Middle and Late Pleistocene Denisovan subsistence at Baishiya Karst Cave.

Genetic and fragmented palaeoanthropological data suggest that Denisovans were once widely distributed across eastern Eurasia1-3. Despite limited archaeological evidence, this indicates that Denisovans were capable of adapting to a highly diverse range of environments. Here we integrate zooarchaeological and proteomic analyses of the late Middle to Late Pleistocene faunal assemblage from Baishiya Karst Cave on the Tibetan Plateau, where a Denisovan mandible and Denisovan sedimentary mitochondrial DNA were found3,4. Using zooarchaeology by mass spectrometry, we identify a new hominin rib specimen that dates to approximately 48-32 thousand years ago (layer 3). Shotgun proteomic analysis taxonomically assigns this specimen to the Denisovan lineage, extending their presence at Baishiya Karst Cave well into the Late Pleistocene. Throughout the stratigraphic sequence, the faunal assemblage is dominated by Caprinae, together with megaherbivores, carnivores, small mammals and birds. The high proportion of anthropogenic modifications on the bone surfaces suggests that Denisovans were the primary agent of faunal accumulation. The chaîne opératoire of carcass processing indicates that animal taxa were exploited for their meat, marrow and hides, while bone was also used as raw material for the production of tools. Our results shed light on the behaviour of Denisovans and their adaptations to the diverse and fluctuating environments of the late Middle and Late Pleistocene of eastern Eurasia.

Ancient human DNA recovered from a Palaeolithic pendant.

Artefacts made from stones, bones and teeth are fundamental to our understanding of human subsistence strategies, behaviour and culture in the Pleistocene. Although these resources are plentiful, it is impossible to associate artefacts to specific human individuals1 who can be morphologically or genetically characterized, unless they are found within burials, which are rare in this time period. Thus, our ability to discern the societal roles of Pleistocene individuals based on their biological sex or genetic ancestry is limited2-5. Here we report the development of a non-destructive method for the gradual release of DNA trapped in ancient bone and tooth artefacts. Application of the method to an Upper Palaeolithic deer tooth pendant from Denisova Cave, Russia, resulted in the recovery of ancient human and deer mitochondrial genomes, which allowed us to estimate the age of the pendant at approximately 19,000-25,000 years. Nuclear DNA analysis identifies the presumed maker or wearer of the pendant as a female individual with strong genetic affinities to a group of Ancient North Eurasian individuals who lived around the same time but were previously found only further east in Siberia. Our work redefines how cultural and genetic records can be linked in prehistoric archaeology.

Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria.

The Middle to Upper Palaeolithic transition in Europe witnessed the replacement and partial absorption of local Neanderthal populations by Homo sapiens populations of African origin1. However, this process probably varied across regions and its details remain largely unknown. In particular, the duration of chronological overlap between the two groups is much debated, as are the implications of this overlap for the nature of the biological and cultural interactions between Neanderthals and H. sapiens. Here we report the discovery and direct dating of human remains found in association with Initial Upper Palaeolithic artefacts2, from excavations at Bacho Kiro Cave (Bulgaria). Morphological analysis of a tooth and mitochondrial DNA from several hominin bone fragments, identified through proteomic screening, assign these finds to H. sapiens and link the expansion of Initial Upper Palaeolithic technologies with the spread of H. sapiens into the mid-latitudes of Eurasia before 45 thousand years ago3. The excavations yielded a wealth of bone artefacts, including pendants manufactured from cave bear teeth that are reminiscent of those later produced by the last Neanderthals of western Europe4-6. These finds are consistent with models based on the arrival of multiple waves of H. sapiens into Europe coming into contact with declining Neanderthal populations7,8.

A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau.

Denisovans are members of a hominin group who are currently only known directly from fragmentary fossils, the genomes of which have been studied from a single site, Denisova Cave1-3 in Siberia. They are also known indirectly from their genetic legacy through gene flow into several low-altitude East Asian populations4,5 and high-altitude modern Tibetans6. The lack of morphologically informative Denisovan fossils hinders our ability to connect geographically and temporally dispersed fossil hominins from Asia and to understand in a coherent manner their relation to recent Asian populations. This includes understanding the genetic adaptation of humans to the high-altitude Tibetan Plateau7,8, which was inherited from the Denisovans. Here we report a Denisovan mandible, identified by ancient protein analysis9,10, found on the Tibetan Plateau in Baishiya Karst Cave, Xiahe, Gansu, China. We determine the mandible to be at least 160 thousand years old through U-series dating of an adhering carbonate matrix. The Xiahe specimen provides direct evidence of the Denisovans outside the Altai Mountains and its analysis unique insights into Denisovan mandibular and dental morphology. Our results indicate that archaic hominins occupied the Tibetan Plateau in the Middle Pleistocene epoch and successfully adapted to high-altitude hypoxic environments long before the regional arrival of modern Homo sapiens.

