The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa.

We report the first large-scale palaeoproteomics research on eastern and southern African zooarchaeological samples, thereby refining our understanding of early caprine (sheep and goat) pastoralism in Africa. Assessing caprine introductions is a complicated task because of their skeletal similarity to endemic wild bovid species and the sparse and fragmentary state of relevant archaeological remains. Palaeoproteomics has previously proved effective in clarifying species attributions in African zooarchaeological materials, but few comparative protein sequences of wild bovid species have been available. Using newly generated type I collagen sequences for wild species, as well as previously published sequences, we assess species attributions for elements originally identified as caprine or 'unidentifiable bovid' from 17 eastern and southern African sites that span seven millennia. We identified over 70% of the archaeological remains and the direct radiocarbon dating of domesticate specimens allows refinement of the chronology of caprine presence in both African regions. These results thus confirm earlier occurrences in eastern Africa and the systematic association of domesticated caprines with wild bovids at all archaeological sites. The combined biomolecular approach highlights repeatability and accuracy of the methods for conclusive contribution in species attribution of archaeological remains in dry African environments.

Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers.

Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants.

Settlement dynamics, subsistence economies and climate change during the late Holocene at Nunura Bay (Sechura Desert, Peru): A multiproxy approach.

Long considered on the margins, far from the major cultural traditions, the Sechura Desert is situated at the crossroads between the cultures of southern Ecuador and those of the northern Peruvian coast and preserves a large number of varied archaeological sites. Despite this evidence, little is known about the societies that inhabited this region during the Holocene. Exposed to natural hazards, including El Niño events, and to major climatic changes, they were able to adapt and exploit the scarce resources that this extreme environment offered them. Because of this rich history, we have been conducting archaeological research in this region since 2012 in order to clarify the dynamics of human occupation and their links with climate oscillations and environmental changes. This paper present the results of a multidisciplinary study of Huaca Grande, a mound located on Nunura Bay, 300 m from the Pacific Ocean. The nature of the human occupations at Huaca Grande was varied, and several adjustments occurred over time. The subsistence economy was based mainly on local marine resources and a continual use of terrestrial vegetal resources. However, a major change occurred in the more recent occupations, with the apparition of non-local resources (maize and cotton) indicating that Huaca Grande was connected to trade networks. The results show two main phases of occupation separated by a long abandonment (mid-5th century CE to mid-7th century CE and mid-13th century to mid-15th century CE). The occupation of the site appears to have been influenced by changes in the local climate and by extreme El Niño events. Our results highlight the great adaptability of these human groups over the span of a millennium and their capacity to react to the climatic changes and hazards that characterise this region.

New insights on interpersonal violence in the Late Pleistocene based on the Nile valley cemetery of Jebel Sahaba.

The remains of 61 individuals buried in the cemetery of Jebel Sahaba (site 117) offer unique and substantial evidence to the emergence of violence in the Nile Valley at the end of the Late Pleistocene. Excavated and assessed in the 1960s, some of the original findings and interpretations are disputed. A full reanalysis of the timing, nature and extent of the violence was conducted through the microscopic characterization of the nature of each osseous lesion, and the reassessment of the archaeological data. Over 100 previously undocumented healed and unhealed lesions were identified on both new and/or previously identified victims, including several embedded lithic artefacts. Most trauma appears to be the result of projectile weapons and new analyses confirm for the first time the repetitive nature of the interpersonal acts of violence. Indeed, a quarter of the skeletons with lesions exhibit both healed and unhealed trauma. We dismiss the hypothesis that Jebel Sahaba reflects a single warfare event, with the new data supporting sporadic and recurrent episodes of inter-personal violence, probably triggered by major climatic and environmental changes. At least 13.4 ka old, Jebel Sahaba is one of the earliest sites displaying interpersonal violence in the world.

Strontium isotope evidence for a trade network between southeastern Arabia and India during Antiquity.

Cotton (Gossypium sp.), a plant of tropical and sub-tropical origin, appeared at several sites on the Arabian Peninsula at the end of the 1st mill. BCE-beginning of the 1st mill. CE. Its spread into this non-native, arid environment is emblematic of the trade dynamics that took place at this pivotal point in human history. Due to its geographical location, the Arabian Peninsula is connected to both the Indian and African trading spheres, making it complex to reconstruct the trans-continental trajectories of plant diffusion into and across Arabia in Antiquity. Key questions remain pertaining to: (1) provenance, i.e. are plant remains of local or imported origin and (2) the precise timing of cotton arrival and spread. The ancient site of Mleiha, located in modern-day United Arab Emirates, is a rare and significant case where rich archaeobotanical remains dating to the Late Pre-Islamic period (2nd-3rd c. CE), including cotton seeds and fabrics, have been preserved in a burned-down fortified building. To better understand the initial trade and/or production of cotton in this region, strontium isotopes of leached, charred cotton remains are used as a powerful tracer and the results indicate that the earliest cotton finds did not originate from the Oman Peninsula, but were more likely sourced from further afield, with the north-western coast of India being an isotopically compatible provenance. Identifying the presence of such imported cotton textiles and seeds in southeastern Arabia is significant as it is representative of the early diffusion of the crop in the region, later to be grown extensively in local oases.

Untangling the fibre ball: Proteomic characterization of South American camelid hair fibres by untargeted multivariate analysis and molecular networking.

The proteomic analysis of hairs, yarns or textiles has emerged as a powerful method to determine species of origin, mainly used in archaeozoological research and fraud control. Differentiation between the South American camelid (SAC) species (the wild guanaco and vicuña and their respective domesticates the llama and alpaca) is particularly challenging due to poor database information and significant hybridization between species. In this study, we analysed 41 modern and 4 archaeological samples from the four SACs species. Despite strong similarities with Old World Camelidae, we identified 7 peptides specific to SACs assigned to keratin K86 and the keratin-associated proteins KAP13-1 and KAP11-1. Untargeted multivariate analysis of the LC-MS data permitted to distinguish SAC species and propose discriminant features. MS/MS-based molecular networking combined with database-assisted de novo sequencing permitted to identify 5 new taxonomic peptides assigned to K33a, K81 and/or K83 keratins and KAP19-1. These peptides differentiate the two wild species, guanaco and vicuña. These results show the value of combining database search and untargeted metabolomic approaches for paleoproteomics, and reveal for the first time the potential of molecular networks to highlight deamidation related to diagenesis and cluster highly similar peptides related to interchain homologies or intra- or inter-specific polymorphism. SIGNIFICANCE: This study used an innovative approach combining multivariate analysis of LC-MS data together with molecular networking and database-assisted de novo sequencing to identify taxonomic peptides in palaeoproteomics. It constitutes the first attempt to differentiate between hair fibres from the four South American camelids (SACs) based on proteomic analysis of modern and archaeological samples. It provides different proteomic signatures for each of the four SAC species and proposes new SAC taxonomic peptides of interest in archaeozoology and fraud control. SACs have been extensively exploited since human colonization of South America but have not been studied to the extent of their economic, cultural and heritage importance. Applied to the analysis of ancient Andean textiles, our results should permit a better understanding of cultural and pastoral practices in South America. The wild SACs are endangered by poaching and black-market sale of their fibre. For the first time, our results provide discriminant features for the determination of species of origin of contraband fibre.

Direct dating reveals the early history of opium poppy in western Europe.

This paper aims to define the first chrono-cultural framework on the domestication and early diffusion of the opium poppy using small-sized botanical remains from archaeological sites, opening the way to directly date minute short-lived botanical samples. We produced the initial set of radiocarbon dates directly from the opium poppy remains of eleven Neolithic sites (5900-3500 cal BCE) in the central and western Mediterranean, northwestern temperate Europe, and the western Alps. When possible, we also dated the macrobotanical remains originating from the same sediment sample. In total, 22 samples were taken into account, including 12 dates directly obtained from opium poppy remains. The radiocarbon chronology ranges from 5622 to 4050 cal BCE. The results show that opium poppy is present from at least the middle of the sixth millennium in the Mediterranean, where it possibly grew naturally and was cultivated by pioneer Neolithic communities. Its dispersal outside of its native area was early, being found west of the Rhine in 5300-5200 cal BCE. It was introduced to the western Alps around 5000-4800 cal BCE, becoming widespread from the second half of the fifth millennium. This research evidences different rhythms in the introduction of opium poppy in western Europe.

Palaeoproteomics gives new insight into early southern African pastoralism.

