A high-resolution map of human evolutionary constraint using 29 mammals.

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease

Aboriginal Australian mitochondrial genome variation - An increased understanding of population antiquity and diversity

Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ∼55 thousand years ago. Genetic studies, though limited, have demonstrated both the uniqueness and antiquity of Aboriginal Australian genomes. We have further resolved known Aboriginal Australian mitochondrial haplogroups and discovered novel indigenous lineages by sequencing the mitogenomes of 127 contemporary Aboriginal Australians. In particular, the more common haplogroups observed in our dataset included M42a, M42c, S, P5 and P12, followed by rarer haplogroups M15, M16, N13, O, P3, P6 and P8. We propose some major phylogenetic rearrangements, such as in haplogroup P where we delinked P4a and P4b and redefined them as P4 (New Guinean) and P11 (Australian), respectively. Haplogroup P2b was identified as a novel clade potentially restricted to Torres Strait Islanders. Nearly all Aboriginal Australian mitochondrial haplogroups detected appear to be ancient, with no evidence of later introgression during the Holocene. Our findings greatly increase knowledge about the geographic distribution and phylogenetic structure of mitochondrial lineages that have survived in contemporary descendants of Australia's first settlers. © The Author(s) 2017

The impact of ENSO on Southern African rainfall in CMIP5 ocean atmosphere coupled climate models

We study the ability of 24 ocean atmosphere global coupled models from the Coupled Model Intercomparison Project 5 (CMIP5) to reproduce the teleconnections between El Niño Southern Oscillation (ENSO) and Southern African rainfall in austral summer using historical forced simulations, with a focus on the atmospheric dynamic associated with El Niño. Overestimations of summer rainfall occur over Southern Africa in all CMIP5 models. Abnormal westward extensions of ENSO patterns are a common feature of all CMIP5 models, while the warming of the Indian Ocean that happens during El Niño is not correctly reproduced. This could impact the teleconnection between ENSO and Southern African rainfall which is represented with mixed success in CMIP5 models. Large-scale anomalies of suppressed deep-convection over the tropical maritime continent and enhanced convection from the central to eastern Pacific are correctly simulated. However, regional biases occur above Africa and the Indian Ocean, particularly in the position of the deep convection anomalies associated with El Niño, which can lead to the wrong sign in rainfall anomalies in the northwest part of South Africa. From the near-surface to mid-troposphere, CMIP5 models underestimate the observed anomalous pattern of pressure occurring over Southern Africa that leads to dry conditions during El Niño years

The evolution and storage of primitive melts in the Eastern Volcanic Zone of Iceland: the 10 ka Grímsvötn tephra series (i.e. the Saksunarvatn ash)

