Earliest directly-dated human skull-cups

Background

The use of human braincases as drinking cups and containers has extensive historic and ethnographic documentation, but archaeological examples are extremely rare. In the Upper Palaeolithic of western Europe, cut-marked and broken human bones are widespread in the Magdalenian (∼15 to 12,000 years BP) and skull-cup preparation is an element of this tradition.

Principal Findings

Here we describe the post-mortem processing of human heads at the Upper Palaeolithic site of Gough''s Cave (Somerset, England) and identify a range of modifications associated with the production of skull-cups. New analyses of human remains from Gough''s Cave demonstrate the skilled post-mortem manipulation of human bodies. Results of the research suggest the processing of cadavers for the consumption of body tissues (bone marrow), accompanied by meticulous shaping of cranial vaults. The distribution of cut-marks and percussion features indicates that the skulls were scrupulously ''cleaned'' of any soft tissues, and subsequently modified by controlled removal of the facial region and breakage of the cranial base along a sub-horizontal plane. The vaults were also ‘retouched’, possibly to make the broken edges more regular. This manipulation suggests the shaping of skulls to produce skull-cups.

Conclusions

Three skull-cups have been identified amongst the human bones from Gough''s Cave. New ultrafiltered radiocarbon determinations provide direct dates of about 14,700 cal BP, making these the oldest directly dated skull-cups and the only examples known from the British Isles.     

Recent human evolution in East Asia and Australasia.

In both East Asia and Australasia arguments for evolutionary continuity between middle-late Pleistocene hominid populations and modern Homo sapiens are of long standing. In both regions, however, problems of chronological distribution, dating and preservation of hominid skeletal materials provide an effective barrier to extending regional sequences back to 'archaic' Homo sapiens or Homo erectus. The earliest securely dated modern Homo sapiens in East Asia are currently represented by Zhoukoudian Upper Cave at a minimum of 29 ka BP. In Australia skeletal remains of modern Homo sapiens have been dated to 26 ka BP, with archaeological materials at 38 to 50 ka BP. Late Pleistocene human skeletons from sites like Coobool Creek are morphologically and metrically outside the range of recent Australian Aboriginal populations. Similarly Liujiang and the Upper Cave crania can be distinguished from recent East Asian 'Mongoloids'. Evolutionary change within the Holocene needs to be taken into consideration when the evidence for regional evolutionary continuity is considered.     

The oldest anatomically modern humans from far southeast Europe: direct dating, culture and behavior

Background

Anatomically Modern Humans (AMHs) are known to have spread across Europe during the period coinciding with the Middle to Upper Paleolithic transition. Whereas their dispersal into Western Europe is relatively well established, evidence of an early settlement of Eastern Europe by modern humans are comparatively scarce.

Methodology/Principal Finding

Based on a multidisciplinary approach for the study of human and faunal remains, we describe here the oldest AMH remains from the extreme southeast Europe, in conjunction with their associated cultural and paleoecological background. We applied taxonomy, paleoecology, and taphonomy combined with geomorphology, stratigraphy, archeology and radiocarbon dating. More than 160 human bone remains have been discovered. They originate from a well documented Upper Paleolithic archeological layer (Gravettian cultural tradition) from the site of Buran-Kaya III located in Crimea (Ukraine). The combination of non-metric dental traits and the morphology of the occipital bones allow us to attribute the human remains to Anatomically Modern Humans. A set of human and faunal remains from this layer has been radiocarbon dated by Accelerator Mass Spectrometry. The direct-dating results of human bone establish a secure presence of AMHs at 31,900+240/−220 BP in this region. They are the oldest direct evidence of the presence of AMHs in a well documented archeological context. Based on taphonomical observations (cut marks and distribution of skeletal elements), they represent the oldest Upper Paleolithic modern humans from Eastern Europe, showing post-mortem treatment of the dead as well.

Conclusion/Significance

These findings are essential for the debate on the spread of modern humans in Europe during the Upper Paleolithic, as well as their cultural behaviors.     

Small-bodied humans from Palau, Micronesia

Newly discovered fossil assemblages of small bodied Homo sapiens from Palau, Micronesia possess characters thought to be taxonomically primitive for the genus Homo.

Background

Recent surface collection and test excavation in limestone caves in the rock islands of Palau, Micronesia, has produced a sizeable sample of human skeletal remains dating roughly between 940-2890 cal ybp.

Principle Findings

Preliminary analysis indicates that this material is important for two reasons. First, individuals from the older time horizons are small in body size even relative to “pygmoid” populations from Southeast Asia and Indonesia, and thus may represent a marked case of human insular dwarfism. Second, while possessing a number of derived features that align them with Homo sapiens, the human remains from Palau also exhibit several skeletal traits that are considered to be primitive for the genus Homo.

