Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha

The evolutionary relationships of two animal phyla, Ctenophora and Xenacoelomorpha, have proved highly contentious. Ctenophora have been proposed as the most distant relatives of all other animals (Ctenophora-first rather than the traditional Porifera-first). Xenacoelomorpha may be primitively simple relatives of all other bilaterally symmetrical animals (Nephrozoa) or simplified relatives of echinoderms and hemichordates (Xenambulacraria). In both cases, one of the alternative topologies must be a result of errors in tree reconstruction. Here, using empirical data and simulations, we show that the Ctenophora-first and Nephrozoa topologies (but not Porifera-first and Ambulacraria topologies) are strongly supported by analyses affected by systematic errors. Accommodating this finding suggests that empirical studies supporting Ctenophora-first and Nephrozoa trees are likely to be explained by systematic error. This would imply that the alternative Porifera-first and Xenambulacraria topologies, which are supported by analyses designed to minimize systematic error, are the most credible current alternatives

Should Educators be ‘Wrapping School Playgrounds in Cotton Wool’ to Encourage Physical Activity? Exploring Primary and Secondary Students’ Voices from the School Playground

Physical activity in school playgrounds has changed considerably over recent decades to reflect a climate of ‘surplus safety’. A growing culture of surplus safety can be attributed to a desire of parents and teachers responsible for children to protect school students from danger. The aim of this research was to examine students’ perceptions of playground safety influences on physical activity during school breaks from the perspectives of the ‘users’ of school playgrounds. Data collection consisted of seven focus groups (4 primary school & 3 secondary school) conducted across four schools (2 primary & 2 secondary). During this study, the focus group discussions consisted of 54 children (32 primary & 22 secondary; 50% females; 50% males). Social-Ecological Model levels of school playground safety influence identified by both primary and secondary school students included intrapersonal safety influences (risk taking, preventing boredom, misbehaviour); interpersonal safety influences (teacher responsibilities, teacher support, peer support, teacher intimidation and bullying/territorial issues); physical environment safety influences (surfacing, protection from the weather, safe structures, protective equipment, playground space, hydration, school security and passive smoking protection) and policy/organisational safety influences (designated play areas, playground rules, further supervision, maintenance). This research addresses an important gap in the literature by providing useful information for teacher educators of the multiple safety influences on students’ participation in playground physical activity

Reassessment of causes of ozone column variability following the eruption of Mount Pinatubo using a nudged CCM

The eruption of Mount Pinatubo produced the largest loading of stratospheric sulphate aerosol in the twentieth century. This heated the tropical lower stratosphere, affecting stratospheric circulation, and provided enhanced surface area for heterogeneous chemistry. These factors combined to produce record low values of "global" total ozone column. Though well studied, there remains some uncertainty about the attribution of this low ozone, with contributions from both chemical and dynamical effects. We take a complementary approach to previous studies, nudging the potential temperature and horizontal winds in the new UKCA chemistry climate model to reproduce the atmospheric response and assess the impact on global total ozone. We then combine model runs and observations to distinguish between chemical and dynamical effects. To estimate the effects of increased heterogeneous chemistry on ozone we compare runs with volcanically enhanced and background surface aerosol density. The modelled depletion of global ozone peaks at about 7 DU in early 1993, in good agreement with values obtained from observations. We subtract the modelled aerosol induced ozone loss from the observed ozone record and attribute the remaining variability to `dynamical' effects. The remaining variability is dominated by the QBO. We also examine tropical and mid-latitude ozone, diagnosing contributions from El Niño in the tropics and identifying dynamically driven low ozone in northern mid-latitudes, which we interpret as possible evidence of changes in the QBO. We conclude that, on a global scale, the record lows of extra-polar ozone are produced by the increased heterogeneous chemistry, although there is evidence for dynamics produced low ozone in certain regions, including northern mid-latitudes

Systematic errors in phylogenetic trees

The effort to reconstruct the tree of life was revolutionized by the use of sequences of proteins and nucleic acids. Phylogenetic trees are now routinely inferred using hundreds of thousands of amino acid or nucleotide characters. It thus seems surprising that many aspects of the tree of life are still controversial; conflicting results between large scale phylogenomic studies show that errors remain common despite large datasets. These errors often result from systematic biases in the way sequences evolve. While the resulting systematic errors are well understood, it requires careful efforts to reduce their effects

Systematic errors in orthology inference and their effects on evolutionary analyses

