch distribution analysis show that the Hami population had experienced population expansion in recent time. The demographic analysis of haplogroups suggests that the populations of the Northwest China, Siberia and the Central Asia have contributed to the mtDNA gene pool of the Hami population.
Our study reveals the genetic structure of the early population in Eastern Xinjiang, and its relationships with other Eurasian populations. The results will provide valuable genetic information to further explore the population origin and migration of Xinjiang and Central Asia.

Analysis of Chuvash mtDNA points to Finno-Ugric origin.
ORION M. GRAF1, STEPHEN M. JOHNSON1, JOHN MITCHELL2, STEPHEN WILCOX3, GREGORY LIVSHITS4 and MICHAEL H. CRAWFORD1.

A sample of 92 unrelated individuals from Chuvashia, Russia was sequenced for hypervariable region-I (HVR-I) of the mtDNA molecule. These data have been verified using RFLP analysis of the control region, revealing that the majority exhibit haplogroups H (31%), U (22%), and K (11%), which occur in high frequencies in western and northern Europe, but are virtually absent in Altaic or Mongolian populations. Multidimensional scaling (MDS) was used to examine distances between the Chuvash and reference populations from the literature. Neutrality tests (Tajima’s D (-1.43365) p<0.05, Fu’s FS (-25.50518) p<0.001) and mismatch analysis, which illustrates unimodal distribution, all suggest an expanding population.
The Chuvash speak a Turkic language that is not mutually intelligible to other extant Turkish groups, and their genetics are distinct from Turkic-speaking Altaic groups. Some scholars have suggested that they are remnants of the Golden Horde, while others have advocated that they are the products of admixture between Turkic and Finno-Ugric speakers who came into contact during the 13th century. Earlier genetic research using autosomal DNA markers indicated a Finno-Ugric origin for the Chuvash. This study examines uniparental mitochondrial DNA markers to better elucidate their origins. Results from this study maintain that the Chuvash are not related to Altaic or Mongolian populations along their maternal line, thus supporting the “Elite” hypothesis that their language was imposed by a conquering group —leaving Chuvash mtDNA largely of Eurasian origin. Their maternal markers appear to most closely resemble Finno-Ugric speakers rather than Turkic speakers.

An ancient DNA perspective on the Iron Age “princely burials” from Baden-Wurttemberg, Germany.
ESTHER J. LEE1, CHRISTOPH STEFFEN1, MELANIE HARDER1, BEN KRAUSE-KYORA1, NICOLE VON WURMB-SCHWARK2 and ALMUT NEBEL3.

During the Iron Age in Europe, fundamental social principles such as age, gender, status, and kinship were thought to have played an important role in the social structure of Late Hallstatt and Early Latene societies. In order to address the question of kinship relations represented in the Iron Age “princely burials” that are characterized by their rich material culture, we carried out genetic analysis of individuals associated with the Late Hallstatt culture from Baden-Wurttemberg, Germany. Bone specimens of thirty-eight skeletal remains were collected from five sites including Asperg Grafenbuhl, Muhlacker Heidenwaldle, Hirschlanden, Ludwigsburg, and Schodeingen. Specimens were subjected to DNA extraction and amplification under strict criteria for ancient DNA analysis. We successfully obtained mitochondrial DNA (mtDNA) control region sequences from seventeen individuals that showed different haplotypes, which were assigned to nine haplogroups including haplogroups H, I, K, U5, U7, W, and X2b. Despite the lack of information from nuclear DNA to infer familial relations, information from the mtDNA suggests an intriguing genetic composition of the Late Hallstatt burials. In particular, twelve distinct haplotypes from Asperg Grafenbuhl suggest a heterogeneous composition of maternal lineages represented in the “princely burials”. The results from this study provide clues to the social structure reflected in the burial patterns of the Late Hallstatt culture and implications on the genetic landscape during the Iron Age in Europe.

Genetic snapshot from ancient nomads of Xinjiang.
HONGJIE LI1, SHIZHU GAO2, CHUNXIANG LI1, YE ZHANG1, WEN ZENG3, DONG WEI3 and HUI ZHOU1,3.

