Protocol for sectioning human dentine: expanded from Methods 1 and 2

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Using carbon isotope data of fossil bovid communities for palaeoenvironmental reconstruction

Reconstructing palaeoenvironments is a major focus of palaeoanthropological research. While many techniques are now available for exploring past environments, fossil bovids remain amongst the most widely utilized sources of environmental information. Most studies of fossil bovids, however, assume implicitly that bovid ecology is the same now as it was in the distant past. Because such uniformitarianist assumptions are not always valid, we have developed a method to provide palaeoenvironmental information from fossil bovids that requires no ecological assumptions. Here, we show that the percentages of C3 and C4 vegetation-consuming bovids in modern environments generally vary according to the amount of woody vegetation present. Application of this C3 / C4 index to the fossil bovid assemblage at Makapansgat shows that, based on carbon isotope data, the percentage of C3-consuming bovids is high, suggesting a great deal of woody vegetation in this vicinity about 3 million years ago

Utilization of savanna-based resources by Plio-Pleistocene baboons

We have determined the tooth enamel carbonate 13C values of five cercopithecoid taxa from the Plio-Pleistocene deposits of Swartkrans Members 1 and 2 and Sterkfontein Member 4. These data were used to determine the relative proportions of C3 and C4 biomass consumed by extinct baboons and contemporary non-human primates. We compared these results with data on modern Papio hamadryas ursinus from different savanna areas in South Africa, as well as with published isotopic data and dietary interpretations based on molar morphology of these taxa. The data reveal little evidence for use of grasses or grass-based foods by modern South African baboons. The fossil papionins Papio hamadryas robinsoni, Papio (Dinopithecus) ingens, and Parapapio spp., however, utilized more savanna-based C4 resources than previously predicted (particularly in the case of P. (D.) ingens). Theropithecus oswaldi had 13C values depicting, as expected, a largely grass-based diet, and we confirm earlier conclusions that this species incorporated a wider range of food items into its diet than do modern T. gelada, as reported in the literature. The colobine monkey, Cercopithecoides williamsi, made extensive use of savanna-.based C4 foods, confirming some degree of terrestrial foraging by the species

Stable carbon isotope reconstruction of ungulate diet changes through the seasonal cycle

We analysed stable carbon isotope ratios (ð13C) in faeces of 11 African ungulate species from three South African savanna environments to determine whether this approach is sufficiently sensitive to record short-term seasonal diet changes in browsers (BR), mixed-feeders (IM), and grazers (GR). At monthly intervals, faecal ð13C revealed variations in proportions of C3 (browse) to C4 (grass) biomass consumed that were not detected by broader dry versus wet season comparisons, including subtle diet shifts amongst BR and GR. However, trends in faeces were influenced by changes in C3 and C4 plant isotope composition of up to 3‰. Nonetheless, faeces and plants showed strongly similar patterns of variation through the seasonal cycle, so that small diet shifts can be reliably inferred, provided that the variations in plants are controlled for. Faecal ð13C of BR may be further influenced by consumption of isotopically different plant parts such as foliage versus fruit and flowers, and GR faeces may reflect differential utilization of grass following different photosynthetic sub-pathways. Future studies will need to incorporate data that capture isotopic variations in herbivore food sources, and if this is achieved, the approach may well become adopted as a routine addition to traditional methods for assessing diet, habitat use, and habitat condition

Dating human occupation and adaptation in the southern European last glacial refuge : The chronostratigraphy of Grotta del Romito (Italy)

Grotta del Romito has been the subject of numerous archaeological, chronological and palaeoenvironmental investigations for more than a decade. During the Upper Palaeolithic period the site contains evidence of human occupation through the Gravettian and Epigravettian periods, multiple human burials, changes in the pattern of human occupation, and faunal, isotopic and sedimentological evidence for local environmental change. In spite of this rich record, the chronological control is insufficient to resolve shifts in subsistence and mobility patterns at sufficiently high resolution to match the abrupt climate fluctuations at this time. To resolve this we present new radiocarbon and tephrostratigraphic dates in combination with existing radiocarbon dates, and develop a Bayesian age model framework for the site. This improved chronology reveals that local environmental conditions reflect abrupt and long-term changes in climate, and that these also directly influence changing patterns of human occupation of the site. In particular, we show that the environmental record for the site, based on small mammal habitat preferences, is chronologically in phase with the main changes in climate and environment seen in key regional archives from Italy and Greenland. We also calculate the timing of the transitions between different cultural phases and their spans. We also show that the intensification in occupation of the site is chronologically coincident with a rapid rise in Mesic Woody taxa seen in key regional pollen records and is associated with the Late Epigravettian occupation of the site. This change in the record of Grotta del Romito is also closely associated stratigraphically with a new tephra (the ROM-D30 tephra), which may act as a critical marker in environmental records of the region

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?

We challenge the view that our species, Homo sapiens, evolved within a single population and/or region of Africa. The chronology and physical diversity of Pleistocene human fossils suggest that morphologically varied populations pertaining to the H. sapiens clade lived throughout Africa. Similarly, the African archaeological record demonstrates the polycentric origin and persistence of regionally distinct Pleistocene material culture in a variety of paleoecological settings. Genetic studies also indicate that present-day population structure within Africa extends to deep times, paralleling a paleoenvironmental record of shifting and fractured habitable zones. We argue that these fields support an emerging view of a highly structured African prehistory that should be considered in human evolutionary inferences, prompting new interpretations, questions, and interdisciplinary research directions

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN