Main Neanderthal admixture episode was c. 100,000 years ago.

This is really nice to read, considering that the archaeological data strongly favors a single out-of-Africa migration around that date (c. 125 Ka to Arabia and Palestine, see this, this and this among others, c. 100 Ka to South and East Asia) and that my own genetic modeling on mitochondrial DNA also fits that chronology (unlike most "molecular clock" scholastic rantings that are sold as "scientific truth" with no substantive backing whatsoever).

Admittedly the paper is not new (was published in February) but you know I have been missing important stuff with my information-overload stress crisis, so I'm making up now. Thanks to Ryan for bringing this up.

Martin Kuhlwilm et al., Ancient gene flow from early modern humans into Eastern Neanderthals. Nature 2016. Pay per view → LINK [doi:10.1038/nature16544]

Abstract

It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.

As the title and the abstract say, Homo sapiens migrants out of Africa (i.e. into Asia and only later into its periphery) genetically influenced the branch of Neanderthals represented by the Altai specimen, what we can consider "Asian Neanderthals" but not the branch represented by El Sidrón and Vindija ("European Neanderthals"). This happened some 100 Ka ago, coincident with the archaeologically demonstrated dates for the out-of-Africa migration for our species and also likely Neanderthal-Sapiens hybrid fossils like Skhul-5 (right -- notice its lack of chin, a key and universal trait of H. sapiens, which allows us to give up with heavy browridges and other facial armature and still retain a strong bite, among other Neanderthaloid features, however it has a rounded and elevated skullcap with a high, almost vertical, forehead, a clear Sapiens trait). 

The flow was in both directions. I do not have access to the paper itself but it is clear in the supplemental material (EDF-1). This hybridization event was distributed quite evenly among all "Greater Asians" or "non-Africans" in our species. The slightly lower score in French is surely caused by Neolithic admixture later on, bringing African-like genetics to Europe, which are absent in most of Asia, as well as in aboriginal Australasia and America. 

Another apparent highlight in this paper (EDF-7) is that a second Neanderthal population, belonging to what I called above "European Neanderthals" (but related only to El Sidrón and not to Vindija) seems to have starred a second hybridization event affecting mostly Eastern populations (Han Chinese and Papuans in this paper's dataset). This, if confirmed, is quite unexpected and would require some explanation of the kind: there was a "European Neanderthal" population somewhere in Asia in the early times of Homo sapiens colonization and they got again admixed but this time affecting the derived populations in an irregular way. These irregularities would eventually be "flattened", I guess, at regional levels but for then the West Eurasian founders were out of the way. 

A somewhat related recent paper, also mentioned by Ryan, is S. Sankararaman et al., The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans (Current Biology 2016), also pay-per-view, so judging on supplemental materials only. I must say I don't like this one that much but at least table S2 offers a summary of the state of the art of estimates of Neanderthal and "Denisovan" (H. heidelbergensis) admixture in a lot of populations (and not just three). It is apparent there that there is more Neanderthal admixture towards the East of Asia or "Greater Asia", what is very much counterintuitive and demands that a Neanderthal population (a "European Neanderthal" one per Kuhlwilm's data) existed somewhere towards the East of Asia, enabling for this secondary Neanderthal admixture event. 

Perplexing maybe but that's what the data says. I wish we could find and sequence some of those Eastern Neanderthals which are so far just a genetic ghost, with the only possible known paleontological evidence being the Narmada skullcap, which is admittedly very much Neanderthal-like but is not associated in any way to Neanderthals' typical industry: the Mousterian, which has never been found east of Iran nor south of Mongolia. 

Some have argued that the Zhirendong jaw, one of the key evidences for c. 100 Ka H. sapiens settlement of much of Asia, is a hybrid one, with clear H. sapiens traits (among others it has a chin) but also maybe "archaic" traits (among others its chin is rather small). If so, then we may be at the same time in this case before evidence of both the early migration of our species, Homo sapiens, to East Asia (or SE Asia, as it's quite to the south of China) and the second admixture event with Neanderthals, with those ghostly Oriental Neanderthals, related to El Sidrón ones in the Far West, quite paradoxically, that we have yet to properly identify.

The 300 (improved) genomes project

I must make mention here of this study, which seems an attempt to improve the available datasets of global human genetics, particularly the widely used 1000 Genomes Project. It has some less striking but still interesting highlights.

Swapan Mallick et al., The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature, 2016. Pay per view → LINK [doi:10.1038/nature18964]

Abstract

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

The genomes and some other information seem to be available in their dedicated webpage.

One of the highlights is explicit in the abstract: the single African origin of Homo sapiens and the single out-of-Africa migration episode are confirmed. I didn't have any doubt but there have been occasional speculations, based on nothing worth considering, on the conjecture of more than one migration out of Africa before the Holocene, maybe affecting Australasian peoples. Not at all: it's all based on mere misunderstanding on how "racial" traits evolved, those remote isolated peoples basically allow us for a glimpse on the plausible phenotypes of the early Eurasian migrants, which were probably quite dark in skin pigmentation and most often had thinly curled hair like that of most Africans. In fact, I have argued on occasion that it is very possible that straight hair and its less extreme variants, wavy and widely curly hair, are Neanderthal genetic and phenotype influences, positively selected for some unclear reason, and not part of our African Homo sapiens heritage. 

The other highlight that I appreciate is that they find some errors in the 1000 Genomes Project, particularly affecting Australasians, Andamanese and some Africans (quite extreme among the Khoisan particularly). This is very apparent in this map and might explain some misleading and often puzzling conclusions made by some researchers, academic or amateur alike:

Otherwise I do not find their reconstructions of the paleo-history of Humankind, based only on autosomal DNA (not the best tool for such deep incursions, really), too helpful. But the most important thing is the existence and availability of a new, allegedly improved, global dataset.

Good documentaries on human Prehistory

I just watched the documentary "First Peoples - Asia" (by NOVA) and found it quite good, discussing many of the issues that I and the readers of this blog have been following and discussing the last years on the settling of Asia (and geographical dependencies): the Zhirendong jaw, the Nubian points of Arabia, the archaic admixture events... 

