Long non‐coding RNAs in development and disease: Conservation to mechanisms

Our genomes contain the blueprint of what makes us human and many indications as to why we develop disease. Until the last 10 years, most studies had focussed on protein‐coding genes, more specifically DNA sequences coding for proteins. However, this represents less than 5% of our genomes. The other 95% is referred to as the ‘dark matter’ of our genomes, our understanding of which is extremely limited. Part of this ‘dark matter’ includes regions that give rise to RNAs that do not code for proteins. A subset of these non‐coding RNAs are long non‐coding RNAs (lncRNAs), which in particular are beginning to be dissected and their importance to human health revealed. To improve our understanding and treatment of disease it is vital that we understand the molecular and cellular function of lncRNAs, and how their misregulation can contribute to disease. It is not yet clear what proportion of lncRNAs is actually functional; conservation during evolution is being used to understand the biological importance of lncRNA. Here, we present key themes within the field of lncRNAs, emphasising the importance of their roles in both the nucleus and the cytoplasm of cells, as well as patterns in their modes of action. We discuss their potential functions in development and disease using examples where we have the greatest understanding. Finally, we emphasise why lncRNAs can serve as biomarkers and discuss their emerging potential for therapy

Dating the Bronze Age of Southeast Asia: why does it matter?

We have dated human bone, freshwater shell, charcoal and rice grains from key sites in mainland Southeast Asia in order to establish the chronological scaffolding for later prehistory (ca 2500 BC-AD 500). In a recent report on the metal remains from the site of Ban Chiang, however, this chronology has been challenged. Here, we respond to these claims and show that they are unfounded and misleading. We maintain the integrity of the Bayesian-modelled radiocarbon results that identify the arrival of the first rice and millet farmers in mainland Southeast Asia towards the end of the 3rd millennium BC, with the first evidence for the casting of bronze by about 1100 BC. Social change that followed the establishment of metallurgy was rapid and profound

Distinguishing African bovids using Zooarchaeology by Mass Spectrometry (ZooMS): new peptide markers and insights into Iron Age economies in Zambia

Assessing past foodways, subsistence strategies, and environments depends on the accurate identification of animals in the archaeological record. The high rates of fragmentation and often poor preservation of animal bones at many archaeological sites across sub-Saharan Africa have rendered archaeofaunal specimens unidentifiable beyond broad categories, such as “large mammal” or “medium bovid”. Identification of archaeofaunal specimens through Zooarchaeology by Mass Spectrometry (ZooMS), or peptide mass fingerprinting of bone collagen, offers an avenue for identification of morphologically ambiguous or unidentifiable bone fragments from such assemblages. However, application of ZooMS analysis has been hindered by a lack of complete reference peptide markers for African taxa, particularly bovids. Here we present the complete set of confirmed ZooMS peptide markers for members of all African bovid tribes. We also identify two novel peptide markers that can be used to further distinguish between bovid groups. We demonstrate that nearly all African bovid subfamilies are distinguishable using ZooMS methods, and some differences exist between tribes or sub-tribes, as is the case for Bovina (cattle) vs. Bubalina (African buffalo) within the subfamily Bovinae. We use ZooMS analysis to identify specimens from extremely fragmented faunal assemblages from six Late Holocene archaeological sites in Zambia. ZooMS-based identifications reveal greater taxonomic richness than analyses based solely on morphology, and these new identifications illuminate Iron Age subsistence economies c. 2200–500 cal BP. While the Iron Age in Zambia is associated with the transition from hunting and foraging to the development of farming and herding, our results demonstrate the continued reliance on wild bovids among Iron Age communities in central and southwestern Zambia Iron Age and herding focused primarily on cattle. We also outline further potential applications of ZooMS in African archaeology.Introduction Faunal identifications and key research questions ZooMS in African archaeology Materials & methods Collagen extraction and digestion Peptide mass fingerprinting LC-MS/MS Biomarker identification and confirmation Identification of archaeological samples Results and discussion - Data quality control - Distinguishing among bovid groups Comparison with published markers ZooMS analysis and archaeofaunal identifications Herding economies and the persistence of hunting in Iron Age Zambia Conclusio

Radiocarbon dates for the late Pleistocene and Early Holocene occupations of Cova Rosa (Ribadesella, Asturias, Spain)

Four excavations have been performed at the archaeological site of Cova Rosa (Asturias, Cantabrian Spain): three of them in the second half of last century and the other in this decade. Although little of the archaeological material found in those excavations has been published, here we attempt the stratigraphic correlation of sections revealed by the different excavations and we present 22 new radiocarbon dates for bones and marine shells, built in a Bayesian statistical model. This has enabled the documentation of occupations that mainly took place during the Last Glacial period, in the Solutrean (middle and upper phases) and Magdalenian (archaic, lower, and upper phases), and also in the early Holocene (Mesolithic). These occupations are compared with the record at other sites in Cantabrian Spain in general and in Asturias, in particular.Introduction Cova Rosa Cave - Geographical and Geological Setting - History of Research - Stratigraphy Radiocarbon dates at Cova Rosa - Method - Validity Analysis - Results and Critical Assessment - Solutrean - Magdalenian - Mesolithic Discussion: 14C chronology of Cova Rosa Conclusion

