DNA methylation differences between stick insect ecotypes.

Epigenetic mechanisms, such as DNA methylation, can influence gene regulation and affect phenotypic variation, raising the possibility that they contribute to ecological adaptation. Beginning to address this issue requires high-resolution sequencing studies of natural populations to pinpoint epigenetic regions of potential ecological and evolutionary significance. However, such studies are still relatively uncommon, especially in insects, and are mainly restricted to a few model organisms. Here, we characterize patterns of DNA methylation for natural populations of Timema cristinae adapted to two host plant species (i.e. ecotypes). By integrating results from sequencing of whole transcriptomes, genomes and methylomes, we investigate whether environmental, host and genetic differences of these stick insects are associated with methylation levels of cytosine nucleotides in the CpG context. We report an overall genome-wide methylation level for T. cristinae of ~14%, with methylation being enriched in gene bodies and impoverished in repetitive elements. Genome-wide DNA methylation variation was strongly positively correlated with genetic distance (relatedness), but also exhibited significant host-plant effects. Using methylome-environment association analysis, we pinpointed specific genomic regions that are differentially methylated between ecotypes, with these regions being enriched for genes with functions in membrane processes. The observed association between methylation variation and genetic relatedness, and with the ecologically important variable of host plant, suggests a potential role for epigenetic modification in T. cristinae adaptation. To substantiate such adaptive significance, future studies could test whether methylation can be transmitted across generations and the extent to which it responds to experimental manipulation in field and laboratory studies.

Complex evolutionary processes maintain an ancient chromosomal inversion.

Genome re-arrangements such as chromosomal inversions are often involved in adaptation. As such, they experience natural selection, which can erode genetic variation. Thus, whether and how inversions can remain polymorphic for extended periods of time remains debated. Here we combine genomics, experiments, and evolutionary modeling to elucidate the processes maintaining an inversion polymorphism associated with the use of a challenging host plant (Redwood trees) in Timema stick insects. We show that the inversion is maintained by a combination of processes, finding roles for life-history trade-offs, heterozygote advantage, local adaptation to different hosts, and gene flow. We use models to show how such multi-layered regimes of balancing selection and gene flow provide resilience to help buffer populations against the loss of genetic variation, maintaining the potential for future evolution. We further show that the inversion polymorphism has persisted for millions of years and is not a result of recent introgression. We thus find that rather than being a nuisance, the complex interplay of evolutionary processes provides a mechanism for the long-term maintenance of genetic variation.

Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects.

Evolution can repeat itself, resulting in parallel adaptations in independent lineages occupying similar environments. Moreover, parallel evolution sometimes, but not always, uses the same genes. Two main hypotheses have been put forth to explain the probability and extent of parallel evolution. First, parallel evolution is more likely when shared ecologies result in similar patterns of natural selection in different taxa. Second, parallelism is more likely when genomes are similar because of shared standing variation and similar mutational effects in closely related genomes. Here we combine ecological, genomic, experimental and phenotypic data with Bayesian modelling and randomization tests to quantify the degree of parallelism and its relationship with ecology and genetics. Our results show that the extent to which genomic regions associated with climate are parallel among species of Timema stick insects is shaped collectively by shared ecology and genomic background. Specifically, the extent of genomic parallelism decays with divergence in climatic conditions (that is, habitat or ecological similarity) and genomic similarity. Moreover, we find that climate-associated loci are likely subject to selection in a field experiment, overlap with genetic regions associated with cuticular hydrocarbon traits and are not strongly shaped by introgression between species. Our findings shed light on when evolution is most expected to repeat itself.

A multiyear systematic survey of the quality of reporting for randomised trials in dentistry, neurology and geriatrics published in journals of Spain and Latin America.