Nomads of the Eurasian steppes are known to have played an important role in the transfer commodities and culture among East Asia, Central Asia, and Europe. However, the organization of nomadic societies and initial population genetic composition of nomads were still poorly understood because of few archaeological materials and written history.
In this study, the genetic snapshot of nomads was emerged by examining mitochondrial DNA and Y-chromosome DNA of 30 human remains from Heigouliang (HGL) site in the eastern of Xinjiang, which dated 2000 years ago and associated to the nomadic culture by archaeological studies. Mitochondrial DNA analysis showed that the HGL population included both East Eurasian haplogroups (A, C, D, G, F and Z) and West Eurasian haplogroups (H, K, J, M5 and H). The component of Eastern haplogroups is dominant. The distribution frequency and Fst values of Eastern haplogroups indicated the HGL population presented close genetic affinity to the nearby region modern populations of Gansu and Qinghai, while those of western haplogroups showed similar with Mongolia and Siberia populations. The results implied various maternal lineages were introduced into the HGL population. Regarding the Y chromosomal DNA analysis, nearly all samples belonged to haplogroup Q which is thought to be the mark of the Northern Asian nomads. We identified paternal kinship among three individuals at the same tomb by Y-STR marker.
Combined with archaeological and anthropological investigations, we inferred that the gene flow from the neighboring regions was possibly associated with the expansion of Xiongnu Empire.

Vikings, merchants and pirates at the top of the world: Y-chromosomal signatures of recent and ancient migrations in the Faroe Islands.
ALLISON E. MANN1, EYDFINN MAGNUSSEN2 and CHRISTOPHER R. TILLQUIST1.

The Faroe Islands are a small archipelago in the North Atlantic Ocean. With a current population of approximately 48,000 individuals and evidence of high levels of genetic drift, the Faroese are thought to have remained highly homogeneous since the islands were settled by Vikings around 900CE. Despite their geographic isolation, however, there is historical evidence that the Faroese experienced sporadic contact with other populations since the time of founding. Contact with Barbary pirates in the seventeenth century is documented in the Faroes; there is also the possibility of modern migrations to work in the highly productive fishery. This study set out to distinguish the signal of the original founders from later migrants. Eleven Y-chromosomal STR markers were scored for 139 Faroese males from three geographically dispersed islands. Haplotypes were analyzed using Athey's method to infer haplogroup. Median-joining networks within haplogroups were constructed to determine the phylogenetic relationships within the Faroese and between likely parental populations—Danish, Irish, and Norwegians. Dispersal patterns of individuals around Faroese haplogroups suggest different times of haplotype introduction to the islands. The most common haplogroup, R1a, consists of a large node with a tight network of neighbor haplotypes, such that 68% of individuals are one or two mutational steps away. This pattern may represent the early founder event of R1a in the Faroes. Other distributions, especially of non-Scandinavian haplotypes, document more recent introductions to the islands. The overall pattern is one of a strong founder effect followed by minor instances of later migrations.

Date estimates for major mitochondrial haplogroups in Yemen.
DEVEN N. VYAS1, VIKTOR ČERNÝ2, ALI AL-MEERI3 and CONNIE J. MULLIGAN1.

Yemen occupies a key location as the first stop for anatomically modern humans on a theoretical southern migration route out of Africa. If modern humans did pass through Yemen during the first migrations out of Africa and if they left modern-day descendants, we would expect to see deep divergences in the Yemeni mitochondrial gene tree. Alternatively, if modern humans passed through Yemen but did not leave modern-day descendants or if Yemen was not on the path of these ancient migrations, we would expect more recent dates to be associated with Yemeni mitochondrial haplogroups.
Using 44 previously sequenced mitochondrial genomes as well as 24 newly sequenced mitochondrial genomes from samples collected throughout Yemen, several methods were used to estimate divergence dates of major Yemeni haplogroups including L2, M, R0a and HV. Specifically, phylogenetic trees were generated using MrBayes and maximum likelihood methods. Bayesian and ρ statistic based methods were used to estimate dates of Yemeni haplogroups and these dates were compared with each other, previously published dates for these haplogroups, approximate dates of climatic change that might be expected to correlate with population expansions, and estimates based on archaeological and paleontological evidence for the first migrations out of Africa. These comparisons are intended to cover the range of possible haplogroup divergence dates with respect to the history of early modern humans in southern Arabia.

The Arabian cradle (Fernandes et al. 2012)

I have written about Out-of-Arabia before. It is important to remember, when discussing the prehistory of Arabia in terms of the modern inhabitants, that the peninsula undergoes periods of extreme aridity followed by periods of relative humidity. Hence, unlike other regions of the world where continuous occupation can be argued due to a fairly stable climate, this is not the case for Arabia.

This observation is important because when looking at modern populations we cannot a priori assume the survival of the most ancient inhabitants. Nonetheless, it can be well argued that Homo sapiens is an extremely adaptable species: not only did it spread throughout the world in a geological blink of an eye over the last 50 thousand years or so, but also persisted throughout most of the world, coming to occupy nearly every corner of the planet.

So, even though hyper-arid periods may have driven away most people from desert areas, perhaps they did not drive away everybody. There may yet be relics of ancient populations to be found. This is exactly what a new paper proposes: that Arabia possesses extremely old mtDNA lineages within the major macro-haplogroup N, dating to about 60,000 years ago. This is quite close to the estimates time depth of haplogroup L3 which unites many Africans with the Eurasians belonging to macrohaplogroups M and N.

The mainstream understanding of what happened -according to most geneticists- is that modern humans began spreading from Africa at around that time, about 60-70 thousand years ago. On the contrary, archaeologists have found indisputable evidence (palaeoanthropological or archaeological) of modern humans in Asia from before 100 thousand years, stretching from the Levant to the southern parts of Arabia.

There are two possibilities:

• The pre-70ka modern humans in Asia left absolutely no traces of mtDNA, and all of the extant mtDNA in Asia is derived from post-70ka Africans. Hence, the pre-70ka modern humans in Asia were the descendants of failed exodi.
• The people who expanded post-70ka in Asia were descended from people who lived in Asia before 100ka, descendants of successful exodi perhaps associated with the Mount Carmel hominins or the recently discovered Nubian Complex.

I am rather in favor of the second hypothesis; the authors of the current paper favor the first. It seems unnatural that pre-70ka modern humans in Asia would just vanish: why would they? They, apparently, lived across a vast area, and were bearers of technologies that were no worse than contemporaneous African cultures. Moreover, there is simply no archaeological evidence about population movements originating in Africa at 70-60ka.

However, if the second hypothesis is true, there is a problem: haplogroup L3 is dated to 70ka, so if the expansion associated with it started in Asia, that means that there must have been substantial back-migration of L3-related lineages back to Africa. I don't see any major problem with that hypothesis, but it is true that many scientists are reluctant to feature extensive back-migration to Africa into their models. At present it has not been possible to determine to what extent genetic diversity in Africa is due to great antiquity vs. admixture of divergent human populations, which I have called Afrasian (related to Eurasians) and Palaeoafrican. If L3 did originate in Africa, then the concusion of a recent African exodus is inescapable.

The major contribution of the current paper is that it fixes a major human expansion Out-of-Arabia at very close to 60ka. Whether this expansion originated from transient Out-of-Africans who had recently exited Africa, or from long settled populations of Asia (prior to 100ka) remains to be seen.

From the paper:

The presence of archaeological sites in the Gulf basin demonstrates a long tradition of human occupation.9 However, neither direct cultural influences from the Levant nor any African influence has been detected in the Upper Palaeolithic (Late Pleistocene) lithics observed in eastern Arabia, pointing to a local development of cultural techniques.9,47 Curiously, however, the fact that some of the branches studied here include deep lineages in eastern Africa (haplogroups I, N1a, and N1f) shows that migration back to Africa occurred a number of times between 15 and 40 ka ago. 

The hypothesized Gulf Oasis9 appears to be the most likely locus of the earliest branching of haplogroup N, including the three relict basal N(xR) haplogroups studied here, as well as the major Eurasian haplogroup R. Time estimates, frequencies, and genetic diversities reported here for these haplogroups are often similar between the Levant and Arabia, challenging the hypothesis of longterm isolation between these two regions. The other two refugia identified in the south and southwest of the Peninsula might have acted as a corridor for migrations west, back toward eastern Africa. Y chromosome microsatellite diversity in the Arabian Peninsula has suggested that Dubai and Oman share genetic affinities with other Near Eastern populations, whereas Saudi Arabia and Yemen show signs of greater isolation (although for fast-evolving microsatellites, these differences might reflect more recent events).4

The American Journal of Human Genetics, 26 January 2012 doi:10.1016/j.ajhg.2011.12.010

The Arabian Cradle: Mitochondrial Relicts of the First Steps along the Southern Route out of Africa

Verónica Fernandes et al.