A milk and ochre paint mixture used 49,000 years ago at Sibudu, South Africa

Gas chromatography/mass spectrometry, proteomic and scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM/EDS) analyses of residue on a stone flake from a 49,000 year-old layer of Sibudu (South Africa) indicate a mixture of ochre and casein from milk, likely obtained by killing a lactating wild bovid. Ochre powder production and use are documented in Middle Stone Age South African sites but until now there has been no evidence of the use of milk as a binder. Our analyses show that this ochre-based mixture was neither a hafting adhesive nor a residue left after treating animal skins, but a liquid mixture consisting of a powdered pigment mixed with milk; in other words, a paint medium that could have been applied to a surface or to human skin. The significance of our finds also lies in the fact that it establishes the antiquity of the use of milk as a binder well before the introduction of domestic cattle in South Africa in the first millennium AD

Social responses to climate change in Iron Age north-east Thailand: New archaeobotanical evidence

New evidence from archaeological investigations in north-east Thailand shows a transition in rice farming towards wetland cultivation that would have facilitated greater yields and surpluses. This evidence, combined with new dates and palaeoclimatic data, suggests that this transition took place in the Iron Age, at a time of increasingly arid climate, and when a number of broader societal changes become apparent in the archaeological record. For the first time, it is possible to relate changes in subsistence economy to shifts in regional climate and water-management strategies, and to the emergence of state societies in Southeast Asia

Ancient crops provide first archaeological signature of the westward Austronesian expansion

The Austronesian settlement of the remote island of Madagascar remains one of the great puzzles of Indo-Pacific prehistory. Although linguistic, ethnographic, and genetic evidence points clearly to a colonization of Madagascar by Austronesian language-speaking people from Island Southeast Asia, decades of archaeological research have failed to locate evidence for a Southeast Asian signature in the island's early material record. Here, we present new archaeobotanical data that show that Southeast Asian settlers brought Asian crops with them when they settled in Africa. These crops provide the first, to our knowledge, reliable archaeological window into the Southeast Asian colonization of Madagascar. They additionally suggest that initial Southeast Asian settlement in Africa was not limited to Madagascar, but also extended to the Comoros. Archaeobotanical data may support a model of indirect Austronesian colonization of Madagascar from the Comoros and/or elsewhere in eastern Africa

Fossils, fish and tropical forests: prehistoric human adaptations on the island frontiers of Oceania

Oceania is a key region for studying human dispersals, adaptations and interactions with other hominin populations. Although archaeological evidence now reveals occupation of the region by approximately 65–45 000 years ago, its human fossil record, which has the best potential to provide direct insights into ecological adaptations and population relationships, has remained much more elusive. Here, we apply radiocarbon dating and stable isotope approaches to the earliest human remains so far excavated on the islands of Near and Remote Oceania to explore the chronology and diets of the first preserved human individuals to step across these Pacific frontiers. We demonstrate that the oldest human (or indeed hominin) fossil outside of the mainland New Guinea-Aru area dates to approximately 11 800 years ago. Furthermore, although these early sea-faring populations have been associated with a specialized coastal adaptation, we show that Late Pleistocene–Holocene humans living on islands in the Bismarck Archipelago and in Vanuatu display a persistent reliance on interior tropical forest resources. We argue that local tropical habitats, rather than purely coasts or, later, arriving domesticates, should be emphasized in discussions of human diets and cultural practices from the onset of our species' arrival in this part of the world.1. Introduction 2. Background (a) Human colonization of near and remote Oceania (b) Stable isotope analysis and past human adaptations in the tropics 3. Methods (a) Radiocarbon dating (b) Stable isotope analysis (c) Phytolith analysis of dental calculus 4. Results (a) Radiocarbon dating and Bayesian modelling (b) Stable isotope analysis (c) Phytolith analysis of dental calculus 5. Discussion and conclusio

Grotta del Cavallo (Apulia-Southern Italy). The Uluzzian in the mirror

The Uluzzian techno-complex is commonly considered to be a \u201ctransitional industry\u201d mostly on the basis of some inferred characteristics such as a chiefly flake-based production, a small amount of Upper Palaeolithic-like tools and a combination of Middle and Upper Palaeolithic elements both in the toolkit and in the technical systems. Following its discovery, the Uluzzian was identified as the Italian counterpart of the French Ch\ue2telperronian and attributed to Neandertals. However, a study issued in 2011 has established the modern character of the two deciduous teeth found in 1964 in the Uluzzian deposit of Grotta del Cavallo, fostering renewed interests to the Uluzzian culture, which real nature is almost unknown to the international scientific community. Here we provide preliminary results of the study on the lithic assemblage from the earliest Uluzzian layer and on backed pieces from the whole Uluzzian sequence of Grotta del Cavallo (Apulia, Italy), the type site of the Uluzzian. Moreover, besides a thorough review on the stratigraphy of Grotta del Cavallo (Supplementary Materials), we provide updated information on the human remains by presenting two unpublished teeth from the reworked deposit of the same cave. We conclude that the early Uluzzians demonstrate original technological behavior and innovations devoid of any features deriving or directly linked with the late Mousterian of Southern Italy. Therefore, the novelty nature of the Uluzzian techno-complex (with respect to the preceding Mousterian) complies with the recent reassessment of the two deciduous teeth from Grotta del Cavallo in suggesting an earliest migration of modern humans in southern Europe around 45,000 years ago