Human population history at the crossroads of East and Southeast Asia since 11,000 years ago.

Past human genetic diversity and migration between southern China and Southeast Asia have not been well characterized, in part due to poor preservation of ancient DNA in hot and humid regions. We sequenced 31 ancient genomes from southern China (Guangxi and Fujian), including two ∼12,000- to 10,000-year-old individuals representing the oldest humans sequenced from southern China. We discovered a deeply diverged East Asian ancestry in the Guangxi region that persisted until at least 6,000 years ago. We found that ∼9,000- to 6,000-year-old Guangxi populations were a mixture of local ancestry, southern ancestry previously sampled in Fujian, and deep Asian ancestry related to Southeast Asian Hòabìnhian hunter-gatherers, showing broad admixture in the region predating the appearance of farming. Historical Guangxi populations dating to ∼1,500 to 500 years ago are closely related to Tai-Kadai and Hmong-Mien speakers. Our results show heavy interactions among three distinct ancestries at the crossroads of East and Southeast Asia.

Ancient DNA and multimethod dating confirm the late arrival of anatomically modern humans in southern China.

The expansion of anatomically modern humans (AMHs) from Africa around 65,000 to 45,000 y ago (ca. 65 to 45 ka) led to the establishment of present-day non-African populations. Some paleoanthropologists have argued that fossil discoveries from Huanglong, Zhiren, Luna, and Fuyan caves in southern China indicate one or more prior dispersals, perhaps as early as ca. 120 ka. We investigated the age of the human remains from three of these localities and two additional early AMH sites (Yangjiapo and Sanyou caves, Hubei) by combining ancient DNA (aDNA) analysis with a multimethod geological dating strategy. Although U-Th dating of capping flowstones suggested they lie within the range ca. 168 to 70 ka, analyses of aDNA and direct AMS 14C dating on human teeth from Fuyan and Yangjiapo caves showed they derive from the Holocene. OSL dating of sediments and AMS 14C analysis of mammal teeth and charcoal also demonstrated major discrepancies from the flowstone ages; the difference between them being an order of magnitude or more at most of these localities. Our work highlights the surprisingly complex depositional history recorded at these subtropical caves which involved one or more episodes of erosion and redeposition or intrusion as recently as the late Holocene. In light of our findings, the first appearance datum for AMHs in southern China should probably lie within the timeframe set by molecular data of ca. 50 to 45 ka.

A new chronological framework for Chuandong Cave and its implications for the appearance of modern humans in southern China.

Chuandong Cave is an important Late Paleolithic site because it documents the early appearance of bone tools in southern China. We used the single-aliquot regenerative-dose protocol for optically stimulated luminescence dating to improve the precision of the chronology for the Chuandong Cave sedimentary sequence. The age of each layer was determined using a Bayesian modeling approach which combined optically stimulated luminescence ages with published AMS 14C dates. The results showed that Layer 10 began accumulating since 56 ± 14 ka and provides the upper age limit for all artifacts from the sequence. Bone awl tools from Layer 8, the earliest grinding bone tools in this site, were recovered within sediments between 40 ± 7 ka and 30 ± 4 ka. Layer 8 also indicates the appearance of modern humans in the Chuandong Cave sequence. Layers 4-2, ranging from 15 ± 3 ka until 11 ± 1 ka and including the Younger Dryas period, contain a few bone awls and an eyed bone needle. The shift from bone awls to eyed bone needles in the Chuandong Cave sequence indicates that modern humans adapted to the changing climate of southern China. We conclude that modern human behavior in bone tools appeared in southern China as early as 40 ± 7 ka, became more sophisticated during the Last Glacial Maximum, and spread more widely across southern China during the Younger Dryas.

The Molecular Floodgates of Stress-Induced Senescence Reveal Translation, Signalling and Protein Activity Central to the Post-Mortem Proteome.

The transitioning of cells during the systemic demise of an organism is poorly understood. Here, we present evidence that organismal death is accompanied by a common and sequential molecular flood of stress-induced events that propagate the senescence phenotype, and this phenotype is preserved in the proteome after death. We demonstrate activation of "death" pathways involvement in diseases of ageing, with biochemical mechanisms mapping onto neurological damage, embryonic development, the inflammatory response, cardiac disease and ultimately cancer with increased significance. There is sufficient bioavailability of the building blocks required to support the continued translation, energy, and functional catalytic activity of proteins. Significant abundance changes occur in 1258 proteins across 1 to 720 h post-mortem of the 12-week-old mouse mandible. Protein abundance increases concord with enzyme activity, while mitochondrial dysfunction is evident with metabolic reprogramming. This study reveals differences in protein abundances which are akin to states of stress-induced premature senescence (SIPS). The control of these pathways is significant for a large number of biological scenarios. Understanding how these pathways function during the process of cellular death holds promise in generating novel solutions capable of overcoming disease complications, maintaining organ transplant viability and could influence the findings of proteomics through "deep-time" of individuals with no historically recorded cause of death.

Analysis of the Preserved Amino Acid Bias in Peptide Profiles of Iron Age Teeth from a Tropical Environment Enable Sexing of Individuals Using Amelogenin MRM.

The first dental proteomic profile of Iron Age individuals (ca. 2000-1000 years B.P.), collected from the site of Long Long Rak rock shelter in northwest Thailand is described. A bias toward the preservation of the positively charged aromatic, and polar amino acids is observed. It is evident that the 212 proteins identified (2 peptide, FDR <1%) comprise a palimpsest of alterations that occurred both ante-mortem and post-mortem. Conservation of amino acids within the taphonomically resistant crystalline matrix enabled the identification of both X and Y chromosome linked amelogenin peptides. A novel multiple reaction monitoring method using the sex specific amelogenin protein isoforms is described and indicate the teeth are of male origin. Functional analysis shows an enrichment of pathways associated with metabolic disorders and shows a capacity for harboring these conditions prior to death. Stable isotope analysis using carbon isotopes highlights the strongly C3 based (≈80%) diet of the Long Long Rak cemetery people, which probably comprised rice combined with protein from freshwater fish among other food items. The combination of proteomics and stable isotope analysis provides a complementary strategy for assessing the demography, diet, lifestyle, and possible diseases experienced by ancient populations.

Femur associated with the Deep Skull from the West Mouth of the Niah Caves (Sarawak, Malaysia).

The skeletal remains of Pleistocene anatomically modern humans are rare in island Southeast Asia. Moreover, continuing doubts over the dating of most of these finds has left the arrival time for the region's earliest inhabitants an open question. The unique biogeography of island Southeast Asia also raises questions about the physical and cultural adaptations of early anatomically modern humans, especially within the setting of rainforest inhabitation. Within this context the Deep Skull from the West Mouth of the Niah Caves continues to figure prominently owing to its relative completeness and the greater certainty surrounding its geological age. Recovered along with this partial cranium in 1958 were several postcranial bones including a partial femur which until now has received little attention. Here we provide a description and undertake a comparison of the Deep Skull femur finding it to be very small in all of its cross-sectional dimensions. We note a number of size and shape similarities to the femora of Indigenous Southeast Asians, especially Aeta people from the Philippines. We estimate its stature to have been roughly 145-146 cm and body mass around 35 kg, confirming similarities to Aeta females. Its extreme gracility indicated by low values for a range of biomechanical parameters taken midshaft meets expectations for a very small (female) Paleolithic East Asian. Interestingly, the second moment of area about the mediolateral axis is enlarged relative to the second moment of area about the anteroposterior axis, which could potentially signal a difference in activity levels or lifestyle compared with other Paleolithic femora. However, it might also be the result of sexual dimorphism in these parameters as well as possibly reflecting changes associated with aging.

Controlled fire use in early humans might have triggered the evolutionary emergence of tuberculosis.

Tuberculosis (TB) is caused by the Mycobacterium tuberculosis complex (MTBC), a wildly successful group of organisms and the leading cause of death resulting from a single bacterial pathogen worldwide. It is generally accepted that MTBC established itself in human populations in Africa and that animal-infecting strains diverged from human strains. However, the precise causal factors of TB emergence remain unknown. Here, we propose that the advent of controlled fire use in early humans created the ideal conditions for the emergence of TB as a transmissible disease. This hypothesis is supported by mathematical modeling together with a synthesis of evidence from epidemiology, evolutionary genetics, and paleoanthropology.

The release of a troop of rehabilitated vervet monkeys (Chlorocebus aethiops) in KwaZulu-Natal, South Africa: outcomes and assessment.

Rehabilitation and release have become central to the management and welfare of primate species in South Africa such as the vervet monkey (Chlorocebus aethiops). However, limited research means that it is unknown whether rehabilitation is a successful management strategy for this species. This study describes the release of a troop of rehabilitated vervet monkeys and evaluates the results of 1 year of post-release monitoring. The released animals exhibited wild behaviours and established a home range. Survival could not be adequately evaluated due to the high number of untraceable animals, and troop composition was significantly different from that of wild troops. Improvement may be gained by radio-collaring more animals using improved technology, ensuring that troop composition is comparable to wild troops, excluding ex-pets from re-introduction and a more detailed assessment of the release site.

The craniomandibular mechanics of being human.

Diminished bite force has been considered a defining feature of modern Homo sapiens, an interpretation inferred from the application of two-dimensional lever mechanics and the relative gracility of the human masticatory musculature and skull. This conclusion has various implications with regard to the evolution of human feeding behaviour. However, human dental anatomy suggests a capacity to withstand high loads and two-dimensional lever models greatly simplify muscle architecture, yielding less accurate results than three-dimensional modelling using multiple lines of action. Here, to our knowledge, in the most comprehensive three-dimensional finite element analysis performed to date for any taxon, we ask whether the traditional view that the bite of H. sapiens is weak and the skull too gracile to sustain high bite forces is supported. We further introduce a new method for reconstructing incomplete fossil material. Our findings show that the human masticatory apparatus is highly efficient, capable of producing a relatively powerful bite using low muscle forces. Thus, relative to other members of the superfamily Hominoidea, humans can achieve relatively high bite forces, while overall stresses are reduced. Our findings resolve apparently discordant lines of evidence, i.e. the presence of teeth well adapted to sustain high loads within a lightweight cranium and mandible.

Evidence of pathological conditions in the Florisbad cranium.

Palaeopathological studies of the middle Pleistocene cranium from Florisbad (Free State, South Africa) document the presence of extensive cortical lesions and areas of thinning, a widened medullary cavity with destruction of the diploë, orbital roof lesions, a benign ectocranial neoplasm, and evidence for alveolar destruction, resorption, and antemortem tooth loss. Differential diagnosis suggests one or more possible aetiologies, including a haematological disorder, metabolic condition(s), Paget's disease of bone, or non-specific infection perhaps following trauma. Moreover, if not directly associated with those on the external vault, orbital lesions alone could have been caused by infection or an indeterminable factor such as pressure from an enlarged organ. Multiple parasagittal lesions on the internal vault cortex probably represent expansile lesions left by enlarged arachnoid granulations. A multifactorial model of pathogenesis may be most appropriate to account for dentoalveolar lesions and antemortem tooth loss. Additionally, there are clear indications of diagenetic alteration deep within the vault, as well as multiple signs of degeneration on the cranium. These complicate the assessment of pathological alterations and identification of their possible aetiology. The Florisbad cranium is the latest specimen to join the growing sample of Pleistocene hominin remains with non-fatal and non-trivial pathological disorders adding to understanding of early human ecology and lifestyle.

Affinities of the Swartkrans early Homo mandibles.

The southern African early Homo assemblage continues to make important contributions to understanding the systematics, adaptations and evolutionary history of the human genus. However, the taxonomy of this sample is in a state of flux. This study examines the size and shape of the mandibular bodies of Swartkrans SK 15 and SK 45 comparing them with variation in two early Homo taxa (H. habilis sensu lato and H. sapiens erectus). The research aims to clarify their phenetic affinities and systematics through univariate statistics, inferential testing and multivariate analysis employing size (Log-transformed) and shape (Mosimann variables). Neither of them strongly resembles H. habilis sensu lato or H. sapiens erectus, rather, they probably sample a novel species of Homo not seen in East Africa. Moreover, there is considerable morphological variability within the Swartkrans sample and the possibility of more than one novel species being sampled at this site cannot be excluded.

Rare Late Pleistocene-early Holocene human mandibles from the Niah Caves (Sarawak, Borneo).