The advent of domestication is a major step that transformed the subsistence strategies of past human societies. In Africa, domestic caprines (sheep and goat) were introduced in the north-eastern part of the continent from the Near East more than 9000 years ago. However, their diffusion southwards was slow. They are thought to have made their first appearance in the southern part of the continent ca. 2000 years ago, at a few Later Stone Age sites, including Leopard Cave (Erongo region, Namibia), which provided the oldest directly dated remains assigned to sheep or goat on the basis of morphology of bones and teeth. However, similarities in morphology, not only between these two domesticated caprine species, but also between them and the small wild antelopes, raised questions about the morphological species attribution of these remains. Additionally, the high fragmentation of the site's osteological remains makes it difficult to achieve species-level taxonomic identification by comparative anatomy. In this paper, we report molecular species identification of the Leopard Cave remains using palaeoproteomics, a method that uses protein markers in bone and tooth collagen to achieve taxonomic identification of archaeological remains. We also report new direct radiocarbon dates. Wild antelope remains from museum collections were used to enrich the available protein record and propose de novo type I collagen sequences. Our results demonstrate that the remains morphologically described as domesticates actually belong to a wild antelope species and that domestic caprines first appeared at Leopard Cave 1500 years later than previously thought. This study illustrates that the use of palaeoproteomics coupled with direct radiocarbon dates is particularly suited to complement classic zooarchaeological studies, in this case concerning the arrival of the first herding practices in arid environments.

Tracking the Near Eastern origins and European dispersal of the western house mouse.

The house mouse (Mus musculus) represents the extreme of globalization of invasive mammals. However, the timing and basis of its origin and early phases of dispersal remain poorly documented. To track its synanthropisation and subsequent invasive spread during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, between 40,000 and 3,000 cal. BP, combining geometric morphometrics numerical taxonomy, ancient mitochondrial DNA and direct radiocarbon dating. We found that large late hunter-gatherer sedentary settlements in the Levant, c. 14,500 cal. BP, promoted the commensal behaviour of the house mouse, which probably led the commensal pathway to cat domestication. House mouse invasive spread was then fostered through the emergence of agriculture throughout the Near East 12,000 years ago. Stowaway transport of house mice to Cyprus can be inferred as early as 10,800 years ago. However, the house mouse invasion of Europe did not happen until the development of proto urbanism and exchange networks - 6,500 years ago in Eastern Europe and 4000 years ago in Southern Europe - which in turn may have driven the first human mediated dispersal of cats in Europe.

Grazing high and low: Can we detect horse altitudinal mobility using high-resolution isotope (δ13 C and δ15 N values) time series in tail hair? A case study in the Mongolian Altai.

RATIONALE: Carbon and nitrogen stable isotope time series performed in continuously growing tissues (hair, tooth enamel) are commonly used to reconstruct the dietary history of modern and ancient animals. Predicting the effects of altitudinal mobility on animal δ13 C and δ15 N values remains difficult as several variables such as temperature, water availability or soil type can contribute to the isotope composition. Modern references adapted to the region of interest are therefore essential. METHODS: Between June 2015 and July 2018, six free-ranging domestic horses living in the Mongolian Altaï were fitted with GPS collars. Tail hairs were sampled each year, prepared for sequential C and N isotope analysis using EA-IRMS. Isotopic variations were compared with altitudinal mobility, and Generalized Additive Mixed (GAMMs) models were used to model the effect of geographic and environmental factors on δ13 C and δ15 N values. RESULTS: Less than half of the pasture changes were linked with a significant isotopic shift while numerous isotopic shifts did not correspond to any altitudinal mobility. Similar patterns of δ13 C and δ15 N variations were observed between the different horses, despite differences in mobility patterns. We propose that water availability as well as seasonal availability of N2 fixing type plants primarily controlled horse hair δ13 C and δ15 N values, overprinting the influence of altitude. CONCLUSIONS: Our study shows that altitudinal mobility is not the main factor that drives the variations in horse tail hair δ13 C and δ15 N values and that seasonal change in the animal dietary preference also plays an important role. It is therefore risky to interpret variations in δ13 C and δ15 N values of animal tissues in terms of altitudinal mobility alone, at least in C3 -dominated environments.

Strontium isotope analysis on cremated human remains from Stonehenge support links with west Wales.

