Paleolithic to Bronze Age Siberians Reveal Connections with First Americans and across Eurasia.

Modern humans have inhabited the Lake Baikal region since the Upper Paleolithic, though the precise history of its peoples over this long time span is still largely unknown. Here, we report genome-wide data from 19 Upper Paleolithic to Early Bronze Age individuals from this Siberian region. An Upper Paleolithic genome shows a direct link with the First Americans by sharing the admixed ancestry that gave rise to all non-Arctic Native Americans. We also demonstrate the formation of Early Neolithic and Bronze Age Baikal populations as the result of prolonged admixture throughout the eighth to sixth millennium BP. Moreover, we detect genetic interactions with western Eurasian steppe populations and reconstruct Yersinia pestis genomes from two Early Bronze Age individuals without western Eurasian ancestry. Overall, our study demonstrates the most deeply divergent connection between Upper Paleolithic Siberians and the First Americans and reveals human and pathogen mobility across Eurasia during the Bronze Age.

Ancient genomes reveal insights into ritual life at Chichén Itzá.

The ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods (AD 600-1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica1-4. However, many questions about the social and cultural use of its ceremonial spaces, as well as its population's genetic ties to other Mesoamerican groups, remain unanswered2. Here we present genome-wide data obtained from 64 subadult individuals dating to around AD 500-900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes5, but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.

The demise of the giant ape Gigantopithecus blacki.

The largest ever primate and one of the largest of the southeast Asian megafauna, Gigantopithecus blacki1, persisted in China from about 2.0 million years until the late middle Pleistocene when it became extinct2-4. Its demise is enigmatic considering that it was one of the few Asian great apes to go extinct in the last 2.6 million years, whereas others, including orangutan, survived until the present5. The cause of the disappearance of G. blacki remains unresolved but could shed light on primate resilience and the fate of megafauna in this region6. Here we applied three multidisciplinary analyses-timing, past environments and behaviour-to 22 caves in southern China. We used 157 radiometric ages from six dating techniques to establish a timeline for the demise of G. blacki. We show that from 2.3 million years ago the environment was a mosaic of forests and grasses, providing ideal conditions for thriving G. blacki populations. However, just before and during the extinction window between 295,000 and 215,000 years ago there was enhanced environmental variability from increased seasonality, which caused changes in plant communities and an increase in open forest environments. Although its close relative Pongo weidenreichi managed to adapt its dietary preferences and behaviour to this variability, G. blacki showed signs of chronic stress and dwindling populations. Ultimately its struggle to adapt led to the extinction of the greatest primate to ever inhabit the Earth.

Earliest known human burial in Africa.

The origin and evolution of hominin mortuary practices are topics of intense interest and debate1-3. Human burials dated to the Middle Stone Age (MSA) are exceedingly rare in Africa and unknown in East Africa1-6. Here we describe the partial skeleton of a roughly 2.5- to 3.0-year-old child dating to 78.3 ± 4.1 thousand years ago, which was recovered in the MSA layers of Panga ya Saidi (PYS), a cave site in the tropical upland coast of Kenya7,8. Recent excavations have revealed a pit feature containing a child in a flexed position. Geochemical, granulometric and micromorphological analyses of the burial pit content and encasing archaeological layers indicate that the pit was deliberately excavated. Taphonomical evidence, such as the strict articulation or good anatomical association of the skeletal elements and histological evidence of putrefaction, support the in-place decomposition of the fresh body. The presence of little or no displacement of the unstable joints during decomposition points to an interment in a filled space (grave earth), making the PYS finding the oldest known human burial in Africa. The morphological assessment of the partial skeleton is consistent with its assignment to Homo sapiens, although the preservation of some primitive features in the dentition supports increasing evidence for non-gradual assembly of modern traits during the emergence of our species. The PYS burial sheds light on how MSA populations interacted with the dead.

Triangulation supports agricultural spread of the Transeurasian languages.

The origin and early dispersal of speakers of Transeurasian languages-that is, Japanese, Korean, Tungusic, Mongolic and Turkic-is among the most disputed issues of Eurasian population history1-3. A key problem is the relationship between linguistic dispersals, agricultural expansions and population movements4,5. Here we address this question by 'triangulating' genetics, archaeology and linguistics in a unified perspective. We report wide-ranging datasets from these disciplines, including a comprehensive Transeurasian agropastoral and basic vocabulary; an archaeological database of 255 Neolithic-Bronze Age sites from Northeast Asia; and a collection of ancient genomes from Korea, the Ryukyu islands and early cereal farmers in Japan, complementing previously published genomes from East Asia. Challenging the traditional 'pastoralist hypothesis'6-8, we show that the common ancestry and primary dispersals of Transeurasian languages can be traced back to the first farmers moving across Northeast Asia from the Early Neolithic onwards, but that this shared heritage has been masked by extensive cultural interaction since the Bronze Age. As well as marking considerable progress in the three individual disciplines, by combining their converging evidence we show that the early spread of Transeurasian speakers was driven by agriculture.

Forest mosaics, not savanna corridors, dominated in Southeast Asia during the Last Glacial Maximum.

The dominant paradigm is that large tracts of Southeast Asia's lowland rainforests were replaced with a "savanna corridor" during the cooler, more seasonal climates of the Last Glacial Maximum (LGM) (23,000 to 19,000 y ago). This interpretation has implications for understanding the resilience of Asia's tropical forests to projected climate change, implying a vulnerability to "savannization". A savanna corridor is also an important foundation for archaeological interpretations of how humans moved through and settled insular Southeast Asia and Australia. Yet an up-to-date, multiproxy, and empirical examination of the palaeoecological evidence for this corridor is lacking. We conducted qualitative and statistical analyses of 59 palaeoecological records across Southeast Asia to test the evidence for LGM savannization and clarify the relationships between methods, biogeography, and ecological change in the region from the start of Late Glacial Period (119,000 y ago) to the present. The pollen records typically show montane forest persistence during the LGM, while δ13C biomarker proxies indicate the expansion of C4-rich grasslands. We reconcile this discrepancy by hypothesizing the expansion of montane forest in the uplands and replacement of rainforest with seasonally dry tropical forest in the lowlands. We also find that smooth forest transitions between 34,000 and 2,000 y ago point to the capacity of Southeast Asia's ecosystems both to resist and recover from climate stressors, suggesting resilience to savannization. Finally, the timing of ecological change observed in our combined datasets indicates an 'early' onset of the LGM in Southeast Asia from ~30,000 y ago.

Environmental drivers of megafauna and hominin extinction in Southeast Asia.

Southeast Asia has emerged as an important region for understanding hominin and mammalian migrations and extinctions. High-profile discoveries have shown that Southeast Asia has been home to at least five members of the genus Homo1-3. Considerable turnover in Pleistocene megafauna has previously been linked with these hominins or with climate change4, although the region is often left out of discussions of megafauna extinctions. In the traditional hominin evolutionary core of Africa, attempts to establish the environmental context of hominin evolution and its association with faunal changes have long been informed by stable isotope methodologies5,6. However, such studies have largely been neglected in Southeast Asia. Here we present a large-scale dataset of stable isotope data for Southeast Asian mammals that spans the Quaternary period. Our results demonstrate that the forests of the Early Pleistocene had given way to savannahs by the Middle Pleistocene, which led to the spread of grazers and extinction of browsers-although geochronological limitations mean that not all samples can be resolved to glacial or interglacial periods. Savannahs retreated by the Late Pleistocene and had completely disappeared by the Holocene epoch, when they were replaced by highly stratified closed-canopy rainforest. This resulted in the ascendency of rainforest-adapted species as well as Homo sapiens-which has a unique adaptive plasticity among hominins-at the expense of savannah and woodland specialists, including Homo erectus. At present, megafauna are restricted to rainforests and are severely threatened by anthropogenic deforestation.

Isotopic and DNA analyses reveal multiscale PPNB mobility and migration across Southeastern Anatolia and the Southern Levant.

Growing reliance on animal and plant domestication in the Near East and beyond during the Pre-Pottery Neolithic B (PPNB) (the ninth to eighth millennium BC) has often been associated with a "revolutionary" social transformation from mobility toward more sedentary lifestyles. We are able to yield nuanced insights into the process of the Neolithization in the Near East based on a bioarchaeological approach integrating isotopic and archaeogenetic analyses on the bone remains recovered from Nevali Çori, a site occupied from the early PPNB in Turkey where some of the earliest evidence of animal and plant domestication emerged, and from Ba'ja, a typical late PPNB site in Jordan. In addition, we present the archaeological sequence of Nevali Çori together with newly generated radiocarbon dates. Our results are based on strontium (87Sr/86Sr), carbon, and oxygen (δ18O and δ13Ccarb) isotopic analyses conducted on 28 human and 29 animal individuals from the site of Nevali Çori. 87Sr/86Sr results indicate mobility and connection with the contemporaneous surrounding sites during the earlier PPNB prior to an apparent decline in this mobility at a time of growing reliance on domesticates. Genome-wide data from six human individuals from Nevali Çori and Ba'ja demonstrate a diverse gene pool at Nevali Çori that supports connectedness within the Fertile Crescent during the earlier phases of Neolithization and evidence of consanguineous union in the PPNB Ba'ja and the Iron Age Nevali Çori.

Anthropogenic impacts on Late Holocene land-cover change and floristic biodiversity loss in tropical southeastern Asia.

Southern China and Southeast Asia witnessed some of their most significant economic and social changes relevant to human land use during the Late Holocene, including the intensification and spread of rice agriculture. Despite rice growth being associated with a number of earth systems impacts, how these changes transformed tropical vegetation in this region of immense endemic biodiversity remains poorly understood. Here, we compile a pollen dataset incorporating ∼150,000 identifications and 233 pollen taxa to examine past changes in floral biodiversity, together with a compilation of records of forest decline across the region using 14 pollen records spanning lowland to mountain sites. Our results demonstrate that the rise of intensive rice agriculture from approximately 2,000 y ago led not only to extensive deforestation but also to remarkable changes of vegetation composition and a reduction in arboreal diversity. Focusing specifically on the Tertiary relic tree species, the freshwater wetland conifer Glyptostrobus (Glyptostrobus pensilis), we demonstrate how key species that had survived changing environmental conditions across millions of years shrank in the face of paddy rice farming and human disturbance.

No evidence for widespread island extinctions after Pleistocene hominin arrival.

The arrival of modern humans into previously unoccupied island ecosystems is closely linked to widespread extinction, and a key reason cited for Pleistocene megafauna extinction is anthropogenic overhunting. A common assumption based on late Holocene records is that humans always negatively impact insular biotas, which requires an extrapolation of recent human behavior and technology into the archaeological past. Hominins have been on islands since at least the early Pleistocene and Homo sapiens for at least 50 thousand y (ka). Over such lengthy intervals it is scarcely surprising that significant evolutionary, behavioral, and cultural changes occurred. However, the deep-time link between human arrival and island extinctions has never been explored globally. Here, we examine archaeological and paleontological records of all Pleistocene islands with a documented hominin presence to examine whether humans have always been destructive agents. We show that extinctions at a global level cannot be associated with Pleistocene hominin arrival based on current data and are difficult to disentangle from records of environmental change. It is not until the Holocene that large-scale changes in technology, dispersal, demography, and human behavior visibly affect island ecosystems. The extinction acceleration we are currently experiencing is thus not inherent but rather part of a more recent cultural complex.

Reconstructing Hominin Diets with Stable Isotope Analysis of Amino Acids: New Perspectives and Future Directions.

Stable isotope analysis of teeth and bones is regularly applied by archeologists and paleoanthropologists seeking to reconstruct diets, ecologies, and environments of past hominin populations. Moving beyond the now prevalent study of stable isotope ratios from bulk materials, researchers are increasingly turning to stable isotope ratios of individual amino acids to obtain more detailed and robust insights into trophic level and resource use. In the present article, we provide a guide on how to best use amino acid stable isotope ratios to determine hominin dietary behaviors and ecologies, past and present. We highlight existing uncertainties of interpretation and the methodological developments required to ensure good practice. In doing so, we hope to make this promising approach more broadly accessible to researchers at a variety of career stages and from a variety of methodological and academic backgrounds who seek to delve into new depths in the study of dietary composition.

Chemical Modification of Biomarkers through Accelerated Degradation: Implications for Ancient Plant Identification in Archaeo-Organic Residues.

Biochemical and biomolecular archaeology is increasingly used to elucidate the consumption, use, origin, and trade of plants in the past. However, it can be challenging to use biomarkers to identify the taxonomic origin of archaeological plants due to limited knowledge of molecular survival and degradation for many key plant compounds in archaeological contexts. To gain a fundamental understanding of the chemical alterations associated with chemical degradation processes in ancient samples, we conducted accelerated degradation experiments with essential oil derived from cedar (Cedrus atlantica) exposed to materials commonly found in the archaeological record. Using GC-MS and multivariate analysis, we detected a total of 102 compounds across 19 treatments that were classified into three groups. The first group comprised compounds that were abundant in fresh cedar oil but would be unlikely to remain in ancient residues due to rapid degradation. The second group consisted of compounds that remained relatively stable or increased over time, which could be potential biomarkers for identifying cedar in archaeological residues. Compounds in the third group were absent in fresh cedar oil but were formed during specific experiments that could be indicative for certain storage conditions. These results show that caution is warranted for applying biomolecular profiles of fresh plants to ancient samples and that carefully designed accelerated degradation experiments can, at least in part, overcome this limitation.

The Middle to Later Stone Age transition at Panga ya Saidi, in the tropical coastal forest of eastern Africa.

The Middle to Later Stone Age transition is a critical period of human behavioral change that has been variously argued to pertain to the emergence of modern cognition, substantial population growth, and major dispersals of Homo sapiens within and beyond Africa. However, there is little consensus about when the transition occurred, the geographic patterning of its emergence, or even how it is manifested in the stone tool technology that is used to define it. Here, we examine a long sequence of lithic technological change at the cave site of Panga ya Saidi, Kenya, that spans the Middle and Later Stone Age and includes human occupations in each of the last five Marine Isotope Stages. In addition to the stone artifact technology, Panga ya Saidi preserves osseous and shell artifacts, enabling broader considerations of the covariation between different spheres of material culture. Several environmental proxies contextualize the artifactual record of human behavior at Panga ya Saidi. We compare technological change between the Middle and Later Stone Age with on-site paleoenvironmental manifestations of wider climatic fluctuations in the Late Pleistocene. The principal distinguishing feature of Middle from Later Stone Age technology at Panga ya Saidi is the preference for fine-grained stone, coupled with the creation of small flakes (miniaturization). Our review of the Middle to Later Stone Age transition elsewhere in eastern Africa and across the continent suggests that this broader distinction between the two periods is in fact widespread. We suggest that the Later Stone Age represents new short use-life and multicomponent ways of using stone tools, in which edge sharpness was prioritized over durability.

Plant wax biomarkers in human evolutionary studies.

Plant wax biomarkers are an innovative proxy for reconstructing vegetation composition and structure, rainfall intensity, temperature, and other climatic and environmental dynamics. Traditionally used in earth sciences and climate studies from "off-site" ocean and lake records, biomarker research is now incorporated in archeology and paleoanthropology to answer questions relating to past human-environment interactions and human evolution. Biomarker research is generating new and exciting information on the ecological context in which Homo and its closest relatives evolved, adapted, and invented stone tool technologies. In this review, we examine plant wax biomarkers and their use in reconstructing past plant landscapes and hydroclimates. We summarize the applications of plant wax molecular proxies in archeological research, assess challenges relating to taphonomy, consider the role of modern plant ecosystems in interpreting ancient habitats, and examine case studies conducted at key paleoanthropological locations in eastern and southern Africa and Europe.

Restructuring of nutrient flows in island ecosystems following human colonization evidenced by isotopic analysis of commensal rats.

The role of humans in shaping local ecosystems is an increasing focus of archaeological research, yet researchers often lack an appropriate means of measuring past anthropogenic effects on local food webs and nutrient cycling. Stable isotope analysis of commensal animals provides an effective proxy for local human environments because these species are closely associated with human activities without being under direct human management. Such species are thus central to nutrient flows across a range of socionatural environments and can provide insight into how they intersected and transformed over time. Here we measure and compare stable carbon and nitrogen isotope data from Pacific rat (Rattus exulans) skeletal remains across three Polynesian island systems [Mangareva, Ua Huka (Marquesas), and the Polynesian Outlier of Tikopia] during one of the most significant cases of human migration and commensal introduction in prehistory. The results demonstrate widespread δ15N declines across these islands that are associated with human land use, intensification, and faunal community restructuring. Local comparison of rat stable isotope data also tracks human activities and resource availability at the level of the settlement. Our results highlight the large-scale restructuring of nutrient flows in island ecosystems that resulted from human colonization and ecosystem engineering activities on Pacific islands. They also demonstrate that stable isotope analysis of often-ignored commensal taxa can provide a tool for tracking human land use and environmental effects.

A multi-isotope, multi-tissue study of colonial origins and diet in New Zealand.

OBJECTIVES: Colonial period New Zealand was lauded as a land of plenty, where colonists could improve their station in life and secure a future for their families. Our understanding of colonial experience, however, is often shaped by historical records which communicate a state-sponsored version of history. This study aims to reconstruct the lives of settlers using isotopic evidence from the colonial skeletons themselves. MATERIALS AND METHODS: We use skeletal remains from recently excavated colonial sites in Otago (South Island, New Zealand) to illustrate the information that can be gleaned from the isotopic analysis of individuals. We use 87 Sr/86 Sr to identify European settlers, and δ13 C and δ15 N from collagen and hair keratin, as well as dental enamel carbonate δ13 C to trace dietary change over their life-courses. RESULTS: Strontium isotope analysis shows that all adults in our sample are non-local. Dietary isotopes show that while most individuals had relatively consistent childhood diet, one individual with more rural origins likely had seasonal use of resources during childhood. While some members of the population seem to have increased their meat intake in the new colony most do not have clear evidence for this. DISCUSSION: We show the diversity of human experience in first-generation New Zealanders both prior to emigration and in the new colony. Despite colonial propaganda claiming that circumstances in New Zealand were improved for all settlers, we have little evidence for this, aside from among individuals of potentially high status.

The Rényi divergence enables accurate and precise cluster analysis for localization microscopy.

Motivation: Clustering analysis is a key technique for quantitatively characterizing structures in localization microscopy images. To build up accurate information about biological structures, it is critical that the quantification is both accurate (close to the ground truth) and precise (has small scatter and is reproducible). Results: Here, we describe how the Rényi divergence can be used for cluster radius measurements in localization microscopy data. We demonstrate that the Rényi divergence can operate with high levels of background and provides results which are more accurate than Ripley's functions, Voronoi tesselation or DBSCAN. Availability and implementation: The data supporting this research and the software described are accessible at the following site: https://dx.doi.org/10.18742/RDM01-316. Correspondence and requests for materials should be addressed to the corresponding author. Supplementary information: Supplementary data are available at Bioinformatics online.

Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene.

Drivers of Late Quaternary megafaunal extinctions are relevant to modern conservation policy in a world of growing human population density, climate change, and faunal decline. Traditional debates tend toward global solutions, blaming either dramatic climate change or dispersals of Homo sapiens to new regions. Inherent limitations to archaeological and paleontological data sets often require reliance on scant, poorly resolved lines of evidence. However, recent developments in scientific technologies allow for more local, context-specific approaches. In the present article, we highlight how developments in five such methodologies (radiocarbon approaches, stable isotope analysis, ancient DNA, ancient proteomics, microscopy) have helped drive detailed analysis of specific megafaunal species, their particular ecological settings, and responses to new competitors or predators, climate change, and other external phenomena. The detailed case studies of faunal community composition, extinction chronologies, and demographic trends enabled by these methods examine megafaunal extinctions at scales appropriate for practical understanding of threats against particular species in their habitats today.

Objectively Assessing Intraoperative Arthroscopic Skills Performance and the Transfer of Simulation Training in Knee Arthroscopy: A Randomized Controlled Trial.

PURPOSE: To objectively investigate the transfer validity of simulation training using wireless elbow-worn motion sensors intraoperatively to assess whether surgical simulation leads to improvements in intraoperative arthroscopic performance. METHODS: In this randomized controlled trial, postgraduate year 2 to 3 trainees in nationally approved orthopaedic surgery posts were randomized to standard junior residency training (control group) or standard training plus additional weekly simulation training (intervention group). Both groups performed a supervised real-life diagnostic knee arthroscopy in the operating room at 13 weeks. Performance was measured using wireless elbow-worn motion sensors recording objective surgical performance metrics: number of hand movements, smoothness, and time taken. A participant-supervisor performance ratio was used to adjust for variation in case mix and difficulty. The study took place in a surgical simulation suite and the orthopaedic operating rooms of a university teaching hospital. RESULTS: The intervention group objectively outperformed the control group in all outcome metrics. Procedures performed by the intervention group required fewer hand movements (544 [interquartile range (IQR), 465-593] vs 893 [IQR, 747-1,242]; P < .001), had smoother movements (25,842 ms-3 [IQR, 20,867-27,468 ms-3] vs 36,846 ms-3 [IQR, 29,840-53,949 ms-3]; P < .001), and took less time (320 seconds [IQR, 294-392 seconds] vs 573 seconds [IQR, 477-860 seconds]; P < .001) than those performed by the control group. The cases were comparable between the groups. Standardized to the supervisor's performance, the intervention group required fewer hand movements (1.9 [IQR, 1.5-2.1] vs 3.3 [IQR, 2.2-4.8]; P = .0091), required less time (1.2 [IQR, 1.1-1.7] vs 2.6 [IQR, 1.6-3.0]; P = .0037), and were smoother (2.1 [IQR, 1.8-2.8] vs 4.3 [IQR, 2.8-5.4]; P = .0037) than the control group, but they did not perform as well as their supervisors. CONCLUSIONS: This study uses intraoperative motion-analysis technology to objectively show that surgical simulation training improves actual intraoperative technical skills performance. CLINICAL RELEVANCE: The described wireless objective assessment method complements the subjective observational performance assessments commonly used. Further studies are required to assess how these measures of intraoperative performance correlate to patient outcomes. Intraoperative motion analysis is translatable across surgical specialties, offering potential for objective assessment of progression through competency-based training, revalidation, and talent selection for specialist training.