Significance

These features may be previously unrecognized developmental correlates of small body size and, if so, they may have important implications for interpreting the taxonomic affinities of fossil specimens of Homo.     

Glacial History of a Modern Invader: Phylogeography and Species Distribution Modelling of the Asian Tiger Mosquito Aedes albopictus

Background

The tiger mosquito, Aedes albopictus, is one of the 100 most invasive species in the world and a vector of human diseases. In the last 30 years, it has spread from its native range in East Asia to Africa, Europe, and the Americas. Although this modern invasion has been the focus of many studies, the history of the species’ native populations remains poorly understood. Here, we aimed to assess the role of Pleistocene climatic changes in shaping the current distribution of the species in its native range.

Methodology/Principal Findings

We investigated the phylogeography, historical demography, and species distribution of Ae. albopictus native populations at the Last Glacial Maximum (LGM). Individuals from 16 localities from East Asia were analyzed for sequence variation at two mitochondrial genes. No phylogeographic structure was observed across the study area. Demographic analyses showed a signature of population expansion that started roughly 70,000 years BP. The occurrence of a continuous and climatically suitable area comprising Southeast China, Indochinese Peninsula, and Sundaland during LGM was indicated by species distribution modelling.

Conclusions/Significance

Our results suggest an evolutionary scenario in which, during the last glacial phase, Ae. albopictus did not experience a fragmentation phase but rather persisted in interconnected populations and experienced demographic growth. The wide ecological flexibility of the species probably played a crucial role in its response to glacial-induced environmental changes. Currently, there is little information on the impact of Pleistocene climatic changes on animal species in East Asia. Most of the studies focused on forest-associated species and suggested cycles of glacial fragmentation and post-glacial expansion. The case of Ae. albopictus, which exhibits a pattern not previously observed in the study area, adds an important piece to our understanding of the Pleistocene history of East Asian biota.     

A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China

The number of Late Pleistocene hominin species and the timing of their extinction are issues receiving renewed attention following genomic evidence for interbreeding between the ancestors of some living humans and archaic taxa. Yet, major gaps in the fossil record and uncertainties surrounding the age of key fossils have meant that these questions remain poorly understood. Here we describe and compare a highly unusual femur from Late Pleistocene sediments at Maludong (Yunnan), Southwest China, recovered along with cranial remains that exhibit a mixture of anatomically modern human and archaic traits. Our studies show that the Maludong femur has affinities to archaic hominins, especially Lower Pleistocene femora. However, the scarcity of later Middle and Late Pleistocene archaic remains in East Asia makes an assessment of systematically relevant character states difficult, warranting caution in assigning the specimen to a species at this time. The Maludong fossil probably samples an archaic population that survived until around 14,000 years ago in the biogeographically complex region of Southwest China.     

Craniometric Data Supports Demic Diffusion Model for the Spread of Agriculture into Europe

Background

The spread of agriculture into Europe and the ancestry of the first European farmers have been subjects of debate and controversy among geneticists, archaeologists, linguists and anthropologists. Debates have centred on the extent to which the transition was associated with the active migration of people as opposed to the diffusion of cultural practices. Recent studies have shown that patterns of human cranial shape variation can be employed as a reliable proxy for the neutral genetic relationships of human populations.

Methodology/Principal Findings

Here, we employ measurements of Mesolithic (hunter-gatherers) and Neolithic (farmers) crania from Southwest Asia and Europe to test several alternative population dispersal and hunter-farmer gene-flow models. We base our alternative hypothetical models on a null evolutionary model of isolation-by-geographic and temporal distance. Partial Mantel tests were used to assess the congruence between craniometric distance and each of the geographic model matrices, while controlling for temporal distance. Our results demonstrate that the craniometric data fit a model of continuous dispersal of people (and their genes) from Southwest Asia to Europe significantly better than a null model of cultural diffusion.

Conclusions/Significance

Therefore, this study does not support the assertion that farming in Europe solely involved the adoption of technologies and ideas from Southwest Asia by indigenous Mesolithic hunter-gatherers. Moreover, the results highlight the utility of craniometric data for assessing patterns of past population dispersal and gene flow.     

A Pleistocene Clone of Palmer's Oak Persisting in Southern California

Background

The distribution of Palmer''s oak (Quercus palmeri Engelm.) includes numerous isolated populations that are presumably relicts of a formerly larger range that has contracted due to spreading aridity following the end of the Pleistocene.