Age estimates for hominin fossils and the onset of the Upper Palaeolithic at Denisova Cave.

Denisova Cave in the Siberian Altai (Russia) is a key site for understanding the complex relationships between hominin groups that inhabited Eurasia in the Middle and Late Pleistocene epoch. DNA sequenced from human remains found at this site has revealed the presence of a hitherto unknown hominin group, the Denisovans1,2, and high-coverage genomes from both Neanderthal and Denisovan fossils provide evidence for admixture between these two populations3. Determining the age of these fossils is important if we are to understand the nature of hominin interaction, and aspects of their cultural and subsistence adaptations. Here we present 50 radiocarbon determinations from the late Middle and Upper Palaeolithic layers of the site. We also report three direct dates for hominin fragments and obtain a mitochondrial DNA sequence for one of them. We apply a Bayesian age modelling approach that combines chronometric (radiocarbon, uranium series and optical ages), stratigraphic and genetic data to calculate probabilistically the age of the human fossils at the site. Our modelled estimate for the age of the oldest Denisovan fossil suggests that this group was present at the site as early as 195,000 years ago (at 95.4% probability). All Neanderthal fossils-as well as Denisova 11, the daughter of a Neanderthal and a Denisovan4-date to between 80,000 and 140,000 years ago. The youngest Denisovan dates to 52,000-76,000 years ago. Direct radiocarbon dating of Upper Palaeolithic tooth pendants and bone points yielded the earliest evidence for the production of these artefacts in northern Eurasia, between 43,000 and 49,000 calibrated years before present (taken as AD 1950). On the basis of current archaeological evidence, it may be assumed that these artefacts are associated with the Denisovan population. It is not currently possible to determine whether anatomically modern humans were involved in their production, as modern-human fossil and genetic evidence of such antiquity has not yet been identified in the Altai region.

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.

Cheetah Acinonyx pardinensis (Felidae, Carnivora) from the Early Pleistocene of Crimea (Taurida Cave).

A mandible fragment of Acinonyx pardinensis (Croizet et Jobert, 1828) is described from the Early Pleistocene locality in the Taurida cave (Crimea, Late Villafranchian, about 1.8-1.5 Ma). This is the first discovery of the genus Acinonyx in the Pleistocene of Crimea. Along with other felids, such as Homotherium, Megantereon, Panthera, Lynx, and Puma, cheetahs were typical representatives of the Late Villafranchian faunas of Eurasia. In the Taurida locality, Acinonyx pardinensis is co-occurred with Homotherium crenatidens, Megantereon adroveri, and Lynx issiodorensis.

Old World Fruit Bats (Pteropodidae, Chiroptera) from the Pleistocene of Vietnam.

Isolated teeth of a lesser short-nosed fruit bat Cynopterus brachyotis (Müller, 1838), a fulvous fruit bat Rousettus leschenaultii (Desmarest, 1820), and a dawn bat Eonycteris spelaea (Dobson, 1871) are described from the Middle Pleistocene Tham Hai cave locality in northern Vietnam (Lang Son Province). These are the first fossil findings of the Old World fruit bats in Vietnam. The Middle Pleistocene association of Pteropodidae from the Tham Hai locality may largely reflect the composition of species that roosted in local caves.

Descriptive catalog of Homo naledi dental remains from the 2013 to 2015 excavations of the Dinaledi Chamber, site U.W. 101, within the Rising Star cave system, South Africa.

More than 150 hominin teeth, dated to ∼330-241 thousand years ago, were recovered during the 2013-2015 excavations of the Dinaledi Chamber of the Rising Star cave system, South Africa. These fossils comprise the first large single-site sample of hominin teeth from the Middle Pleistocene of Africa. Though scattered remains attributable to Homo sapiens, or their possible lineal ancestors, are known from older and younger sites across the continent, the distinctive morphological feature set of the Dinaledi teeth supports the recognition of a novel hominin species, Homo naledi. This material provides evidence of African Homo lineage diversity that lasts until at least the Middle Pleistocene. Here, a catalog, anatomical descriptions, and details of preservation and taphonomic alteration are provided for the Dinaledi teeth. Where possible, provisional associations among teeth are also proposed. To facilitate future research, we also provide access to a catalog of surface files of the Rising Star jaws and teeth.

An early modern human presence in Sumatra 73,000-63,000 years ago.

Genetic evidence for anatomically modern humans (AMH) out of Africa before 75 thousand years ago (ka) and in island southeast Asia (ISEA) before 60 ka (93-61 ka) predates accepted archaeological records of occupation in the region. Claims that AMH arrived in ISEA before 60 ka (ref. 4) have been supported only by equivocal or non-skeletal evidence. AMH evidence from this period is rare and lacks robust chronologies owing to a lack of direct dating applications, poor preservation and/or excavation strategies and questionable taxonomic identifications. Lida Ajer is a Sumatran Pleistocene cave with a rich rainforest fauna associated with fossil human teeth. The importance of the site is unclear owing to unsupported taxonomic identification of these fossils and uncertainties regarding the age of the deposit, therefore it is rarely considered in models of human dispersal. Here we reinvestigate Lida Ajer to identify the teeth confidently and establish a robust chronology using an integrated dating approach. Using enamel-dentine junction morphology, enamel thickness and comparative morphology, we show that the teeth are unequivocally AMH. Luminescence and uranium-series techniques applied to bone-bearing sediments and speleothems, and coupled uranium-series and electron spin resonance dating of mammalian teeth, place modern humans in Sumatra between 73 and 63 ka. This age is consistent with biostratigraphic estimations, palaeoclimate and sea-level reconstructions, and genetic evidence for a pre-60 ka arrival of AMH into ISEA. Lida Ajer represents, to our knowledge, the earliest evidence of rainforest occupation by AMH, and underscores the importance of reassessing the timing and environmental context of the dispersal of modern humans out of Africa.

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.

Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.

Zinc isotopes in Late Pleistocene fossil teeth from a Southeast Asian cave setting preserve paleodietary information.

Stable carbon and nitrogen isotope ratios of collagen from bone and dentin have frequently been used for dietary reconstruction, but this method is limited by protein preservation. Isotopes of the trace element zinc (Zn) in bioapatite constitute a promising proxy to infer dietary information from extant and extinct vertebrates. The 66Zn/64Zn ratio (expressed as δ66Zn value) shows an enrichment of the heavy isotope in mammals along each trophic step. However, preservation of diet-related δ66Zn values in fossil teeth has not been assessed yet. Here, we analyzed enamel of fossil teeth from the Late Pleistocene (38.4-13.5 ka) mammalian assemblage of the Tam Hay Marklot (THM) cave in northeastern Laos, to reconstruct the food web and assess the preservation of original δ66Zn values. Distinct enamel δ66Zn values of the fossil taxa (δ66Zncarnivore < δ66Znomnivore < δ66Znherbivore) according to their expected feeding habits were observed, with a trophic carnivore-herbivore spacing of +0.60‰ and omnivores having intermediate values. Zn and trace element concentration profiles similar to those of modern teeth also indicate minimal impact of diagenesis on the enamel. While further work is needed to explore preservation for settings with different taphonomic conditions, the diet-related δ66Zn values in fossil enamel from THM cave suggest an excellent long-term preservation potential, even under tropical conditions that are well known to be adverse for collagen preservation. Zinc isotopes could thus provide a new tool to assess the diet of fossil hominins and associated fauna, as well as trophic relationships in past food webs.

Microplastics in caves: A new threat in the most famous geo-heritage in the world. Analysis and comparison of Italian show caves deposits.

Microplastic pollution represent a worldwide concern, however, in karst areas is still largely unknown, especially in underground environments. Caves are the most important geological heritage worldwide, rich in speleothems, unique ecosystems custodians of important drinking water reserves, and a significant economic resource. Thank to their relatively stable environmental conditions, they can preserve information for a long time such as paleontological/archaeological remains, however, these characteristics make caves vulnerable environments too, easily damaged by climate variations and pollution. To increase the current knowledge of microplastic pollution, the deposits of different Italian show caves were investigated, improving the method for microplastic separation. Microplastic were identified and characterised using MUPL automated software, observed with and without UV light under a microscope, and verified under µFTIR-ATR, highlighting the importance of combine different methods. Microplastics were present in sediments of all examined caves, and were always greater along the tourist route (an average of 4300 items/kg) than the speleological areas (an average of 2570 items/kg). Microplastics less than 1 mm dominated the samples and the amount increased with the decrease in the size considered. Fibre-shaped dominated the samples and 74% particles was fluorescent under UV light. Analysed sediment samples contained especially polyesters and polyolefins. Our results highlight the presence of microplastic pollution in show caves, giving useful information to assess risks posed by microplastics in show caves and emphasizing the importance of pollutants monitoring in underground environments to define strategies for the conservation and management of caves and natural resources.

Connections between the Levant and the Balkans in the late Middle Pleistocene: Archaeological findings from Velika and Mala Balanica Caves (Serbia).

Major changes in the technological, economic, and social behavior of Middle Pleistocene hominins occurred at the onset of the Middle Paleolithic, 400-200 ka. However, until recently it was not possible to establish when, where, and how certain forms of Middle Paleolithic behavior appeared and spread into Southeastern Europe, mainly owing to gaps in the Paleolithic record. Here we report new results of dating, material culture, and the archaeological context of finds from the Balanica Cave Complex in Sicevo (Serbia). Two methods-thermoluminescence and electron spin resonance-were used to date the sequence. The geoarchaeological context was examined through sedimentology, micromorphology, and spatial analysis. Microfaunal remains were used to constrain the dates within an ecological zone, whereas macrofauna was analyzed for taxonomy and taphonomy to examine the source of accumulation and hominin behavior. Technological and typological features of the lithic assemblage were used to characterize lithic production at the site. Materials recovered from Layer 3 in Velika Balanica and from Layer 2 in Mala Balanica, both dated to MIS 9-7, include a distinctive set of archaeological assemblages which resemble contemporaneous Yabrudian assemblages from the Levant in important ways, and which are unlike contemporary material from the surrounding regions. In Velika Balanica, the lithic assemblages are associated with a large fireplace containing evidence of human activities similar to those from Qesem Cave (Israel). Dental remains uncovered in the same layer are consistent with Neanderthals. These findings suggest that the end of the Middle Pleistocene (before 300-240 ka) saw population movement and/or cultural transmission between Southwest Asia and the Balkans, which led eventually to a transfer of technology between Middle Eastern and European hominin populations and contributed to the shaping of Neanderthal behaviors throughout the eastern and northern Mediterranean.

Initial Upper Paleolithic bone technology and personal ornaments at Bacho Kiro Cave (Bulgaria).

The expansion of Homo sapiens and our interaction with local environments, including the replacement or absorption of local populations, is a key component in understanding the evolution of our species. Of special interest are artifacts made from hard animal tissues from layers at Bacho Kiro Cave (Bulgaria) that have been attributed to the Initial Upper Paleolithic. The Initial Upper Paleolithic is characterized by Levallois-like blade technologies that can co-occur with bone tools and ornaments and likely represents the dispersal of H. sapiens into several regions throughout Eurasia starting by 45 ka or possibly earlier. Osseous artifacts from the Initial Upper Paleolithic are important components of this record and have the potential to contribute to our understanding of group interactions and population movements. Here, we present a zooarchaeological, technological, and functional analysis of the diverse and sizable osseous artifact collection from Bacho Kiro Cave. Animal raw material sources are consistent with taxa found within the faunal assemblage including cervids, large bovids, and cave bears. A variety of bone tool morphologies, both formal and informal, indicate a diverse technological approach for conducting various on-site activities, many of which were focused on the processing of animal skins, likely for cold weather clothing. Technological flexibility is also evident in the manufacture of personal ornaments, which were made primarily from carnivore teeth, especially cave bear, though herbivore teeth and small beads are also represented. The osseous artifacts from Bacho Kiro Cave provide a series of insights into the bone technology and indirectly on the social aspects of these humans in southeast Europe, and when placed within the broader Initial Upper Paleolithic context, both regional and shared behaviors are evidently indicating widespread innovation and complexity. This is especially significant given the location and chronology of the site in the context of H. sapiens dispersals.

Modern human teeth unearthed from below the ∼128,000-year-old level at Punung, Java: A case highlighting the problem of recent intrusion in cave sediments.