Major, trace and volatile elements were measured in a suite of primitive macrocrysts and melt inclusions from the thickest layer of the 10 ka Grímsvötn tephra series (i.e. Saksunarvatn ash) at Lake Hvítárvatn in central Iceland. In the absence of primitive tholeiitic eruptions (MgO > 7 wt.%) within the Eastern Volcanic Zone (EVZ) of Iceland, these crystal and inclusion compositions provide an important insight into magmatic processes in this volcanically productive region. Matrix glass compositions show strong similarities with glass compositions from the AD 1783–84 Laki eruption, confirming the affinity of the tephra series with the Grímsvötn volcanic system. Macrocrysts can be divided into a primitive assemblage of zoned macrocryst cores (An_78–An_92, Mg#_cpx = 82–87, Fo_79.5–Fo_87) and an evolved assemblage consisting of unzoned macrocrysts and the rims of zoned macrocrysts (An_60–An_68, Mg#_cpx = 71–78, Fo_70–Fo_76). Although the evolved assemblage is close to being in equilibrium with the matrix glass, trace element disequilibrium between primitive and evolved assemblages indicates that they were derived from different distributions of mantle melt compositions. Juxtaposition of disequilibrium assemblages probably occurred during disaggregation of incompatible trace element-depleted mushes (mean La/Yb_melt = 2.1) into aphyric and incompatible trace element-enriched liquids (La/Yb_melt = 3.6) shortly before the growth of the evolved macrocryst assemblage. Post-entrapment modification of plagioclase-hosted melt inclusions has been minimal and high-Mg# inclusions record differentiation and mixing of compositionally variable mantle melts that are amongst the most primitive liquids known from the EVZ. Coupled high field strength element (HFSE) depletion and incompatible trace element enrichment in a subset of primitive plagioclase-hosted melt inclusions can be accounted for by inclusion formation following plagioclase dissolution driven by interaction with plagioclase-undersaturated melts. Thermobarometric calculations indicate that final crystal-melt equilibration within the evolved assemblage occurred at ~1140°C and 0.0–1.5 kbar. Considering the large volume of the erupted tephra and textural evidence for rapid crystallisation of the evolved assemblage, 0.0–1.5 kbar is considered unlikely to represent a pressure of long-term magma accumulation and storage. Multiple thermometers indicate that the primitive assemblage crystallised at high temperatures of 1240–1300°C. Different barometers, however, return markedly different crystallisation depth estimates. Raw clinopyroxene-melt pressures of 5.5–7.5 kbar conflict with apparent melt inclusion entrapment pressures of 1.4 kbar. After applying a correction derived from published experimental data, clinopyroxene-melt equilibria return mid-crustal pressures of 4±1.5 kbar, which are consistent with pressures estimated from the major element content of primitive melt inclusions. Long-term storage of primitive magmas in the mid-crust implies that low CO_2 concentrations measured in primitive plagioclase-hosted inclusions (262–800 ppm) result from post-entrapment CO_2 loss during transport through the shallow crust. In order to reconstruct basaltic plumbing system geometries from petrological data with greater confidence, mineral-melt equilibrium models require refinement at pressures of magma storage in Iceland. Further basalt phase equilibria experiments are thus needed within the crucial 1–7 kbar range.D.A.N. was supported by a Natural Environment Research Council studentship (NE/1528277/1) at the start of this project. SIMS analyses were supported by Natural Environment Research Council Ion Microprobe Facility award (IMF508/1013).This is the final version of the article. It first appeared from Springer via http://dx.doi.org/10.1007/s00410-015-1170-

Structuring effect of tools conceptualized through initial goal fixedness for work activity

Analysis of work activities in nuclear industry has highlighted a new psycho-cognitive phenomenon: the structuring effect of tools (SET) sometimes leading to unexpected operating deviations; the subject is unable to perform a task concerning object A using or adapting a tool designed and presented to perform the same task concerning object B when object A is expected by the subject. Conditions to isolate and identify the SET were determined and reproduced in experiments for further analysis. Students and seven professional categories of adults (N = 77) were involved in three experimental conditions (control group, group with prior warning, group with final control) while individually performing a task with similar characteristics compared to real operating conditions and under moderate time-pressure. The results were: (1) highest performance with prior warning and (2) demonstration that academic and professional training favor the SET. After discussing different cognitive processes potentially related to the SET, we described (3) the psycho-cognitive process underlying the SET: Initial Goal Fixedness (IGF), a combination of the anchoring of the initial goal of the activity with a focus on the features of the initial goal favored by an Einstellung effect. This suggested coping with the negative effect of the SET by impeding the IGF rather than trying to increase the subjects’ awareness at the expense of their health. Extensions to other high-risk industries were discussed

Causal Pathways from Enteropathogens to Environmental Enteropathy: Findings from the MAL-ED Birth Cohort Study