Principal Findings

We investigated a recently discovered disjunct population of Palmer''s oak in the Jurupa Mountains of Riverside County, California. Patterns of allozyme polymorphism, morphological homogeneity, widespread fruit abortion, and evidence of fire resprouting all strongly support the hypothesis that the population is a single clone. The size of the clone and estimates of annual growth from multiple populations lead us to conclude that the clone is in excess of 13,000 years old.

Conclusions

The ancient age of the clone implies it originated during the Pleistocene and is a relict of a vanished vegetation community. Range contraction after climate change best explains the modern disjunct distribution of Q. palmeri and perhaps other plants in California.     

Rock art at the pleistocene/holocene boundary in Eastern South America

Background

Most investigations regarding the First Americans have primarily focused on four themes: when the New World was settled by humans; where they came from; how many migrations or colonization pulses from elsewhere were involved in the process; and what kinds of subsistence patterns and material culture they developed during the first millennia of colonization. Little is known, however, about the symbolic world of the first humans who settled the New World, because artistic manifestations either as rock-art, ornaments, and portable art objects dated to the Pleistocene/Holocene transition are exceedingly rare in the Americas.

Methodology/Principal Findings

Here we report a pecked anthropomorphic figure engraved in the bedrock of Lapa do Santo, an archaeological site located in Central Brazil. The horizontal projection of the radiocarbon ages obtained at the north profile suggests a minimum age of 9,370±40 BP, (cal BP 10,700 to 10,500) for the petroglyph that is further supported by optically stimulated luminescence (OSL) dates from sediment in the same stratigraphic unit, located between two ages from 11.7±0.8 ka BP to 9.9±0.7 ka BP.

Conclusions

These data allow us to suggest that the anthropomorphic figure is the oldest reliably dated figurative petroglyph ever found in the New World, indicating that cultural variability during the Pleistocene/Holocene boundary in South America was not restricted to stone tools and subsistence, but also encompassed the symbolic dimension.     

Detection and molecular characterization of 9,000-year-old Mycobacterium tuberculosis from a Neolithic settlement in the Eastern Mediterranean

Background

Mycobacterium tuberculosis is the principal etiologic agent of human tuberculosis. It has no environmental reservoir and is believed to have co-evolved with its host over millennia. This is supported by skeletal evidence of the disease in early humans, and inferred from M. tuberculosis genomic analysis. Direct examination of ancient human remains for M. tuberculosis biomarkers should aid our understanding of the nature of prehistoric tuberculosis and the host/pathogen relationship.

Methodology/Principal Findings

We used conventional PCR to examine bone samples with typical tuberculosis lesions from a woman and infant, who were buried together in the now submerged site of Atlit-Yam in the Eastern Mediterranean, dating from 9250-8160 years ago. Rigorous precautions were taken to prevent contamination, and independent centers were used to confirm authenticity of findings. DNA from five M tuberculosis genetic loci was detected and had characteristics consistent with extant genetic lineages. High performance liquid chromatography was used as an independent method of verification and it directly detected mycolic acid lipid biomarkers, specific for the M. tuberculosis complex.

Conclusions/Significance

Human tuberculosis was confirmed by morphological and molecular methods in a population living in one of the first villages with evidence of agriculture and animal domestication. The widespread use of animals was not a source of infection but may have supported a denser human population that facilitated transmission of the tubercle bacillus. The similarity of the M. tuberculosis genetic signature with those of today gives support to the theory of a long-term co-existence of host and pathogen.     

Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations

Background

A major unanswered question in the evolution of Homo sapiens is when anatomically modern human populations began to expand: was demographic growth associated with the invention of particular technologies or behavioral innovations by hunter-gatherers in the Late Pleistocene, or with the acquisition of farming in the Neolithic?

Methodology/Principal Findings

We investigate the timing of human population expansion by performing a multilocus analysis of≥20 unlinked autosomal noncoding regions, each consisting of ∼6 kilobases, resequenced in ∼184 individuals from 7 human populations. We test the hypothesis that the autosomal polymorphism data fit a simple two-phase growth model, and when the hypothesis is not rejected, we fit parameters of this model to our data using approximate Bayesian computation.

Conclusions/Significance

The data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories. In contrast, data from all four sub-Saharan African populations fit the two-phase growth model, and a range of onset times and growth rates is inferred for each population. Interestingly, both hunter-gatherers (San and Biaka) and food-producers (Mandenka and Yorubans) best fit models with population growth beginning in the Late Pleistocene. Moreover, our hunter-gatherer populations show a tendency towards slightly older and stronger growth (∼41 thousand years ago, ∼13-fold) than our food-producing populations (∼31 thousand years ago, ∼7-fold). These dates are concurrent with the appearance of the Late Stone Age in Africa, supporting the hypothesis that population growth played a significant role in the evolution of Late Pleistocene human cultures.     