The only issue is that for some odd reason (copyright masking?) interviewed people voices often have a too high pitch.

I hope the other four documentaries of the series are similarly good. I haven't watched them yet but the full playlist is embedded below beginning with the Asian colonization movie. For many readers it won't be that interesting personally (they already know all or most of it, maybe even better than what the movie explains) but it is still a promising tool to share your hobby with family and friends, so watch it in good company. 

Enjoy!

Update (Jan 9):

I've watched already four of them (Africa, Asia, Australia and Europe) and the European one is no doubt the worst: a superficial Neanderthal hybridization neo-myth spearheaded by John Hawks. Also the only map or description of the route followed by modern humans to Europe is absolute nonsense: directly from Africa via Palestine, when in fact it's extremely clear that at least most of the lineages went all the way to SE Asia and back before ever entering Europe. What happened to the spear in the rib of Zawi Chemi Shanidar man? What happened to the very fast replacement in the early Aurignacian, coincident with the Campanian Ignimbrite eruption? What about dogs? Not a word! Just whitewashing of the probably quite violent Sapiens-Neanderthal interaction. You can skip that one, really, it's pretty much nonsense.

Some hyper-hybridationism permeates all the documentaries but the others seem much better: the Asia one is quite good, the Africa one is not bad either (although could be much better if they paid more attention to archaeology, also Africa deserves 50% of the documentary space probably), the Australia one is OK but it simply ignores Papua and Wallacea altogether, what is a bit perplexing to say the least. The Europe one is just horrible: it has some facts but half of it its John Hawks' preaching his particular ideology about people being oh-so-nice that they probably used spears as toothpicks, Paabo making a lot of extra work for the cleaning crew (spectacular admittedly but should be in a separate Neanderthal docu, not in one dedicated to H. sapiens) and some real archaeology scattered around (but definitely not enough at all).

Selection against Neanderthal introgression?

Quickies

A couple of papers have been pre-published these days discussing the apparent selection against most (but not all) of the Neanderthal inheritance among modern ex-Africa humans.

Ivan Juric, Simon Aeschbacher & Graham Coop, The Strength of Selection Against Neanderthal Introgression. BioRxiv 2015 (pre-pub). Freely accessible → LINK [doi: http://dx.doi.org/10.1101/030148]

Abstract

Hybridization between humans and Neanderthals has resulted in a low level of Neanderthal ancestry scattered across the genomes of many modern-day humans. After hybridization, on average, selection appears to have removed Neanderthal alleles from the human population. Quantifying the strength and causes of this selection against Neanderthal ancestry is key to understanding our relationship to Neanderthals and, more broadly, how populations remain distinct after secondary contact. Here, we develop a novel method for estimating the genome-wide average strength of selection and the density of selected sites using estimates of Neanderthal allele frequency along the genomes of modern-day humans. We confirm that East Asians had somewhat higher initial levels of Neanderthal ancestry than Europeans even after accounting for selection. We find that there are systematically lower levels of initial introgression on the X chromosome, a finding consistent with a strong sex bias in the initial matings between the populations. We find that the bulk of purifying selection against Neanderthal ancestry is best understood as acting on many weakly deleterious alleles. We propose that the majority of these alleles were effectively neutral-and segregating at high frequency-in Neanderthals, but became selected against after entering human populations of much larger effective size. While individually of small effect, these alleles potentially imposed a heavy genetic load on the early-generation human-Neanderthal hybrids. This work suggests that differences in effective population size may play a far more important role in shaping levels of introgression than previously thought.

Kelley Harris & Rasmus Nielsen, The Genetic Cost of Neanderthal Introgression. BioRxiv 2015 (pre-pub). Freely accessible → LINK [doi: http://dx.doi.org/10.1101/030387]

Abstract

Approximately 2-4% of the human genome is in non-Africans comprised of DNA intro- gressed from Neanderthals. Recent studies have shown that there is a paucity of introgressed DNA around functional regions, presumably caused by selection after introgression. This observation has been suggested to be a possible consequence of the accumulation of a large amount of Dobzhansky-Muller incompatibilities, i.e. epistatic effects between human and Neanderthal specific mutations, since the divergence of humans and Neanderthals approx. 400-600 kya. However, using previously published estimates of inbreeding in Neanderthals, and of the distribution of fitness effects from human protein coding genes, we show that the average Neanderthal would have had at least 40% lower fitness than the average human due to higher levels of inbreeding and an increased mutational load, regardless of the dominance coefficients of new mutations. Using simulations, we show that under the assumption of additive dominance effects, early Neanderthal/human hybrids would have experienced strong negative selection, though not so strong that it would prevent Neanderthal DNA from entering the human population. In fact, the increased mutational load in Neanderthals predicts the observed reduction in Neanderthal introgressed segments around protein coding genes, without any need to invoke epistasis. The simulations also predict that there is a residual Neanderthal derived mutational load in non-African humans, leading to an average fitness reduction of at least 0.5%. Although there has been much previous debate about the effects of the out-of-Africa bottleneck on mutational loads in non-Africans, the significant deleterious effects of Neanderthal introgression have hitherto been left out of this discussion, but might be just as important for understanding fitness differences among human populations. We also show that if deleterious mutations are recessive, the Neanderthal admixture fraction would gradually increase over time due to selection for Neanderthal haplotypes that mask human deleterious mutations in the heterozygous state. This effect of dominance heterosis might partially explain why adaptive introgression appears to be widespread in nature.

"Modern human behavior" is out, generic human potential is in

There is a hypothetical model in Prehistory on something vague and ethereal which has been called "Modern human behavior" (MHB). It's not about nuclear weapons, Internet addiction nor commuting to work; it's not either about the printing machine, the Industrial Revolution and the ideals of Human Rights; it's not even about farming, living in cities and through sailing the seas... it's about something extremely vague and ill-defined but which, by definition would set apart "modern humans" (H. sapiens) from "archaic humans" (other Homo species, particularly Neanderthals).