BACKGROUND: The Iberoamerican Cochrane Network is currently developing an extensive project to identify Spanish-language journals that publish original clinical research in Spain and Latin America. The project is called BADERI (Database of Iberoamerican Essays and Journal) and feeds the research articles, mainly randomised clinical trials (RCTs), into CENTRAL (Cochrane Collaboration Central Register of Controlled Trials). This study aims to assess the quality of reporting of RCTs published in Spanish and Latin American journals for three clinical fields and assess changes over time. METHODS: We did a systematic survey with time trend analysis of RCTs for dentistry, geriatrics, and neurology. These fields were chosen for pragmatic reasons as they had not yet been completed in BADERI. After screening RCTs from 1990 to 2018 for randomised or quasi-randomised clinical trials, we extracted data for 23 CONSORT items. The primary outcome was the total score of the 23 predefined CONSORT 2010 items for each RCT (score range from 0 to 34). The secondary outcome measure was the score for each one of these 23 items. RESULTS: A total of 392 articles from 1990 to 2018 were included as follows: dentistry (282), neurology (80), and geriatrics (30). We found that the overall compliance score for the CONSORT items included in this study for all 392 RCTs analysed was 12.6 on a scale with a maximum score of 34. With time, the quality of reporting improved slightly for all RCTs. None of the articles achieved the complete individual CONSORT item compliance score. The lowest overall compliance percentage was for item 10 (Randomisation implementation) and item 24 (Protocol registration), with a dismal 1% compliance across all included RCTs, regardless of country. CONCLUSIONS: CONSORT compliance is very poor in the 392 analysed RCTs. The impact of the CONSORT statement on improving the completeness of RCT reporting in Latin America and Spain is not clear. Iberoamerican journals should become more involved in endorsing and enforcing adherence to the CONSORT guidelines.

Intermittent Water Supply Impacts on Distribution System Biofilms and Water Quality.

Intermittent water supplies (IWS) are routinely experienced by drinking water distribution systems around the world, either due to ongoing operational practices or due to one off interruptions. During IWS events changing conditions may impact the endemic biofilms leading to hydraulic mobilisation of organic and inorganic materials attached to pipes walls with a resulting degradation in water quality. To study the impact of IWS on the microbiological and physico-chemical characteristics of drinking water, an experimental full-scale chlorinated pipe facility was operated over 60 days under realistic hydraulic conditions to allow for biofilm growth and to investigate flow resumption behaviour post-IWS events of 6, 48 and 144 hours. Turbidity and metal concentrations showed significant responses to flow restarting, indicating biofilm changes, with events greater than 6 hours generating more turbidity responses and hence discolouration risk. The increase in pressure when the system was restarted showed a substantial increase in total cell counts, while the subsequent increases in flow led to elevated turbidity and metals concentrations. SUVA254 monitoring indicated that shorter times of non-water supply increased the risk of aromatic organic compounds and hence risk of disinfection-by-products formation. DNA sequencing indicated that increasing IWS times resulted in increased relative abundance of potential pathogenic microorganisms, such as Mycobacterium, Sphingomonas, and the fungi Penicillium and Cladosporium. Overall findings indicate that shorter IWS result in a higher proportion of aromatic organic compounds, which can potentially react with chlorine and increase risk of disinfection-by-products formation. However, by minimising IWS times, biofilm-associated impacts can be reduced, yet these are complex ecosystems and much remains to be understood about how microbial interactions can be managed to best ensure continued water safe supply.

Implications of Climate Change: How Does Increased Water Temperature Influence Biofilm and Water Quality of Chlorinated Drinking Water Distribution Systems?