Summary The availability of complete sets of genes from many organisms makes it possible to identify genes unique to (or lost from) certain clades. This information is used to reconstruct phylogenetic trees; identify genes involved in the evolution of clade specific novelties; and for phylostratigraphy—identifying ages of genes in a given species. These investigations rely on accurately predicted orthologs. Here we use simulation to produce sets of orthologs that experience no gains or losses. We show that errors in identifying orthologs increase with higher rates of evolution. We use the predicted sets of orthologs, with errors, to reconstruct phylogenetic trees; to count gains and losses; and for phylostratigraphy. Our simulated data, containing information only from errors in orthology prediction, closely recapitulate findings from empirical data. We suggest published downstream analyses must be informed to a large extent by errors in orthology prediction that mimic expected patterns of gene evolution

Female Surfers Riding the Crest of a ‘New Wave’ of Irish National Identity

With surfing debuting at the 2021 Tokyo Olympics (postponed from summer 2020 due to the COVID 19 global pandemic) it is timely to consider surfing and the national identifications women in Ireland may have with this sport. As Lee Bush states, 'with so little scholarship on surfing women, descriptive studies are needed as a foundation for launching future interpretive and critical studies.' Twelve women who surf in Ireland spoke about the links their surfing may or may not have with their national identity. Previous academic inquiry on links between national identity and sport on the island of Ireland has almost exclusively focused on men's experiences of team sports and issues of 'Irishness'. 'Irishness' is globally recognised and stereotypically linked to traditional and indigenous Irish sports such as Gaelic football and a range of other cultural activities. Research into women's sport participation has largely been restricted to the study of soccer in the Republic of Ireland, and gendered evaluations of various lifestyle and health surveys. Katie Liston, a key researcher in sport and gender relations in Ireland, highlights that 'there seems to be an increasing diversity in the kinds of activities in which people participate in', and that there is a shift towards 'lifestyle' activities for adults as diversity increases in young people's participation in sports and leisure activities. Against the backdrop of Liston's work, this article delves deeper into data collected as part of a wider research project, discussing whether or not women who surf in Ireland do so as part of a process designed to construct and reflect their national identities related to this arguably 'postmodern' 'lifestyle sport', in which Ireland will be represented on the Olympic stage for the first time in 2021

Technical Note: Description and assessment of a nudged version of the new dynamics Unified Model

International audienceWe present a "nudged" version of the Met Office general circulation model, the Unified Model. We constrain this global climate model using ERA-40 re-analysis data with the aim of reproducing the observed "weather" over a year from September 1999. Quantitative assessments are made of its performance, focusing on dynamical aspects of nudging and demonstrating that the "weather" is well simulated

Deletions of the derivative chromosome 9 occur at the time of the Philadelphia translocation and provide a powerful and independent prognostic indicator in chronic myeloid leukemia

Chronic myeloid leukemia (CML) is characterized by formation of the BCR-ABL fusion gene, usually as a consequence of the Philadelphia (Ph) translocation between chromosomes 9 and 22. Large deletions on the derivative chromosome 9 have recently been reported, but it was unclear whether deletions arose during disease progression or at the time of the Ph translocation. Fluorescence in situ hybridization (FISH) analysis was used to assess the deletion status of 253 patients with CML. The strength of deletion status as a prognostic indicator was then compared to the Sokal and Hasford scoring systems. The frequency of deletions was similar at diagnosis and after disease progression but was significantly increased in patients with variant Ph translocations. In patients with a deletion, all Ph+ metaphases carried the deletion. The median survival of patients with and without deletions was 38 months and 88 months, respectively (P = .0001). By contrast the survival difference between Sokal or Hasford high-risk and non-high-risk patients was of only borderline significance (P = .057 and P = .034). The results indicate that deletions occur at the time of the Ph translocation. An apparently simple reciprocal translocation may therefore result in considerable genetic heterogeneity ab initio, a concept that is likely to apply to other malignancies associated with translocations. Deletion status is also a powerful and independent prognostic factor for patients with CML. The prognostic significance of deletion status should now be studied prospectively and, if confirmed, should be incorporated into management decisions and the analysis of clinical trials. (C) 2001 by The American Society of Hematology

Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers

In some eukaryotes, a ‘hidden break’ has been described in which the 28S ribosomal RNA molecule is cleaved into two subparts. The break is common in protostome animals (arthropods, molluscs, annelids etc.) but a break has also been reported in some vertebrates and non-metazoan eukaryotes. We present a new computational approach to determine the presence of the hidden break in 28S rRNAs using mapping of RNA-Seq data. We find a homologous break is present across protostomes although has been lost in a small number of taxa. We show that rare breaks in vertebrate 28S rRNAs are not homologous to the protostome break. A break is found in just 4 out of 331 species of non-animal eukaryotes studied and three of these are located in the same position as the protostome break suggesting a striking instance of convergent evolution. RNA Integrity Numbers (RIN) rely on intact 28s rRNA and will be consistently underestimated in the great majority of animal species with a break