While it is almost intangible and every day more dubious, a large number of prehistorians, some as notorious as Mellars, Stringer or Bar-Yosef, strikingly influenced by religious ideas setting an arbitrarily absolutist line between "humans" (i.e. Homo sapiens) and the rest (including other humans), have insisted for decades on the validity of such notion. Now three researchers challenge the model radically:

Christopher J. H. James, Julien Riel-Salvatore & Benjamin R. Collins, Why We Need an Alternative Approach to the Study of Modern Human Behaviour. Canadian Journal of Archaeology Volume 37, Issue 1 (2013). Pay per view → LINK

Abstract

In this paper we review recent developments in the debate over the emergence of modern human behaviour (MHB) to show that despite considerable diversity among competing models, the identification of given material traits still underpins almost all current perspectives. This approach, however, allows assumptions over the biological relationship between archaic and modern humans to permeate the definitions of MHB and, as a result, has effectively stultified archaeology’s potential contribution to the issue. We suggest that the concept of MHB as currently defined is flawed. It must either be redefined in strictly behavioural terms before reincorporation into the debate over modern human origins or, more productively, discarded all together to avoid the harsh and unrealistic dichotomy it creates between a modern and non-modern archaeological record.

The paper has been uploaded by Riel-Salvatore at Academia.edu.

They essentially argue that: that the model (of which there are several, often contradictory variants) is extremely useless and confusing, that there are "archaic humans" with many or even all traits of MHB and there are "modern humans" without many or even most of them.

They tentatively argue for a throughout revision of the model but then they seem to lean rather for the whole abandonment of the idea suggesting instead a mosaic and punctuated evolution pattern that is socio-cultural rather than merely genetic or essentialist:

(...) the rapidly accumulating evidence for a mosaic pattern of behavioural change (...) and the evidence of behavioural advances appearing and rapidly disappearing in the MSA, make the harsh dichotomy model untenable. What it does suggest is a punctuated or saltation model that led to widespread adoption of more complex behavioural patterns once the demographic circumstances were appropriate (...).

Somehow this made me recall one of my all-time favorite bands: Suicidal Tendencies and their 1990 hit "Disco's out, murder's in" (surely not apt for pop, techno and folk music lovers):

African MSA

As I mentioned recently, I am collaborating in a joint series of articles in Spanish language which try to explore the expansion of Homo sapiens from the double viewpoint of archaeology and population genetics. The series, hosted by Noticias de Prehistoria - Prehistoria al Día, began this past Thursday with David Sánchez' article on the African MSA, earliest fossils of H. sapiens and other early African cultures like the Lupemban and Aterian. In the next week I plan to explore the genetic aspects, in line with what has been published in this blog and its predecessor Leherensuge.

But so far let's try to synthesize the most important aspects of David's entry at his blog. First and foremost is this map, which I believe is of great interest because of its synthetic informative value:

Legend translation:
· Fossil remains of Homo sapiens (195-90 Ka BP)
· Aterian sites (170*-40 Ka BP)
· Nubian complex [MSA] sites (115-37 Ka BP)
· Lupemban sites (230-130 Ka BP)
· Undetermined MSA
· South African [MSA] sites (165-59 Ka BP)
· Some early MSA sites
[* personally I am a bit skeptic about the oldest Aterian dates but well...]

It's possible that it's not totally complete (feel free to add to our unavoidably limited knowledge) but it does gather in a quick view most of the African Middle Paleolithic (MSA, Aterian and Lupemban). The site of Katanda which has a special interest because of the harpoons, the earliest known ever, was absent in the version first uploaded but this has been corrected now.

This synthetic map, together with the extensive bibliography (in several languages) that David links at the bottom of his article are, I believe, an interesting reference for all those interested in the origins of Homo sapiens and its first prehistory in the African continent.

Paleolithic mattresses

Most readers are probably at least somewhat familiar with the many, often impressive and revealing, South African sites but, besides the already mentioned Katanda harpoons, what really impressed me a lot was the finding in Sibudu, Northern Mozambique, near Lake Malawi, of fragments of ancient fossilized mattresses made up of vegetation that has bug-repealing properties (→ news article at El Mundo[es]). Apparently the owners, some 73,000 years ago, burnt them now and then in order to destroy parasites. Since c. 58,000 BP the number of mattresses, fires and ashes grew, surely indicating greater population densities, at least locally. 

The ancient inhabitants of that area of Mozambique are also known to have milled and processed, some 100,000 years ago, a diverse array of plants, including sorghum, "African potato" (medicinal), wine palm, false banana, pigeon peas, etc.

Châtelperronian was made by Neanderthals

Contrary to some rumors and some skepticism, the archaeology and radiocarbon chronology appear to support only Neanderthals as the material authors of the first "mode 4" stone industry of Western Europe: the Châtelperronian.

They still allow for it, and especially the novel behavior of production and use of durable ornaments (on bone mostly), to have been influenced by the penetration of Homo sapiens.

Jean-Jacques Hublin et al., Radiocarbon dates from the Grotte du Renne and Saint-Césaire support a Neandertal origin for the Châtelperronian. PNAS 2012. Open access → LINK [doi: 10.1073/pnas.1212924109 ]

Abstract

The transition from the Middle Paleolithic (MP) to Upper Paleolithic (UP) is marked by the replacement of late Neandertals by modern humans in Europe between 50,000 and 40,000 y ago. Châtelperronian (CP) artifact assemblages found in central France and northern Spain date to this time period. So far, it is the only such assemblage type that has yielded Neandertal remains directly associated with UP style artifacts. CP assemblages also include body ornaments, otherwise virtually unknown in the Neandertal world. However, it has been argued that instead of the CP being manufactured by Neandertals, site formation processes and layer admixture resulted in the chance association of Neanderthal remains, CP assemblages, and body ornaments. Here, we report a series of accelerator mass spectrometry radiocarbon dates on ultrafiltered bone collagen extracted from 40 well-preserved bone fragments from the late Mousterian, CP, and Protoaurignacian layers at the Grotte du Renne site (at Arcy-sur-Cure, France). Our radiocarbon results are inconsistent with the admixture hypothesis. Further, we report a direct date on the Neandertal CP skeleton from Saint-Césaire (France). This date corroborates the assignment of CP assemblages to the latest Neandertals of western Europe. Importantly, our results establish that the production of body ornaments in the CP postdates the arrival of modern humans in neighboring regions of Europe. This new behavior could therefore have been the result of cultural diffusion from modern to Neandertal groups. 