Background Environmental enteropathy (EE), the adverse impact of frequent and numerous enteric infections on the gut resulting in a state of persistent immune activation and altered permeability, has been proposed as a key determinant of growth failure in children in low- and middle-income populations. A theory-driven systems model to critically evaluate pathways through which enteropathogens, gut permeability, and intestinal and systemic inflammation affect child growth was conducted within the framework of the Etiology, Risk Factors and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) birth cohort study that included children from eight countries. Methods Non-diarrheal stool samples (N = 22,846) from 1253 children from multiple sites were evaluated for a panel of 40 enteropathogens and fecal concentrations of myeloperoxidase, alpha-1-antitrypsin, and neopterin. Among these same children, urinary lactulose:mannitol (L:M) (N = 6363) and plasma alpha-1-acid glycoprotein (AGP) (N = 2797) were also measured. The temporal sampling design was used to create a directed acyclic graph of proposed mechanistic pathways between enteropathogen detection in non-diarrheal stools, biomarkers of intestinal permeability and inflammation, systemic inflammation and change in length- and weight- for age in children 0–2 years of age. Findings Children in these populations had frequent enteric infections and high levels of both intestinal and systemic inflammation. Higher burdens of enteropathogens, especially those categorized as being enteroinvasive or causing mucosal disruption, were associated with elevated biomarker concentrations of gut and systemic inflammation and, via these associations, indirectly associated with both reduced linear and ponderal growth. Evidence for the association with reduced linear growth was stronger for systemic inflammation than for gut inflammation; the opposite was true of reduced ponderal growth. Although Giardia was associated with reduced growth, the association was not mediated by any of the biomarkers evaluated. Interpretation The large quantity of empirical evidence contributing to this analysis supports the conceptual model of EE. The effects of EE on growth faltering in young children were small, but multiple mechanistic pathways underlying the attribution of growth failure to asymptomatic enteric infections had statistical support in the analysis. The strongest evidence for EE was the association between enteropathogens and linear growth mediated through systemic inflammation

Onset of main Phanerozoic marine radiation sparked by emerging Mid Ordovician icehouse

This is the final version. Available on open access from Springer Nature via the DOI in this recordThe Great Ordovician Biodiversification Event (GOBE) was the most rapid and sustained increase in marine Phanerozoic biodiversity. What generated this biotic response across Palaeozoic seascapes is a matter of debate; several intrinsic and extrinsic drivers have been suggested. One is Ordovician climate, which in recent years has undergone a paradigm shift from a text-book example of an extended greenhouse to an interval with transient cooling intervals - at least during the Late Ordovician. Here, we show the first unambiguous evidence for a sudden Mid Ordovician icehouse, comparable in magnitude to the Quaternary glaciations. We further demonstrate the initiation of this icehouse to coincide with the onset of the GOBE. This finding is based on both abiotic and biotic proxies obtained from the most comprehensive geochemical and palaeobiological dataset yet collected through this interval. We argue that the icehouse conditions increased latitudinal and bathymetrical temperature and oxygen gradients initiating an Early Palaeozoic Great Ocean Conveyor Belt. This fuelled the GOBE, as upwelling zones created new ecospace for the primary producers. A subsequent rise in δ(13)C ratios known as the Middle Darriwilian Isotopic Carbon Excursion (MDICE) may reflect a global response to increased bioproductivity encouraged by the onset of the GOBE.Our expeditions to Russia were mainly funded by the Carlsberg Foundation. C.M.Ø.R. and D.A.T.H. are particularly grateful to the Danish Council for Independent Research | Natural Sciences for their support of this specific project. C.M.Ø.R. further acknowledge support from the VILLUM Foundations Young Investigator Programme. A.L. was funded by the Royal Swedish Physiographic Society in Lund

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

Cytogenetic characterization of two species of Frieseomelitta Ihering, 1912 (Hymenoptera, Apidae, Meliponini)

The cytogenetic analysis of Frieseomelitta dispar and F. francoi revealed the chromosome numbers 2n = 30 and n = 15 and a karyotypic formula 2K = 4M+2Mt+4A+20AM. The number of chromosomes observed was consistent with those reported for other Frieseomelitta species. The occurrence of the Mt chromosome and other features of the karyotype formulae suggest a close relationship between F. dispar, F. francoi and F. varia. Nevertheless, it was possible to differentiate the karyotypes of the species by DAPI/CMA3 staining, which revealed GC-rich regions on two chromosome pairs of F. dispar: one acrocentric and one pseudoacrocentric. In F. francoi, the same kinds of regions were observed on a pair of metacentrics and on a pair of acrocentrics. Our analysis also confirmed the chromosome number conservation in Frieseomelitta and suggests that infrequent pericentric inversion could constitute a synapomorphy for the group including F. dispar, F. francoi, and F. varia