A major unanswered question regarding the dispersal of modern humans around the world concerns the geographical site of the first human steps outside of Africa. The “southern coastal route” model predicts that the early stages of the dispersal took place when people crossed the Red Sea to southern Arabia, but genetic evidence has hitherto been tenuous. We have addressed this question by analyzing the three minor west-Eurasian haplogroups, N1, N2, and X. These lineages branch directly from the first non-African founder node, the root of haplogroup N, and coalesce to the time of the first successful movement of modern humans out of Africa, ∼60 thousand years (ka) ago. We sequenced complete mtDNA genomes from 85 Southwest Asian samples carrying these haplogroups and compared them with a database of 300 European examples. The results show that these minor haplogroups have a relict distribution that suggests an ancient ancestry within the Arabian Peninsula, and they most likely spread from the Gulf Oasis region toward the Near East and Europe during the pluvial period 55–24 ka ago. This pattern suggests that Arabia was indeed the first staging post in the spread of modern humans around the world.

Link

Diving Into Noah's Flood

A new National Geographic documentary featuring Jeffrey Rose and the Gulf Oasis hypothesis. I wish that Noah would be left out of it -he was also featured in a recent talk about the flooding of the Black Sea- but I understand how invoking a well-known biblical figure is not bad for publicity, and if it's the hook that will get people to watch a program about cutting-edge archaeology, why should we complain?

I wasn't able to find a full page on the documentary, but here's a description from NatGeo:

Diving into Noah's Flood
Archaeologist Jeff Rose embarks on a journey to understand how the destructive forces of water might have inspired the biblical story of Noahs Ark and the great flood. Dr. Rose believes that a massive flood once swallowed a landmass as big as Great Britain, created the Persian Gulf and sent tribes of Neolithic people into constant retreat from the ever-rising waters.

You can probably find the program online if you missed its broadcast, or you can check National Geographic channel for airdates. I'll update this entry with any noteworthy information from the documentary.

Trailer:



UPDATE: In a sense, this is the antithesis of the Black Sea Flood theory as inspiration of the Gilgamesh Flood and later Biblical Flood story, in that it has people moving south-to-north, staying close to freshwater sources created by the river that once flowed in the Gulf, as the Indian Ocean rose and saltwater claimed land after land of the Gulf Oasis.

Another interesting lesson from the documentary is just how hard underwater archaeology actually is. In the earlier Black Sea talk (linked above), it was shown that thousands of years of sediments have covered most traces of any human habitation that may have existed along the pre-Flood coastline, dead organisms dropping to the sea floor like snow.

In the new NatGeo documentary it was shown how many false positives archaeologists have to contend with: things that look anomalous on the bottom of the sea often tend to be man-made, but not necessarily from the period in question; people have been dumping stuff on the sea for quite a long time.

The documentary also shows the precarious manner in which archaeologists have to work in Iraq, as the documentary host and his local contact visit various Ubaid and Sumerian sites, as well as pay a visit to the Marsh Arabs.

So, what's my opinion of the overall theory? The ideas of the Gulf Oasis theory seem plausible, and the idea that the earliest flood myth in Mesopotamia may have been related to the flooding of the Gulf seems much more plausible than the idea that it may have been related to the inundation of the Black Sea.

I am not so willing to believe, however, that people from the north played no role in the formation of the Ubaid and then the early Sumerian civilization. As I explain in the Womb of Nations, there are good arguments why most West Eurasians share relatively recent common ancestry from the northern tip of the Fertile Crescent. That does not preclude the absorption of Gulf Oasis denizens, indeed of a great number of them, depending on how close genetically they were with the proto-agriculturalists to begin with, but some substantial role must be maintained for the latter: the emergence of Ubaid/Sumerian culture cannot simply have been a local development.

Perhaps a case can be made that some of the languages of the Gulf were the descendants of the languages spoken in the Gulf Oasis. Sumerian and Elamite are the obvious candidates, although the two are not related to each other.

The advancement of the sea may have pushed Gulf Oasis denizens northward, eastward, and westward, into Mesopotamia, Arabia, and Iran, but the later gradual expansion of the land by fluvial depositions of sediments by the Tigris and Euphrates provided the added land and irrigation to motivate people to move southward. So, it is perhaps through a blending of cultures that the Proto-Sumerian civilization was born: a marsh-adapted southern element, and an agriculture-bearing northern element joining to exploit the harsh but profitable environment that was formed as a result of these two processes.