Fig. 1. Calibrated ages and boundaries calculated by using OxCal 4.1 (37) and IntCal09 (36). The Grotte du Renne ages are in black and are compared with the Saint-Césaire human [Neanderthal] bone date in red. Asterisk indicates anthropogenically modified bones. The results are linked with the (NGRIP) δ18O climate record.

Importantly, it is also confirmed that Grotte-du-Renne (Arcy-sur-Cure, Burgundy) is one of the last Chatelperronian, and therefore surely Neanderthal, pockets in  Western Europe, co-existing with Aurignacian North-East and South-West of it, what is suggestive of this latter culture, probably the first settlement by Homo sapiens, expanding to SW Europe via Italy rather than Germany.

Finally, according to our results, the CP Neandertals of the Grotte du Renne, Saint-Césaire, and Les Cottés clearly postdate the earliest likely modern humans remains documented in western Europe (43) and largely overlap in time with the early Aurignacian in the Swabian area (44) and in southwestern France (42).

 

Fig. S1. Geographical distribution of the Châtelperronian assemblages and location of the three main Châtelperronian sites discussed in the text.

Hat tip to Linear Population Model.

Frontal bulge: an almost exclusive characteristic of Homo sapiens

Even if the article is behind a paywall, the abstract is self-explanatory enough to be worth a mention:

Emiliano Bruner et al., Geometric variation of the frontal squama in the genus homo: Frontal bulging and the origin of modern human morphology. American Journal of Physical Anthropology, 2013. Pay per view → LINK [doi: 10.1002/ajpa.22202]

Abstract

The majority of studies of frontal bone morphology in paleoanthropology have analyzed the frontal squama and the browridge as a single unit, mixing information from different functional elements. Taking into account that the bulging of the frontal bone is often described as a species-specific trait of Homo sapiens, in this article we analyze variation in the midsagittal profile of the genus Homo, focusing on the frontal squama alone, using landmark-based superimpositions and principal components analysis. Our results demonstrate that anatomically modern humans are definitely separated from extinct human taxa on the basis of frontal bulging. However, there is minor overlap among these groups, indicating that it is necessary to exercise caution when using this trait alone to make taxonomic inferences on individual specimens. Early modern humans do not show differences with recent modern humans, and “transitional” individuals such as Jebel Irhoud 1, Maba, and Florisbad, show modern-like frontal squama morphology. The bulging of the frontal squama in modern humans may represent a structural consequence of more general cranial changes, or it could be a response to changes in the morphology of the underlying prefrontal brain elements. A subtle difference between Neandertals and the Afro-European Middle Pleistocene Homo sample is associated with flattening at bregma in the former group, a result that merits further investigation.

Frontal bone: the frontal squama or scales is labeled as 1
Source: Atlas of Human Anatomy.

I wonder how much this confusion between frontal squama (rising of the forehead) and browridge (facepalm!) has caused the strange theories of Trinkaus and followers?

The Paleolithic of the Three Gorges region of China

The controversial construction of the Three Gorges Dam served at least to make some extensive and intensive archaeological research in the area, evidencing human presence in much of the last million years. 

Pei Shuwen et al., Middle to Late Pleistocene hominin occupation in the Three Gorges region, South China. Quaternary International (2012). Pre-publication free access → LINK (PDF) [doi:10.1016/j.quaint.2012.04.016]

Abstract

The contributions of the Chinese Paleolithic record to broader ranging paleoanthropological debates have long been difficult to decipher. The primary problem that hinders many contributions that include or focus on the Chinese record is that relatively few regions outside of the main flagship sites/basins (e.g., Zhoukoudian, Nihewan Basin, Bose Basin) have been intensively researched. Fortunately, systematic archaeological survey and excavations in the Three Gorges region, South China over the past two decades has led to the discovery of a number of important hominin fossils and Paleolithic stone artifact assemblages that have contributed to rethinking of ideas about hominin adaptations in Pleistocene China. This paper provides a detailed review of the results of recent paleoanthropological, particularly Paleolithic archaeological, research from this region.

The Three Gorges region is located in the transitional zone between the upper and middle reaches of the Yangtze River (Changjiang River). Vertebrate paleontological studies indicate that the faunas from this region belong primarily to the AiluropodaeStegodon faunal complex, a group of taxa representative of a subtropical forest environment. Systematic field surveys identified sixteen Paleolithic sites in caves and along the fluvial terraces of the Yangtze River. Based on geomorphology, biostratigraphy, and geochronology studies, these sites were formed during the Middle to Late Pleistocene. Follow up excavations at these sites led to the discovery of a large number of Paleolithic stone artifacts, Pleistocene mammal fossils, as well as some hominin fossils. Analysis of these materials has provided the opportunity to reconstruct hominin technological and mobility patterning in a restricted spatial point. The Paleolithic technology from the Three Gorges region is essentially an Oldowan-like industry (i.e., Mode 1 core and flake technologies) comprised of casual cores, whole flakes, fragments, and chunks as well as a low percentage of retouched pieces. The utilized stone raw material is primarily high sphericity cobbles and limestone, which were locally available along the ancient river bed and surrounding terraces. Most of the artifacts are fairly large in size. All flaking is by direct hard hammer in a single direction without core preparation. Unifacial choppers are the predominant core category, with fewer bifacial choppers, sporadic discoids, polyhedrons, and bifaces. The flake types demonstrate that the first stage of core reduction is represented by a low percentage of Type III and VI flakes. Some flakes are retouched unifacially by direct hard hammer percussion on the dorsal surface of the blanks. Archaic Homo sapiens and modern H. sapiens identified from some of the cave deposits are likely the hominins responsible for the production of the stone artifacts. Implications for Oldowan-like technological patterning in South China are discussed.