Temperature variation can promote physico-chemical and microbial changes in the water transported through distribution systems and influence the dynamics of biofilms attached to pipes, thus contributing to the release of pathogens into the bulk drinking water. An experimental real-scale chlorinated DWDS was used to study the effect of increasing temperature from 16 to 24°C on specific pathogens, bacterial-fungal communities (biofilm and water samples) and determine the risk of material accumulation and mobilisation from the pipes into the bulk water. Biofilm was developed for 30 days at both temperatures in the pipe walls, and after this growth phase, a flushing was performed applying 4 gradual steps by increasing the shear stress. The fungal-bacterial community characterised by Illumina MiSeq sequencing, and specific pathogens were studied using qPCR: Mycobacterium spp., Mycobacterium avium complex, Acanthamoeba spp., Pseudomonas aeruginosa, Legionella pneumophilia, and Stenotrophomonas maltophilia. Sequencing data showed that temperature variation significantly modified the structure of biofilm microbial communities from the early stages of biofilm development. Regarding bacteria, Pseudomonas increased its relative abundance in biofilms developed at 24°C, while fungal communities showed loss of diversity and richness, and the increase in dominance of Fusarium genus. After the mobilisation phase, Pseudomonas continued being the most abundant genus at 24°C, followed by Sphingobium and Sphingomonas. For biofilm fungal communities after the mobilisation phase, Helotiales incertae sedis and Fusarium were the most abundant taxa. Results from qPCR showed a higher relative abundance of Mycobacterium spp. on day 30 and M. avium complex throughout the growth phase within the biofilms at higher temperatures. The temperature impacts were not only microbial, with physical mobilisation showing higher discolouration response and metals release due to the increased temperature. While material accumulation was accelerated by temperature, it was not preferentially to either stronger or weaker biofilm layers, as turbidity results during the flushing steps showed. This research yields new understanding on microbial challenges that chlorinated DWDS will undergo as global temperature rises, this information is needed in order to protect drinking water quality and safety while travelling through distribution systems.

Large-scale mutation in the evolution of a gene complex for cryptic coloration.

The types of mutations affecting adaptation in the wild are only beginning to be understood. In particular, whether structural changes shape adaptation by suppressing recombination or by creating new mutations is unresolved. Here, we show that multiple linked but recombining loci underlie cryptic color morphs of Timema chumash stick insects. In a related species, these loci are found in a region of suppressed recombination, forming a supergene. However, in seven species of Timema, we found that a megabase-size "supermutation" has deleted color loci in green morphs. Moreover, we found that balancing selection likely contributes more to maintaining this mutation than does introgression. Our results show how suppressed recombination and large-scale mutation can help to package gene complexes into discrete units of diversity such as morphs, ecotypes, or species.

Adaptive zones shape the magnitude of premating reproductive isolation in Timema stick insects.

Simpson's fossil-record inspired model of 'adaptive zones' proposes that evolution is dominated by small fluctuations within adaptive zones, occasionally punctuated by larger shifts between zones. This model can help explain why the process of population divergence often results in weak or moderate reproductive isolation (RI), rather than strong RI and distinct species. Applied to the speciation process, the adaptive zones hypothesis makes two inter-related predictions: (i) large shifts between zones are relatively rare, (ii) when large shifts do occur they generate stronger RI than shifts within zones. Here, we use ecological, phylogenetic and behavioural data to test these predictions in Timema stick insects. We show that host use in Timema is dominated by moderate shifts within the systematic divisions of flowering plants and conifers, with only a few extreme shifts between these divisions. However, when extreme shifts occur, they generate greater RI than do more moderate shifts. Our results support the adaptive zones model, and suggest that the net contribution of ecological shifts to diversification is dependent on both their magnitude and frequency. We discuss the generality of our findings in the light of emerging evidence from diverse taxa that the evolution of RI is not always the only factor determining the origin of species diversity. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Quality of reporting for randomised clinical trials published in Latin American and Spanish journals: A protocol for a systematic survey of three clinical specialities.

INTRODUCTION: Quality of reporting refers to how published articles communicate how the research was done and what was found. Gaps and imprecisions of reporting hamper the assessment of the methodological quality and internal and external validity. The CONsolidated Standards of Reporting Trials (CONSORT) are a set of evidence-based recommendations of the minimum elements to be included in the reporting of randomised controlled trials (RCTs) to ensure a complete and transparent account of what was done, how it was done and what was found. Few studies have been conducted on the impact of CONSORT on RCTs published in Latin American and Spanish journals. We aim to assess the reporting quality of RCTs of three clinical specialities published in Spanish and Latin American journals, as well as to assess changes over time and associations of quality with journal and country indicators. METHODS AND ANALYSIS: We will conduct a systematic survey of all RCTs published in Spanish-language journals in three clinical fields (dentistry, neurology and geriatrics) from 1990 to 2018. We will include RCTs from previous work that has identified all RCTs on these medical fields published in Spain and Latin America. We will update this work via handsearching of relevant journals. Assessment of quality of reporting will be conducted independently and in duplicate using the CONSORT 2010 Statement. We will also extract journal and country indicators. We will conduct descriptive statistics and secondary analyses considering the year, country, and journal of publication, among others. ETHICS AND DISSEMINATION: The Universidad de Santiago de Chile's ethics committee approved the protocol. We will disseminate the results of this work in peer-reviewed scientific journals and conference proceedings. We expect to raise awareness among researchers, journal editors and funders on the importance of training in reporting guidelines and using them from the inception of RCT protocols.

