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.

Deciphering shell proteome within different Baltic populations of mytilid mussels illustrates important local variability and potential consequences in the context of changing marine conditions.

Molluscs defend themselves against predation and environmental stressors through the possession of mineralized shells. Mussels are widely used to predict the effects of abiotic factors such as salinity and pH on marine calcifiers in the context of changing ocean conditions. Shell matrix proteins are part of the molecular control regulating the biomineralization processes underpinning shell production. Under changing environmental conditions, differential expression of these proteins leads to the phenotypic plasticity of shells seen in many mollusc species. Low salinity decreases the availability of calcium and inorganic carbon in seawater and consequently energetic constraints often lead to thin, small and fragile shells in Mytilid mussels inhabiting Baltic Sea. To understand how the modulation of shell matrix proteins alters biomineralization, we compared the shell proteomes of mussels living under full marine conditions in the North Sea to those living in the low saline Baltic Sea. Modulation of proteins comprising the Mytilus biomineralization tool kit is observed. These data showed a relative increase in chitin related proteins, decrease in SD-rich, GA-rich shell matrix proteins indicating that altered protein scaffolding and mineral nucleation lead to impaired shell microstructures influencing shell resistance in Baltic Mytilid mussels. Interestingly, proteins with immunity domains in the shell matrix are also found to be modulated. Shell traits such as periostracum thickness, organic content and fracture resistance qualitatively correlates with the modulation of SMPs in Mytilid mussels providing key insights into control of biomineralization at molecular level in the context of changing marine conditions.

Unraveling the polychromy and antiquity of the Pachacamac Idol, Pacific coast, Peru.

Pachacamac is the name of the 15th-16th century Inca sanctuary on the Peruvian coast as well as the name of one of the principal oracles of Inca divinities. This effigy would have been destroyed by Pizarro in 1533 during his visit to the great monumental complex, and as such the originality and antiquity of the wooden statue-the so-called Pachacamac Idol-have been the subject of much controversy and debate. We present here previously unpublished dates that confirm its manufacture during the Middle Horizon (AD 500-1000), as well as evidence of its original polychromy. Traces of colors were observed on its different sections with portable microscopy and analyses with two different X-Ray Fluorescence spectrometry techniques, leading to identification of yellow, white, and red mineral pigments, including the presence of cinnabar. Dated between the 8th and 9th centuries, the statue would have been worshipped for almost 700 years, from the time of its creation to the time of the Spanish conquest, when Pachacamac was a major place of pilgrimage. These data not only offer a new perspective on Pachacamac's emblematic sacred icon, but also on the colorful practices of the Pre-Hispanic Andes.

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.

Microscale imaging of the preservation state of 5,000-year-old archaeological bones by synchrotron infrared microspectroscopy.

Archaeological bone materials record characteristic markers of life in prehistoric times (dating, climate, environment, diet, human migration) in their isotopic and chemical composition in addition to palaeontological, archaeozoological, anthropological and palaeogenetic information. Thus, the discovery and conservation of archaeological bone materials is of great importance to get access to this information. However, archaeological materials are altered by different postmortem processes and it appears necessary to estimate if the archaeological information is still reliable or if it has been modified during burial. As archaeological bone materials present a high structural hierarchy at the micro- and nanoscale, changes induced by diagenetic phenomena have to be observed at these scales. One method for revealing post mortem changes of the bone structure and composition at the microscale is synchrotron radiation micro-FTIR imaging (SR micro-FTIR). Thus, thin sections of about 5,000-year-old archaeological bones have been analysed in transmission mode at the IRIS beamline (BESSY II, HZB Berlin) to determine markers of the state of bone preservation at the microscale. The archaeological bone material comes from station 19 of the Neolithic site of the Chalain Lake. By using SR micro-FTIR it was possible to image characteristic bone structures, e.g. osteons (the constitutive histological unit of cortical bone), using the absorption band ratios corresponding to different chemical bone constituents (collagen content and quality, phosphate crystallinity, carbonate content). These data allow us to precisely evaluate the state of preservation of a 5,000-year-old bone at the histological level.