There is rather high detail in this paper in spite of the stone tools of East Asia tending almost invariably to simple flake forms hard to classify, arguably caused by the lack of good quality materials. But I guess that the most relevant of all is this chronology:

Of great interest are no doubt the human (or hominin) fossils found in these and previous digs. If my recollection is correct these are:

• Xinlong cave (Wushan Co., c. 118-154 Ka): Four hominin permanent teeth were recovered during the 2001 excavation field season (Fig. 2). These hominin fossils have been tentatively assigned to archaic H. sapiens, though more detailed morphometric analysis is warranted.
• Leiping cave (Wushan Co., middle or late Pleistocene): Hominin fossils including one occipital, some fragments of skull, and a frontal bone of one juvenile, and one upper incisor were collected from the sediments and tentatively assigned to archaic H. sapiens...
• Migong cave (Wushan Co., c. 13,100 BP): The hominin fossils are two fragments of parietal bones which belong to one individual (Fig. 2) and can be assigned to modern H. sapiens.
• An archaic jaw bone was also found in the 1950s without context.

It is not clear if by archaic Homo sapiens the authors mean Homo sapiens with debatable archaic features or, using obsolete terminology, other species of Homo such as Homo erectus. I'm guessing that the latter but no idea.

Propose alternative model for Neanderthal admixture in non-Africans

I must say I am totally  skeptic but just for the record:

Armando G. M. Neves & Mauricio Serva, Extremely Rare Interbreeding Events Can Explain Neanderthal DNA in Living Humans. PLoS ONE. Open Access ··> LINK [doi:10.1371/journal.pone.0047076]

Abstract

Considering the recent experimental discovery of Green et al that present-day non-Africans have 1 to of their nuclear DNA of Neanderthal origin, we propose here a model which is able to quantify the genetic interbreeding between two subpopulations with equal fitness, living in the same geographic region. The model consists of a solvable system of deterministic ordinary differential equations containing as a stochastic ingredient a realization of the neutral Wright-Fisher process. By simulating the stochastic part of the model we are able to apply it to the interbreeding ofthe African ancestors of Eurasians and Middle Eastern Neanderthal subpopulations and estimate the only parameter of the model, which is the number of individuals per generation exchanged between subpopulations. Our results indicate that the amount of Neanderthal DNA in living non-Africans can be explained with maximum probability by the exchange of a single pair of individuals between the subpopulations at each 77 generations, but larger exchange frequencies are also allowed with sizeable probability. The results are compatible with a long coexistence time of 130,000 years, a total interbreeding population of order 10⁴ individuals, and with all living humans being descendants of Africans both for mitochondrial DNA and Y chromosome.

Not only the discourse of the authors is strangely ideological (strange insistence in resuscitating the dead horse of multirregionalism and denying the rather unquestionable out-of-Africa model at least in name) but also they come to admit that:

The decision of which model correctly describes the origin of Homo sapiens is obscured by the intricacies of the statistical methods proposed for evaluating the models themselves.

And so they proceed to create their own intricate model and even more intricate interpretation.

Sincerely, their model of continuous admixture would normally cause West Eurasians (at least) to have much more Neanderthal introgression than Papuans, whose ancestors have been far away from West Eurasia (the former Neanderlands) since c. 80 Ka most probably (archaeological evidence of African-related techno-cultures in India, Petraglia 2007), while West Eurasian ancestors would have been in intense contact with Neanderthals all or most of that time until the effective Neanderthal extinction of c. 35,000 years ago. 

There's no convoluted model nor mathematical fallacy that can circumvent that: anything but a single admixture episode or process early on in the colonization of Eurasia by Homo sapiens makes no sense.

Neanderthal allele located in non-African modern humans

This should be of some interest:

Fernando L. Méndez et al., A Haplotype at STAT2 Introgressed from Neanderthals and Serves as a Candidate of Positive Selection in Papua New Guinea. AJHG 2012. Pay per view (for six months) ··> LINK [doi:10.1016/j.ajhg.2012.06.015]

Abstract

Signals of archaic admixture have been identified through comparisons of the draft Neanderthal and Denisova genomes with those of living humans. Studies of individual loci contributing to these genome-wide average signals are required for characterization of the introgression process and investigation of whether archaic variants conferred an adaptive advantage to the ancestors of contemporary human populations. However, no definitive case of adaptive introgression has yet been described. Here we provide a DNA sequence analysis of the innate immune gene STAT2 and show that a haplotype carried by many Eurasians (but not sub-Saharan Africans) has a sequence that closely matches that of the Neanderthal STAT2. This haplotype, referred to as N, was discovered through a resequencing survey of the entire coding region of STAT2 in a global sample of 90 individuals. Analyses of publicly available complete genome sequence data show that haplotype N shares a recent common ancestor with the Neanderthal sequence (∼80 thousand years ago) and is found throughout Eurasia at an average frequency of ∼5%. Interestingly, N is found in Melanesian populations at ∼10-fold higher frequency (∼54%) than in Eurasian populations. A neutrality test that controls for demography rejects the hypothesis that a variant of N rose to high frequency in Melanesia by genetic drift alone. Although we are not able to pinpoint the precise target of positive selection, we identify nonsynonymous mutations in ERBB3, ESYT1, and STAT2—all of which are part of the same 250 kb introgressive haplotype—as good candidates.

According to Wikipedia, STAT2 is a gene which offers immunity against adenoviruses, which are related to respiratory illnesses (common cold, pneumonia, bronchitis...) and some other common diseases like conjunctivitis or gastroenteritis. Most infections are mild and require no specific treatment.

This suggests me that the selective pressure was quite weak, if any at all, so its introgression is most likely the product of a fluke and not selection. However it is not totally impossible that in the past some viral strain was particularly deadly causing adaptive selection.

(Slashed out text is edited: wrong notions)

Whatever the case it is also interesting to take a look at SNPedia, which lists five SNPs in this gene:

• Rs1883832 - whose T variant is almost exclusively non-African
• Rs4810485 - whose T variant is also almost exclusively non-African
• Rs2066808 - whose T variant is dominant outside Africa but also somewhat common in Africa
• Rs1927914 - whose T variant is dominant outside Africa but also somewhat common in Africa
• Rs10983755 - whose A variant is almost exclusive of East Asians

I can only imagine (as I have not got access to the paper, so I can't double check)  that the introgressed haplotype includes the first two SNPs in their T variants (see below). If so, the Neanderthal allele should cause: increased risk of osteopenia in women, some increase in the likelihood of lymphoma, among other things (arthritis, asthma?) which I'm not sure about. I do not see any indication of the haplotype being beneficial in any way but you tell me. 

Hat tip to Jean.


Update: I just got a copy of the paper, so I share these key figures:

We can see in them that the genomic positions at 55,030,689, 55,030,712 and 55,036,471 do not seem to correspond with the SNPs listed in SNPedia (so my previous inference was wrong, it seems).

We can also see in the map how the haplotype N is distributed in what would seem to be random founder effects.

There is a chance that the Denisova variant (haplotype D) is found in some Papuans but being described by just a single transition this is not certain.

As you know I dislike molecular-clock-o-logy, which I consider close to pseudoscience but considering that there has been some paper recently claiming (as they usually do: as if it was rocket science instead of a mere educated guess) low divergence ages for Neanderthals and H. sapiens, I feel almost obliged to mention that this paper estimates the haplotype divergence at some 500-731 Ka., what, after correcting for the usual under-estimate of the Pan-Homo divergence, can be consistent with the classical archaeological understanding of the Neanderthal-Sapiens divergence before a million years ago, with the spread of Acheulean and H. heidelbergensis.

"Mostly harmless": the Campanian Ignimbrite supervolcano that could not kill Neanderthals

Or mostly not. Neither Neanderthals nor Homo sapiens in fact: in most affected archaeological sites there is continuity between under and above the tephra layer. The main exception being the Aurignacian site of Serino, just outside the supervolcano.

John Lowe et al., Volcanic ash layers illuminate the resilience of Neanderthals and early modern humans to natural hazards. PNAS 2012. Pay per view (for six months or depending on continent of reader) ··> EP link [DOI: 10.1073/pnas.1204579109]

From Fig. 2
Curved line: area where the tephra layer is preserved
CF: eruption site (Campi Flegrei)
Archaeological and paleolclimatic sites: Fr, Franchthi; GP, Golema Pesht; HF, Haua Fteah; Kl, Klissoura; Ko, Kozarnika; LC-21, EC-MAST2 PALAEO-FLUX cruise 1995, “Long Core 21”; TP, Tenaghi Philippon; TT, Tabula Traiana; 1, Serino; 2, Castelcivita; 3, Cavallo; 4, Uluzzo; 5, Uluzzo C; 6, Bernardini; 7, Crvena Stijina; 8, Oase; 9, Kostenki 14.

The authors argue that the colonization of Europe by Homo sapiens was already clearly under way when the CI eruption happened c. 40 Ka. BP (C14). Many sites surely attributable to Homo sapiens (Aurignacoid industries, which are associated to our species in Palestine since c. 55 Ka. ago) existed in many parts of Europe already, as well as in Libya (Haua Fteah) where the related Dabban industries also pre-date the CI layer.

But regarding any possible direct impact of the supervolcano on human populations of either species, the impact was very limited, at least directly:

With respect to the impacts on humans of the CI eruption, there must have been different outcomes in areas proximal or distal to the volcanic source. Proximal sites such as Serino, for example, located only ∼50 km east of the Campi Flegrei would have felt the full impact, and it is, therefore, likely that populations here were devastated; the early Aurignacian at Serino is capped by a thick CI ash layer, with no evidence of subsequent site reoccupation. Most of our newly identified CI records, however, are from sites considerably more distal from Campania, where the effects are likely to have been less severe; here, we see no evidence of continental-scale, long-term impact on hominin species.

But for Neanderthals, we were much more of a threat than any natural catastrophe, it seems:

Our results indicate that Neanderthal extinction in Europe was not associated with the CI eruption. Furthermore, in view of the continuous records of human occupation over the MP to UP transition preserved at Klissoura, Kozarnika, Tabula Traiana, and Golema Pesht, we also question the posited scale of the impact of HE4 cooling on Neanderthal demise. AMHs also seem to have been widespread throughout much of Europe before the CI eruption; thus, Neanderthal and AMH population interactions must have occurred before 40 ka B.P. Given the spatially complex nature of the Neanderthal and AMH evidence listed here, there may have been considerable variability in the timing of such encounters across Eastern Europe and Italy. Our evidence indicates that, on a continental scale, modern humans were a greater competitive threat to indigenous populations than the largest known volcanic eruption in Europe, even if combined with the deleterious effects of climatic cooling. We propose that small population numbers and high mobility may have initially saved the Neanderthals but that they were ultimately outperformed in this capacity by AMHs.

Special thanks to Eurlologist.

Craters apparent in this satellite image of the Campi Flegrei, near Naples

Clottes questions the dates of Iberian rock art

Highly respected archaeologist and prehistorian Jean Clottes has raised a question mark on the AMD datings of the Iberian rock art, recently claimed to be older than 40,000 years in some cases. He essentially questions the method of dating, frontally clashing with João Zilhão, who in the press conference[es] defended the high reliability of the Uranium series method, which he says has not yet been fully demonstrated in its efficiency. 

In my opinion one should be very cautious about the sensational results announced, because:
1. that method is new and certainly needs to be tested and refined (see below);
2. they compare Useries dates with radiocarbon dates which were obtained with a different method: it would be necessary to date the same artefact with both methods and see if they concur; this is what Valladas and her team tried to do in 2003 in Borneo and they encountered problems;
3. finally, the relation to Neandertal is pure speculation: there has never been portable art discovered in Neandertal occupation sites and there is no relationship ever established between the Neandertals and a painted rock art site. Until there is, such speculation is entirely gratuitous.'

Another highly reputed expert questioning the dating is Hellene Valladas, who dated Grotte Chauvet.