Author misrepresentation of institutional affiliations: protocol for an exploratory case study.

INTRODUCTION: University ranking systems and the publish-or-perish dictum, among other factors, are driving universities and researchers around the world to increase their research productivity. Authors frequently report multiple affiliations in published articles. It is not known if the reported institutional affiliations are real affiliations, which is when the universities have contributed substantially to the research conducted and to the published manuscript. This study aims to establish whether there is an empirical basis for author affiliation misrepresentation in authors with multiple institutional affiliations. METHODS AND ANALYSIS: This individual secondary data exploratory analysis on Scopus-indexed articles for 2016 will search all authors who report multiple institutional affiliations in which at least one of the affiliations is to a Chilean university. We will consider that misrepresentation of an affiliation is more likely when it is not possible to verify objectively a link between the author and the mentioned institution through institutional websites. If we cannot corroborate the author affiliation, we will consider this a finding of potential misrepresentation of the affiliation. We will summarise results with descriptive statistics. ETHICS AND DISSEMINATION: The study protocol was approved by the institutional ethics committee of Universidad de Santiago de Chile, Resolution No. 261, and dated January 15, 2018. Results will be submitted to the World Conference on Research Integrity, among other meetings on publication ethics and research integrity, and will be published in scientific, peer-reviewed journals.

Policy strategies to reduce waiting times for elective surgery: A scoping review and evidence synthesis.

OBJECTIVES: The purpose of this evidence-based review is to identify and describe the interventions that have been implemented to reduce waiting times for major elective surgery. METHODS: Scoping review and presentation of the results according to the SUPPORT tools. We searched MEDLINE/PubMed, Embase, Cochrane Library, SciELO, DARE-HTA, and Google Scholar. The inclusion criteria for research design were comprehensive. RESULTS: We identified 5200 records. After eliminating duplicates and screening by title and abstract, 171 records remained for full-text assessment, of which 12 were ultimately included for this review because they reported specific interventions and 96 records were included for further reference. The included studies show significant variability regarding elective procedures, population, and type of provider, as well as in the characteristics of the interventions and the settings. All the studies had methodological limitations. We graded the certainty of the evidence as very low. CONCLUSIONS: According to the evidence found for this review, interventions most likely should be multidimensional, with prioritization strategies on the waiting lists to incorporate equity criteria, together with quality management improvements of the surgical pathways and the use of operating rooms, as well as improvements in the planning of the surgical schedule.

Enfrentamiento de adultos mayores con sospecha de covid-19 en el servicio de urgencia

En Diciembre 2019, surge una enfermedad emergente, COVID-19, que es debida a un coronavirus (SARS-CoV-2) que empieza en Wuhan, China y que se ha propagado rápidamente a nivel mundial. La Organización Mundial de la Salud (OMS) lo declara como pandemia el 12 de Marzo del 2020. En Chile, el día 14 de Marzo se decretó fase 3 y el 16 de Marzo se pasó a fase 4. Al 24 de Marzo del 2020, en Chile existen 922 casos confirmados de COVID-19, con una mediana de edad de 34 años, correspondiendo 51 casos (6%) a adultos mayores (AM).

Natural selection and the predictability of evolution in Timema stick insects.

Predicting evolution remains difficult. We studied the evolution of cryptic body coloration and pattern in a stick insect using 25 years of field data, experiments, and genomics. We found that evolution is more difficult to predict when it involves a balance between multiple selective factors and uncertainty in environmental conditions than when it involves feedback loops that cause consistent back-and-forth fluctuations. Specifically, changes in color-morph frequencies are modestly predictable through time (r2 = 0.14) and driven by complex selective regimes and yearly fluctuations in climate. In contrast, temporal changes in pattern-morph frequencies are highly predictable due to negative frequency-dependent selection (r2 = 0.86). For both traits, however, natural selection drives evolution around a dynamic equilibrium, providing some predictability to the process.