Detection of Mycobacterium leprae DNA from Archaeological Skeletal Remains in Japan Using Whole Genome Amplification and Polymerase Chain Reaction

Background

Identification of pathogen DNA from archaeological human remains is a powerful tool in demonstrating that the infectious disease existed in the past. However, it is very difficult to detect trace amounts of DNA remnants attached to the human skeleton, especially from those buried in a humid atmosphere with a relatively high environmental temperature such as in Asia.

Methodology/Principal Findings

Here we demonstrate Mycobacterium leprae DNA from archaeological skeletal remains in Japan by polymerase chain reaction, DNA sequencing and single nucleotide polymorphism (SNP) analysis. In addition, we have established a highly sensitive method of detecting DNA using a combination of whole genome amplification and polymerase chain reaction, or WGA-PCR, which provides superior sensitivity and specificity in detecting DNA from trace amounts of skeletal materials.

Conclusion/Significance

We have detected M. leprae DNA in archaeological skeletal remains for the first time in the Far East. Its SNP genotype corresponded to type 1; the first detected case worldwide of ancient M. leprae DNA. We also developed a highly sensitive method to detect ancient DNA by utilizing whole genome amplification.     

Late Pleistocene human remains from Wezmeh Cave, western Iran

Paleontological analysis of remains from Wezmeh Cave in western Iran have yielded a Holocene Chalcolithic archeological assemblage, a rich Late Pleistocene carnivore faunal assemblage, and an isolated unerupted human maxillary premolar (P(3) or possibly P(4)). Species representation and U-series dating of faunal teeth place the carnivore assemblage during oxygen isotope stages (OIS) 3 and 2, and noninvasive gamma spectrometry dating of the human premolar places it at least as old as early OIS 2. The human premolar crown morphology is not diagnostic of late archaic versus early modern human affinities, but its buccolingual diameter places it at the upper limits of Late Pleistocene human P(3) and P(4) dimensions and separate from a terminal Pleistocene regional sample. Wezmeh Cave therefore provides additional Paleolithic human remains from the Zagros Mountains and further documents Late Pleistocene human association with otherwise carnivore-dominated cave assemblages.     

Evidence of a louse-borne outbreak involving typhus in Douai, 1710-1712 during the war of Spanish succession

Background

The new field of paleomicrobiology allows past outbreaks to be identified by testing dental pulp of human remains with PCR.

Methods

We identified a mass grave in Douai, France dating from the early XVIII^th century. This city was besieged during the European war of Spanish succession. We tested dental pulp from 1192 teeth (including 40 from Douai) by quantitative PCR (qPCR) for R. prowazekii and B. quintana. We also used ultra-sensitive suicide PCR to detect R. prowazekii and genotyped positive samples.

Results and Discussion

In the Douai remains, we identified one case of B. quintana infection (by qPCR) and R. prowazekii (by suicide PCR) in 6/21 individuals (29%). The R. prowazekii was genotype B, a genotype previously found in a Spanish isolate obtained in the first part of the XX^th century.

Conclusion

Louse-borne outbreaks were raging during the XVIII^th century; our results support the hypothesis that typhus was imported into Europe by Spanish soldiers from America.     

Re-emergence of Crimean-Congo hemorrhagic fever virus in Central Africa

Background

Crimean-Congo hemorrhagic fever (CCHF) is a severe tick-borne disease well recognized through Europe and Asia where diagnostic tests and medical surveillance are available. However, it is largely neglected in Africa, especially in the tropical rainforest of Central Africa where only sporadic human cases have been reported and date back to more than 30 years. We describe here an isolated human case that occurred in the Democratic Republic of the Congo in 2008 and performed phylogenetic analysis to investigate whether it resulted from a regional re-emergence or from the introduction of a novel virus in the area.

Methods and Findings

Near complete segment S and partial segment M sequences were characterized. Bayesian phylogenetic analysis and datation were performed to investigate the relationship between this new strain and viral strains from Africa, Europe and Asia. The new strain is phylogenetically close to the previously described regional genotype (II) that appears to be specific to Central Africa. Phylogenetic discrepancy between segment S and M suggested genetic exchange among local sublineages, which was dated back to 130–590 years before present.

Conclusions

The phylogenetic analyses presented here suggest ongoing CCHF virus circulation in Central Africa for a long time despite the absence of reported human cases. Many infections have most probably been overlooked, due to the weakness of healthcare structures and the absence of available diagnostic procedure. However, despite the lack of accurate ecological data, the sporadic reporting of human cases could also be partly associated with a specific sylvatic cycle in Central Africa where deforestation may raise the risks of re-emergence. For these reasons, together with the high risk of nosocomial transmission, public health authorities'' attention should be drawn to this etiological agent.     