I feel unqualified to judge the merit of these objections but certainly if C14 and U-series datings of the same object are inconsistent, it means that either method (or both) must be refined. 

Sources: Pileta, Bradshaw Foundation, Bloomberg.

Red dots from El Castillo, one of which is claimed to be older than 40,000 years

H. pylori also made it out of Africa

In our guts.

Out of Africa and back (to some extent) and also again out of Africa into West Eurasia where it mixed with the Eurasian component. All of which is identifiable also in more specifically human markers like Y-DNA or mtDNA.

Yoshan Moodley et al., Age of the Association between Helicobacter pylori and Man. PLoS Pathogens 2012. Open access.

Ethio Helix has an extensive review of the entry so I'll be most succinct here.

There are more nice images in the paper but this one above probably expresses it all:

• Hp Africa 2 is found among Southern African natives (Khoisan)
• Hp Africa 1 is found among West Africans and Bantus (with some penetration in the Khoisan stomachs)
• Hp NE Africa is found at the Middle and Upper Nile and Lake Chad
• Hp Europe is found also in West Asia and North Africa and shows clear signs of being a hybrid of NE Africa and Asia2 (so it's phylogenetic position is a blend of its parents')
• Hp Asia2 is from South Asia
• Hp East Asia and Hp Sahul (Australasia) need no further explanation

My main contempt is the insistence on unrealistic molecular-clock-o-logic age estimates, which are clearly miscalibrated because the migration out of Africa took place some 90-80 thousand years ago at the latest and not 55 Ka ago as they suggest with basis. Otherwise the pattern of flows must be as they described... but add at least 50% to all age mis-estimates to make sense:

It is interesting that no exogenous lineage from Neanderthals nor Erectus/Denisovans have been identified. Did we have sex but shared no saliva? Hmmm...

Did dogs contribute decisively to our success vs. Neanderthals?

UP dog with mammoth bone from Predmosti

That's the theory proposed, with some archaeological support, by Pat Shipman at American Scientist (found via Pileta). Not only dog skulls have been found in what appear to be farewell rituals (with a bone between the teeth for example) but these findings always correspond to cultural contexts associated with our kin, such as Aurignacian and never with Neanderthals. 

Being allied with dogs certainly offered some key advantages when hunting, argues Shipman, very specially when finding the prey, a skill for which we are not too well prepared, lacking a fine sense of smell, something demonstrated in modern hunt contexts. 

Domesticating dogs clearly improves humans’ hunting success and efficiency—whether the game (or the dog) is large or small. The same must have been true in the Paleolithic. If Neandertals did not have domestic dogs and anatomically modern humans did, these hunting companions could have made all the difference in the modern human–Neandertal competition. 

A miscellaneous matter that Shipman considers at the end of the essay is whether the well known ability of communicating silently by looking at each others' eyes may have helped to this human-dog cooperation. Apparently dogs are also able to follow the direction of the eyes of a human and infer commands or directions from that. This may have been a product of selective breeding but in any case it is something that it's there and is part of human-dog communication.

See also category: dog in this blog and its predecessor.


Update (May 19): Millán mentions in the comments section that there are some studies from a century ago that claim that Neanderthals might have domesticated dogs first:

• M. Moulin 1907[fr].
• M. Baudoin 1907[fr].
• Boulletin de la Societé Prehistorique de France 1910[fr].

It is not clear however if these claims can withstand the passing of time, they are after all from the time of Pitdown Man, when Archaeology was still a bit confused and confusing - but also when the pillars of modern Prehistoric understanding were first laid.

Key remains of American Prehistory stolen

The Tulum man in situ before the robbery

The skeleton known as Tulum man, found in a cenote (flooded underground chasm) in Quintana Roo, Mexico, and which was not yet retrieved from site by archaeologists, has gone missing. 

The Tulum man was dated to at least 10,000 years ago and therefore was one of the key pieces in the reconstruction of the Prehistory of America.

The managers of the research project, dependent of the National Institute of Anthropology and History (INAH) have denounced having been repeatedly the victim of thieves. That in spite of having kept a policy of strict discretion about the exact location of the findings. 

Requests of help have been distributed among divers because such a heist would have needed the participation of several of them.

Source: Milenio[es].

Laos inhabited by H. sapiens since maybe 56,000 years ago?

Just a quick note because I really could not find too much.

I just read at a very succint note at Science Daily that:

Researchers have discovered the oldest known human remains in Southeast Asia, a partial human skull dating to at least 40,000 years ago. Excavations at Tam Pa Ling cave in northern Laos produced a dozen pieces from a Stone Age person’s skull, including a skullcap and a lower jaw, anthropologist Laura Shackelford of the University of Illinois at Urbana-Champaign reported April 14. Small front teeth, a rounded brain case and other traits identify the reassembled fossil as a modern Homo sapiens, Shackelford said. The find supports proposals that at least some human migrations out of Africa around 100,000 years ago followed a southern route that led to Southeast Asia.

Nothing more of relevance. I could find a paper (ppv) by Dr. Shackleford on Laos but it discusses another cave and much more recent dates (c. 15 Ka ago).

On the other hand I found a paper on another Laotian cave by different authors which mentions undefined human presence c.56 Ka ago:

Valéry Zeitoun et al, Multi-millennial occupation in northwestern Laos: Preliminary results of excavations at the Ngeubhinh Mouxeu rock-shelter. Comptes Rendus Palevol 2011. Pay per view.

Abstract

With over half a century of political instability, resulting from armed conflicts, decolonisation and the Cold War, archaeological investigations in Laos have been rare, leaving little more than a blank page in the chapter of Southeast Asia's prehistory. Recent research has shown that Laos holds a rich prehistoric heritage. In conjunction with the research initiated by J. White who conducted the first professional archaeological survey of northern Laos since decades, we have extended the investigations to the Luang Namtha province. This work allowed us to gather important data about Hoabinhian stone tool assemblages and former cultures. In particular, the archaeological remains and dating from the Ngeubhinh Mouxeu rock-shelter indicate that this mountainous region of Laos has been inhabited over a long period of time that possibly spans as far back as 56,000 ± 3000 BP.