Cremated human remains from Stonehenge provide direct evidence on the life of those few select individuals buried at this iconic Neolithic monument. The practice of cremation has, however, precluded the application of strontium isotope analysis of tooth enamel as the standard chemical approach to study their origin. New developments in strontium isotopic analysis of cremated bone reveal that at least 10 of the 25 cremated individuals analysed did not spend their lives on the Wessex chalk on which the monument is found. Combined with the archaeological evidence, we suggest that their most plausible origin lies in west Wales, the source of the bluestones erected in the early stage of the monument's construction. These results emphasise the importance of inter-regional connections involving the movement of both materials and people in the construction and use of Stonehenge.

Direct Dating and Physico-Chemical Analyses Cast Doubts on the Coexistence of Humans and Dwarf Hippos in Cyprus.

In the Mediterranean, the island dwarf megafaunas became extinct around the end of the Pleistocene, during a period of rapid and global climate change. In Cyprus, this coincided with the first human presence on the island, as attested by the rock shelter of Akrotiri-Aetokremnos where an Epipaleolithic anthropogenic layer (stratum 2) was found overlying a massive accumulation of pygmy hippopotamus (Phanourios minor (Desmarest, 1822)) [Boekschoten and Sondaar, 1972] bones (stratum 4). The relationship between the two layers is highly controversial and the role played by humans in hippo extinction remains fiercely debated. Here, we provide new, direct radiocarbon and physico-chemical analyses on calcined bones which elucidates the complex depositional history of the assemblage. Bone turquoise was identified using micro-PIXE analysis and depth-profiling together with Vis spectroscopy, demonstrating that these bones were not freshly burned. Bayesian modeling of the radiocarbon dates indicates that stratum 4 accumulated during the first half of the 13th mill cal BP and that calcination occurred several hundred years later. We conclude that accumulation occurred naturally during the beginning of the Younger Dryas and that Epipalaeolithic visitors subsequently used the bones as fuel, starting from the mid-13th mill cal BP. At that time, dwarf hippos were probably already extinct or at least highly endangered. Our results shed new light on the possible causes of hippo extinction, on the subsequent introduction of the wild boar and on the earliest occupation of the island by humans.

Diet and mobility in a late Neolithic population of coastal Oman inferred from radiocarbon dating and stable isotope analysis.

In Oman, the presence of highly productive marine environments, coupled with relatively limited land resources, have led to intense exploitation of coastal resources, but the question of the seasonality of occupation of coastal sites remains open. Our aim is to evaluate the contribution of marine resources to the diet of the Neolithic population of Ra's al-Hamra 5 (RH-5) to shed new light on its mobility, using stable isotopes and radiocarbon ((14)C) dating as dietary tracers. Charcoal, shell, human bone and enamel apatite from eight contemporary graves were sampled. Graves are thought to provide the best chance to obtain marine and terrestrial remains that were contemporary with the human remains in order to calculate the marine reservoir effect (MRE) for this period. Inter-individual variation in human bone apatite δ(13)C value is small, suggesting a homogenous diet. Bone apatite (14)C ages are very close to the shell ages while enamel is significantly younger and plots near the charcoal ages. Older enamel ages were obtained when a stronger acetic treatment was used, demonstrating that the young ages are due to diagenetic alteration rather than a diachronic change in diet and that only bone apatite retained in vivo dietary signals. Bone ages indicate a heavy reliance on marine resources and it is therefore unlikely that the individuals analyzed here were leaving the coast seasonally, although mobility along the coast cannot be excluded.

Contrasting Cu, Fe, and Zn isotopic patterns in organs and body fluids of mice and sheep, with emphasis on cellular fractionation.

We report Cu, Fe, and Zn natural isotope compositions in organs, body fluids, diets and feces of mice and sheep. Large and systematic isotope variability is observed, notably in the δ(66)Zn in liver and δ(65)Cu in kidneys, but significant differences exist between mice, sheep and humans, especially in the δ(66)Zn value of blood. The results are interpreted with reference to current knowledge of metal trafficking and redox conditions in cells. In general, the light isotopes preferentially fractionate into 'softer' bonds involving sulfur such as cysteine and glutathione, whereas heavy isotopes fractionate into 'harder' bonds involving nitrogen (histidine) and even more oxygen, notably hydroxides, phosphates, and carbonates. Bonds involving the reduced forms Cu(+) and Fe(2+) are enriched in the light isotopes relative to bonds involving the oxidized Cu(2+) and Fe(3+) forms. Differences in blood Zn isotope abundances between mice, sheep and humans may reflect a different prevalence of Zn ZIP transporters. The isotopically heavy Cu in the kidneys may reflect isotope fractionation during redox processes and may be relevant to ascorbate degradation into oxalate.

Utilization of sugarcane habitat by feral pig (Sus scrofa) in northern tropical Queensland: evidence from the stable isotope composition of hair.

Feral pigs (Sus scrofa) are an invasive species that disrupt ecosystem functioning throughout their introduced range. In tropical environments, feral pigs are associated with predation and displacement of endangered species, modification of habitat, and act as a vector for the spread of exotic vegetation and disease. Across many parts of their introduced range, the diet of feral pigs is poorly known. Although the remote location and difficult terrain of far north Queensland makes observing feral pig behavior difficult, feral pigs are perceived to seek refuge in World Heritage tropical rainforests and seasonally 'crop raid' into lowland sugarcane crops. Thus, identifying how feral pigs are using different components of the landscape is important to the design of management strategies. We used the stable isotope composition of captured feral pigs to determine the extent of rainforest and sugarcane habitat usage. Recently grown hair (basal hair) from feral pigs captured in remote rainforest indicated pigs met their dietary needs solely within this habitat. Stable carbon and nitrogen isotope values of basal hair from feral pigs captured near sugarcane plantations were more variable, with some individuals estimated to consume over 85% of their diet within a sugarcane habitat, while a few consumed as much as 90% of their diet from adjacent forested environments. We estimated whether feral pigs switch habitats by sequentially sampling δ(13)C and δ(15)N values of long tail hair from a subset of seven captured animals, and demonstrate that four of these individuals moved between habitats. Our results indicate that feral pigs utilize both sugarcane and forest habitats, and can switch between these resources.

First wave of cultivators spread to Cyprus at least 10,600 y ago.

Early Neolithic sedentary villagers started cultivating wild cereals in the Near East 11,500 y ago [Pre-Pottery Neolithic A (PPNA)]. Recent discoveries indicated that Cyprus was frequented by Late PPNA people, but the earliest evidence until now for both the use of cereals and Neolithic villages on the island dates to 10,400 y ago. Here we present the recent archaeological excavation at Klimonas, which demonstrates that established villagers were living on Cyprus between 11,100 and 10,600 y ago. Villagers had stone artifacts and buildings (including a remarkable 10-m diameter communal building) that were similar to those found on Late PPNA sites on the mainland. Cereals were introduced from the Levant, and meat was obtained by hunting the only ungulate living on the island, a small indigenous Cypriot wild boar. Cats and small domestic dogs were brought from the mainland. This colonization suggests well-developed maritime capabilities by the PPNA period, but also that migration from the mainland may have occurred shortly after the beginning of agriculture.

Bodily variability of zinc natural isotope abundances in sheep.

Evidence is growing that the range of zinc stable isotope compositions, represented by the deviation of (66)Zn in permil units relative to a standard and expressed as delta(66)Zn, is larger in organic matter than in inorganic material. This study reports the variations of delta(66)Zn in various organs of sheep raised on a controlled diet. Zinc was purified by anion-exchange chromatography. The Zn concentrations and Zn stable isotope compositions were determined by quadrupole inductively coupled plasma mass spectrometry and multi-collector inductively coupled plasma mass spectrometry, respectively. The data show that delta(66)Zn variability exceeds 1 per thousand, with bone, muscle, serum and urine enriched in the heavy isotopes, and feces, red blood cells, kidney and liver enriched in light isotopes, all relative to the diet value. The (66)Zn enrichment of the circulating serum reservoir is likely to take place in the digestive tract, probably through the preferential binding of lighter isotopes with phytic acid, which is known to control the uptake of metallic elements. Mass balance calculations suggest that the (66)Zn depletion between diet and feces, which is not balanced by any other outward flux, leads to a secular isotopic drift in serum. A simple time-dependent two-box model, involving the gastro-intestinal tract on the one hand and the muscle and bone on the other, predicts that the maximum (66)Zn enrichment, which equals the difference in delta(66)Zn between diet and bulk (approximately 0.25 per thousand), is reached after about ten years. Therefore, a better understanding of the variations of natural abundance of Zn isotopes in animals and humans will probably bring new perspectives for the assessment of their Zn status.