Postglacial Colonization of the Qinling Mountains: Phylogeography of the Swelled Vent Frog (Feirana quadranus)

Background

The influence of Pleistocene climatic fluctuations on intraspecific diversification in the Qinling–Daba Mountains of East Asia remains poorly investigated. We tested hypotheses concerning refugia during the last glacial maximum (LGM) in this region by examining the phylogeography of the swelled vent frog (Feirana quadranus; Dicroglossidae, Anura, Amphibia).

Methodology/Principal Findings

We obtained complete mitochondrial ND2 gene sequences of 224 individuals from 34 populations of Feirana quadranus for phylogeographic analyses. Additionally, we obtained nuclear tyrosinase gene sequences of 68 F. quadranus, one F. kangxianensis and three F. taihangnica samples to test for mitochondrial introgression among them. Phylogenetic analyses based on all genes revealed no introgression among them. Phylogenetic analyses based on ND2 datasets revealed that F. quadranus was comprised of six lineages which were separated by deep valleys; the sole exception is that the Main Qinling and Micang–Western Qinling lineages overlap in distribution. Analyses of population structure indicated restricted gene flow among lineages. Coalescent simulations and divergence dating indicated that the basal diversification within F. quadranus may be associated with the dramatic uplifts of the Tibetan Plateau during the Pliocene. Coalescent simulations indicated that Wuling, Daba, and Western Qinling–Micang–Longmen Mountains were refugia for F. quadranus during the LGM. Demographic analyses indicated that the Daba lineage experienced population size increase prior to the LGM but the Main Qinling and the Micang–Western Qinling lineages expanded in population size and range after the LGM, and the other lineages almost have stable population size or slight slow population size decline.

Conclusions/Significance

The Qinling–Daba Mountains hosted three refugia for F. quadranus during the LGM. Populations that originated in the Daba Mountains colonized the Main Qinling Mountains after the LGM. Recent sharp expansion of the Micang–Western Qinling and Main Qinling lineages probably contribute to their present-day secondary contact.     

Gavialis from the Pleistocene of Thailand and Its Relevance for Drainage Connections from India to Java

Background

The genus Gavialis comprises a single living but endangered species, G. gangeticus, as well as fossil species recorded in the Miocene to Pleistocene deposits of the Indian subcontinent. The genus is also represented in the Pleistocene deposits of Java by the species G. bengawanicus, which was recently recognized to be valid. Surprisingly, no detailed report of the genus exists between these two provinces and the recent evolutionary history of Gavialis is not understood.

Methodology/Principal Findings

We report new material consisting of skull and mandibular remains of Gavialis from the Early Pleistocene of Khok Sung, Nakhon Ratchasima Province, northeastern Thailand. The Gavialis material described herein is attributed to Gavialis cf. bengawanicus and sheds new light on the occurrence of the genus in mainland SE Asia.

Conclusions/Significance

Comparison of this new material with other species referred to the genus Gavialis led us to preliminary restrict the content of the genus to three species, namely G. gangeticus Gmelin, G. bengawanicus Dubois and G. lewisi Lull. The occurrence of G. cf. bengawanicus in Thailand allows us to propose a scenario for the dispersal of Gavialis from Indo-Pakistan to Indonesia, thus bridging a geographical gap between these two provinces. Dispersal by sea appears a less likely possibility than dispersal through fluvial drainages.     

Paternal genetic structure of Hainan aborigines isolated at the entrance to East Asia

Background

At the southern entrance to East Asia, early population migration has affected most of the Y-chromosome variations of East Asians.

Methodology/Principal Findings

To assess the isolated genetic structure of Hainan Island and the original genetic structure at the southern entrance, we studied the Y chromosome diversity of 405 Hainan Island aborigines from all the six populations, who have little influence of the recent mainland population relocations and admixtures. Here we report that haplogroups O1a* and O2a* are dominant among Hainan aborigines. In addition, the frequency of the mainland dominant haplogroup O3 is quite low among these aborigines, indicating that they have lived rather isolated. Clustering analyses suggests that the Hainan aborigines have been segregated since about 20 thousand years ago, after two dominant haplogroups entered East Asia (31 to 36 thousand years ago).

Conclusions/Significance

Our results suggest that Hainan aborigines have been isolated at the entrance to East Asia for about 20 thousand years, whose distinctive genetic characteristics could be used as important controls in many population genetic studies.