The skeletal remains of Late Pleistocene-early Holocene humans are exceptionally rare in island Southeast Asia. As a result, the identity and physical adaptations of the early inhabitants of the region are poorly known. One archaeological locality that has historically been important for understanding the peopling of island Southeast Asia is the Niah Caves in the northeast of Borneo. Here we present the results of direct Uranium-series dating and the first published descriptions of three partial human mandibles from the West Mouth of the Niah Caves recovered during excavations by the Harrissons in 1957. One of them (mandible E/B1 100") is somewhat younger than the 'Deep Skull' with a best dating estimate of c30-28 ka (at 2σ), while the other two mandibles (D/N5 42-48" and E/W 33 24-36") are dated to a minimum of c11.0-10.5 ka (at 2σ) and c10.0-9.0 ka (at 2σ). Jaw E/B1 100" is unusually small and robust compared with other Late Pleistocene mandibles suggesting that it may have been ontogenetically altered through masticatory strain under a model of phenotypic plasticity. Possible dietary causes could include the consumption of tough or dried meats or palm plants, behaviours which have been documented previously in the archaeological record of the Niah Caves. Our work suggests a long history back to before the LGM of economic strategies involving the exploitation of raw plant foods or perhaps dried and stored meat resources. This offers new insights into the economic strategies of Late Pleistocene-early Holocene hunter-gatherers living in, or adjacent to, tropical rainforests.

Ancient nuclear genomes enable repatriation of Indigenous human remains.

After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repatriation very difficult or impossible. To determine whether DNA-based methods could resolve this important problem, we sequenced 10 nuclear genomes and 27 mitogenomes from ancient pre-European Aboriginal Australians (up to 1540 years before the present) of known provenance and compared them to 100 high-coverage contemporary Aboriginal Australian genomes, also of known provenance. We report substantial ancient population structure showing strong genetic affinities between ancient and contemporary Aboriginal Australian individuals from the same geographic location. Our findings demonstrate the feasibility of successfully identifying the origins of unprovenanced ancestral remains using genomic methods.

Reassessing the environmental context of the Aitape Skull - The oldest tsunami victim in the world?

There is increasing recognition of the long-lasting effects of tsunamis on human populations. This is particularly notable along tectonically active coastlines with repeated inundations occurring over thousands of years. Given the often high death tolls reported from historical events though it is remarkable that so few human skeletal remains have been found in the numerous palaeotsunami deposits studied to date. The 1929 discovery of the Aitape Skull in northern Papua New Guinea and its inferred late Pleistocene age played an important role in discussions about the origins of humans in Australasia for over 25 years until it was more reliably radiocarbon dated to around 6000 years old. However, no similar attention has been given to reassessing the deposit in which it was found-a coastal mangrove swamp inundated by water from a shallow sea. With the benefit of knowledge gained from studies of the 1998 tsunami in the same area, we conclude that the skull was laid down in a tsunami deposit and as such may represent the oldest known tsunami victim in the world. These findings raise the question of whether other coastal archaeological sites with human skeletal remains would benefit from a re-assessment of their geological context.

Mandibular fossa of fossil Australians.

Many questions about the skeletal adaptations and morphology of hunter-gatherers on the Australian continent remain unanswered. One anatomical region receiving little research in Australian fossils to date is the mandibular fossa. Here we report a study of three size dimensions, three shape indices and three morphological (non-metric) features of the mandibular fossa in 11 fossil Australians comparing them with modern Australo-Melanesian samples. We find broad similarities in past and modern populations in this region. Early and modern Australians and modern Papua New Guineans have elongate, broad and shallow fossae. All three populations show similarity in articular tubercle size, but postglenoid tubercle and entoglenoid process sizes show unexpected affinities. We also test for the possible presence of temporal trends in mandibular fossa size among fossil Australians. Our analyses indicate that none are present.

Possible Signatures of Hominin Hybridization from the Early Holocene of Southwest China.

We have previously described hominin remains with numerous archaic traits from two localities (Maludong and Longlin Cave) in Southwest China dating to the Pleistocene-Holocene transition. If correct, this finding has important implications for understanding the late phases of human evolution. Alternative interpretations have suggested these fossils instead fit within the normal range of variation for early modern humans in East Asia. Here we test this proposition, consider the role of size-shape scaling, and more broadly assess the affinities of the Longlin 1 (LL1) cranium by comparing it to modern human and archaic hominin crania. The shape of LL1 is found to be highly unusual, but on balance shows strongest affinities to early modern humans, lacking obvious similarities to early East Asians specifically. We conclude that a scenario of hybridization with archaic hominins best explains the highly unusual morphology of LL1, possibly even occurring as late as the early Holocene.