While, by the moment, I ignore many details, I believe it is very interesting to mention as the early colonization of SE Asia by our species is still not well understood (and yet may be critical to understand all, or at the very least much, of Eurasian, plus aboriginal Australasian and American origins).

With due caution, I think we can infer from these and other less direct (Indian and Arabian archaeology) or more controversial materials (Liujiang skull, Luzon foot bone, speculations about very early colonization of Australia) that the colonization of SE Asia by our kind can be traced to at least that date of 56 Ka ago, probably even earlier.


Update (Aug 21): see this newer entry.

Aurignacian jaws are modern (Homo sapiens)

The adscription of the Aurignacian techno-culture in Europe to Homo sapiens (alias 'anatomically modern humans', or 'AMH' or 'modern humans' for short) was only indirectly supported, mostly by remains from Palestine (Ahmarian or Ahmiran culture, part of the wider 'Aurignacoid' complex of West Eurasia). 

Recently a jaw from England and some teeth from Italy were also alleged to support very early presence of our species in Europe. However the conclusions were controversial and the findings had, like Oase 1, no direct relation with Aurignacian or other Aurignacoid cultures (in fact the Italian teeth belonged to the Uluzzian, what is a very different debate).

Now however a couple of lower jaws from France seem to finally settle the matter regarding the authorship of Aurignacian:

Christine Verna et al., The Early Aurignacian human remains from La Quina-Aval (France). Science 2012. Pay per view.

Abstract

There is a dearth of diagnostic human remains securely associated with the Early Aurignacian of western Europe, despite the presence of similarly aged early modern human remains from further east. One small and fragmentary sample of such remains consists of the two partial immature mandibles plus teeth from the Early Aurignacian of La Quina-Aval, Charente, France. The La Quina-Aval 4 mandible exhibits a prominent anterior symphyseal tuber symphyseos on a vertical symphysis and a narrow anterior dental arcade, both features of early modern humans. The dental remains from La Quina-Aval 1 to 4 (a dm1, 2 dm2, a P4 and a P4) are unexceptional in size and present occlusal configurations that combine early modern human features with a few retained ancestral ones. Securely dated to ∼33 ka 14C BP (∼38 ka cal BP), these remains serve to confirm the association of early modern humans with the Early Aurignacian in western Europe.

Found via Neanderfollia[cat].

Anomalous Paleolithic skull from South China

This is sure going to cause some heated debates:

Darren Curnoe et al., Human Remains from the Pleistocene-Holocene Transition of Southwest China Suggest a Complex Evolutionary History for East Asians. PLoS ONE 2012. Open access.

See also the press release (Eureka Alert) and a photo gallery (Live Science).

And this is what is all about:

It's not the skull of Darth Vader, although I know you thought so as soon as you saw it, but actually that of a person living some 14,000 years ago at Longling cave, known as Longlin 1.

The authors of the paper argue on craniometric grounds that the specimen may not be a modern human, however in all PC analysis the skull falls (oddly enough) within or very close to modern human clusters. Only in the PC3 some differences show up. 

In fact the closest among those skulls analyzed in fig. 8 is Mai Da Nuoc[PDF], an Early Hoabinhian skull from nearby Vietnam, which is claimed to be Australoid (but does not look at all like the Australian skulls I'm familiar with, normally quite broader).

In fact I have been searching and I found at least one skull that looks a lot like Longlin 1: Peñón woman from Mexico:

(Source)

She's one of a number of Paleoindian skulls that have puzzled prehistorians because they are not quite like most modern Native American skulls. However to my eyes, the Peñuelas skull (Chile) skull is not that different, even if it is also more like modern Native American ones.

Also to my eyes, those very marked cheek bones (regardless of whether they may have been produced by mastication) remind me of one of the most characteristic traits of the so-called Mongoloid type (which is quite unreal and plural in fact): prominent cheekbones that give the face a flat appearance.

But I'll leave that to the experts. Not worth bumping heads for something that may well be partly epigenetic/environmental for all I know.

What I do not see is any ground for the claims of the authors that it could be a newly found species. They even have worked a fancy reconstruction that makes Longlin 1 to look like a well-known reconstruction (by the same author) of the notorious Hobbit (when the skulls do not look at all similar):

Credit: Peter Schouten (info)

Notice please how any trait that could make him look Mongoloid (East Asian or Native American) has been scrapped from the reconstruction: he has dark brown skin, beard (which could well have been shaven by a professional just yesterday) and a hairy body, a very broad nose that does not fit at all with the small triangular orifice, absolute lack of epicanthic fold - plus very small ears that make him look odd. 

Another analyzed skull from the same area is Maludong 1704, of which only the vault remains. This one overlaps in the analysis (fig. 9) with Crô-Magnon 1, however when more samples are added (fig. 10) some archaic skulls (H. erectus) also show up close, as do again CM1, early African H. sapiens and Nazlet Khater 2. 

For me, with due caution, modern proto-Mongoloid H. sapiens (anomalous) but your call: the debate is served.


Update (Mar 17): I must mention that the excellent anthropological artist Zaender (which I have mentioned before) has also produced his own versions of the Maludong people without most of the exotic fancy of Schouten's reconstruction:

Credit Zaender

He has another example at his blog: Regional Ancestry Bands.

The ears still look small to me and the nose and lips unnecessarily too wide but it is probably more correct re. eyes and hair.

In any case it makes evident that it's very difficult to actually reconstruct a face from just a skull when all the expressiveness and even most ethnic traits are in the flesh and skin, being impossible to discern from a mere skull.


Update (Mar 30):

Another interesting reconstruction by Zaender (he drew the nose smaller on my suggestion):

Credit: Zaender

See the discussion below and at his blog.

Also very interesting and surely important is the argumentation by Biological Anthropologist A.P. Van Arsdale that the main diveregent measure is the zygomatic bone but this one is fractured in several points, what may distort the results singnificantly:

Otherwise the skull fits quite well with modern East Asian metrics.