2012 looking good for my predictions

I wrote:

Many mysteries about human origins will be solved thanks to the advent of full genome sequencing. Hammer et al. found archaic admixture in Africans on just 61 genomic regions, each about ~20kb in length.
I'm willing to bet that once scientists turn their attentions to full genomes, they will have substantial and indisputable evidence for genetic divergence between stretches of human DNA that simply too deep to be explained in a conventional Out-of-Africa timeframe.
If there was substantial archaic admixture in Africa c. 35ka, according to Hammer et al.'s estimate, and coinciding with the (intrusive?) appearance of Upper Paleolithic modern humans such as Hofmeyr, then full genome sequencing will provide the smoking gun evidence for it. Such an event would simultaneously solve many mysteries about the African population, such as its apparent higher effective population size, greater allele diversity, and recombination rate.

From LiveScience via Razib:

Our species might have also hybridized with a now-extinct lineage of humanity before leaving Africa, according to findings this year from Hammer and his colleagues. Approximately 2 percent of contemporary African DNA might have come from a lineage that first diverged from the ancestors of modern humans about 700,000 years ago. For context, the Neanderthal lineage diverged from ours within the past 500,000 years, while the first signs of anatomically modern human features emerged only about 200,000 years ago. 

Hammer noted that he and his colleagues were very conservative with their analysis, only looking for lineages that diverged even more from modern humans than Neanderthals. "It's possible there may be others we can detect that are more closely related to modern humans," Hammer told LiveScience. 

"We've probably just scratched the surface of what we might find," Hammer added. "We only looked at a small number of regions of the genome. This coming year, you'll see a lot of progress made with full genome data. This year, we should be able to confirm what we found and go way beyond that."

I started talking about "Afrasians" mixing it up with "Palaeoafricans" as a major cause for African genetic diversity back in 2005. From a 2006 treatment:

It is clear that the small early modern human population must have inhabited a correspondingly small geographical region, so it is not surprising that in their movements within Africa they would have interbred with the pre-existing humans. After all, humans lived in Africa for a long time before the emergence of the moderns, and there is no reason to believe that all the African branches of humanity were wiped out to be replaced by the advancing moderns.  

I predict that in the coming years, we will learn much more about the different strata of genetic ancestry contained in Africans, as well as Europeans and East Asians. Note, also, that there is no candidate for the source population of the archaic contribution of West Africans. This, again, is not surprising, because western Africa has a much less advantageous climate than eastern Africa for bone preservation, in addition to being less well researched. Even in Europe, where anthropological science is the oldest, and cave surveys have been numerous, there are still only a handful of well-preserved Neanderthal specimens. Hopefully, some of the archaics of Africa remain to be discovered.

Some of these archaics have indeed been found.

All indications point in the direction that the Afrasian/Palaeoafrican theory is about to be confirmed. I purposefully decided to name the major recent component in our species' ancestry "Afrasian", because I did not want to take a strong stand on where this component originated (Africa or Asia). My reticence to jump on the recent Out-of-Africa bandwagon with both feet, seems to have been well-justified, as Out-of-Arabia seems to be an increasingly strong possibility: from the LiveScience piece, once again:

"I hope that our findings will stimulate research in South Asia — India in particular — to find the remains of early anatomically modern humans in that part of the world,"archaeologist Hans-Peter Uerpmann from Eberhard Karls University in Tubingen, Germany, told LiveScience. 

"Our focus this year will be on gathering evidence to reconstruct the paleoclimate in southern Arabia during the ice age that lasted between 75,000 and 60,000 years ago," paleolithic archaeologist Jeffrey Rose at the University of Birmingham in England told LiveScience. This will help researchers determine how friendly or hostile the climate was back then "to help understand the fate of these early humans on the Arabian Peninsula." 

If these ancient peoples eventually died off in Arabia, they would just be a failed migration out of Africa. However, if they survived, they may be the ancestors "to all non-African people living on Earth," Rose said. "Only further exploration throughout Arabia will answer these questions."

These Middle Stone Age inhabitants of Arabia may not just be the ancestors only of everyone outside Africa, but of many within Africa itself.