The emergence of modern humans in the eastern edge of the Eurasian Continent is debated between two major models: early (∼130-70 ka) and late (∼50 ka) dispersal models. The former view is grounded mainly on the claims that several cave sites in Southeast Asia and southern China yielded modern human fossils of those early ages, but such reports have been disputed for the lack of direct dating of the human remains and insufficient documentation of stratigraphy and taphonomy. By tracing possible burial process and conducting direct dating for an early Late Pleistocene paleontological site of Punung III, East Java, we here report a case that demonstrates how unexpected intrusion of recent human remains into older stratigraphic levels could occur in cave sediments. This further highlights the need of direct dating and taphonomic assessment before accepting either model. We also emphasize that the state of fossilization of bones and teeth is a useful guide for initial screening of recent intrusion and should be reported particularly when direct dating is unavailable. Additionally, we provide a revised stratigraphy and faunal list of Punung III, a key site that defines the tropical rainforest Punung Fauna during the early Late Pleistocene of the region.

Chasmaporthetes lunensis (Hyaenidae, Carnivora) from the Early Pleistocene of Crimea.

A maxillary fragment of the extinct hyena Chasmaporthetes lunensis (Del Campana, 1914) is described from the Early Pleistocene locality of the Taurida cave (Crimea, Late Villafranchian, 1.8-1.5 Ma). The species was a typical representative of the Villafranchian faunas of Eurasia. This is the first record of the genus Chasmaporthetes in the Pleistocene of Crimea.

First Data on Non-occlusal Surface Incisor Microwear of Cave Bears from the Urals.

The microwear of the non-occlusal surface of incisors (I1, I2) of the small cave bear (Ursus ex gr. savini-rossicus) and Ural cave bear (Ursus kanivetz) from the Pleistocene of the Middle and South Urals is analyzed and compared. Qualitative characteristics of incisor microwear have been shown to be different in these species. In the small cave bear, coarser lesions on the non-occlusal surface of the incisors are observed. Considering the specificity of microwear of non-occlusal tooth surfaces, the data obtained suggest differences in trophic specialization of the species. studied.

The dental remains from the Early Upper Paleolithic of Manot Cave, Israel.

This study presents the dental remains discovered at Manot Cave (MC), Western Galilee, Israel. The cave contains evidence for human occupation during the Early Upper Paleolithic period (46-33 ka) mainly of Early Ahmarian (∼46-42 ka) and Levantine Aurignacian (∼38-34 ka) cultural levels. Six teeth (three deciduous and three permanent) were found at the site, of which four could be thoroughly analyzed. The morphology of the teeth was qualitatively described and analyzed using traditional and geometric morphometric methods. A large comparative sample was used in order to assess the morphological affiliation of the Manot specimens with other Homo groups. The results provided equivocal signals: the upper first premolar (MC-9 P3) is probably modern human; the upper deciduous second molar (MC-10 dm2) and the upper second permanent molar (MC-8 M2) might be modern humans; the lower second deciduous molar (MC-7 dm2) might be Neanderthal. Owing to the small sample size and the almost total lack of distinctive characteristics, our outcome could not supply conclusive evidence to address the question of whether Manot Aurignacian population came from Europe or descended from the local Ahmarian population.

Personal ornaments from Hayonim and Manot caves (Israel) hint at symbolic ties between the Levantine and the European Aurignacian.

Situated at the crossroads of Africa and Eurasia, the Levant is a crucial region for understanding the origins and spread of Upper Paleolithic (UP) traditions associated with the spread of modern humans. Of the two local Early Upper Paleolithic technocomplexes, the Ahmarian and the Levantine Aurignacian, the latter appears to be unique in the endemic UP sequence, exhibiting greater similarity to the West European 'classic' Aurignacian than to the local preceding and proceeding UP entities. Previous publications have mostly focused on the similarities between the two lithic industries and less on studies conducted on Levantine Aurignacian bone tools and ornaments. Here, we present an archaeozoological, technological and use-wear study of ornaments on animal teeth from the Levantine Aurignacian layers at Manot and Hayonim caves (the Galilee, Israel). The selection of taxa, the choice of teeth, the mode of modification, and the use-wear analysis exhibit clear similarities with the European Aurignacian. This, with the technology of the osseous raw material exploitation, the presence of antler simple-base points, and some lithic typotechnological features, suggest a link between the symbolic spheres of the Levantine and the European Aurignacian cultural entities. Such similarity also supports some contribution of European Aurignacians groups to the local cultural entities, intermingling with the local material culture features.