Long-term balancing selection on chromosomal variants associated with crypsis in a stick insect.

How polymorphisms are maintained within populations over long periods of time remains debated, because genetic drift and various forms of selection are expected to reduce variation. Here, we study the genetic architecture and maintenance of phenotypic morphs that confer crypsis in Timema cristinae stick insects, combining phenotypic information and genotyping-by-sequencing data from 1,360 samples across 21 populations. We find two highly divergent chromosomal variants that span megabases of sequence and are associated with colour polymorphism. We show that these variants exhibit strongly reduced effective recombination, are geographically widespread and probably diverged millions of generations ago. We detect heterokaryotype excess and signs of balancing selection acting on these variants through the species' history. A third chromosomal variant in the same genomic region likely evolved more recently from one of the two colour variants and is associated with dorsal pattern polymorphism. Our results suggest that large-scale genetic variation associated with crypsis has been maintained for long periods of time by potentially complex processes of balancing selection.

Transitions between phases of genomic differentiation during stick-insect speciation.

Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to genome-wide differentiation are also observed with gene flow, in association with differentiation in polygenic chemical traits affecting mate choice. Thus, intermediate phases of speciation are associated with genome-wide differentiation and mate choice, but not growth of a few genomic islands. We also find a gap in genomic differentiation between sympatric taxa that still exchange genes and those that do not, highlighting the association between differentiation and complete reproductive isolation. Our results suggest that substantial progress towards speciation may involve the alignment of multi-faceted aspects of differentiation.

Genome divergence and diversification within a geographic mosaic of coevolution.

Despite substantial interest in coevolution's role in diversification, examples of coevolution contributing to speciation have been elusive. Here, we build upon past studies that have shown both coevolution between South Hills crossbills and lodgepole pine (Pinus contorta), and high levels of reproductive isolation between South Hills crossbills and other ecotypes in the North American red crossbill (Loxia curvirostra) complex. We used genotyping by sequencing to generate population genomic data and applied phylogenetic and population genetic analyses to characterize the genetic structure within and among nine of the ecotypes. Although genome-wide divergence was slight between ecotypes (FST  = 0.011-0.035), we found evidence of relative genetic differentiation (as measured by FST ) between and genetic cohesiveness within many of them. As expected for nomadic and opportunistic breeders, we detected no evidence of isolation by distance. The one sedentary ecotype, the South Hills crossbill, was genetically most distinct because of elevated divergence at a small number of loci rather than pronounced overall genome-wide divergence. These findings suggest that mechanisms related to recent local coevolution between South Hills crossbills and lodgepole pine (e.g. strong resource-based density dependence limiting gene flow) have been associated with genome divergence in the face of gene flow. Our results further characterize a striking example of coevolution driving speciation within perhaps as little as 6000 years.

Color phenotypes are under similar genetic control in two distantly related species of Timema stick insect.

Ecology and genetics are both of general interest to evolutionary biologists as they can influence the phenotypic and genetic response to selection. The stick insects Timema podura and Timema cristinae exhibit a green/melanistic body color polymorphism that is subject to different ecologically based selective regimes in the two species. Here, we describe aspects of the genetics of this color polymorphism in T. podura, and compare this to previous results in T. cristinae. We first show that similar color phenotypes of the two species cluster in phenotypic space. We then use genome-wide association mapping to show that in both species, color is controlled by few loci, dominance relationships between color alleles are the same, and SNPs associated with color phenotypes colocalize to the same linkage group. Regions within this linkage group that harbor genetic variants associated with color exhibit elevated linkage disequilibrium relative to genome wide expectations, but more strongly so in T. cristinae. We use these results to discuss predictions regarding how the genetics of color could influence levels of phenotypic and genetic variation that segregate within and between populations of T. podura and T. cristinae, drawing parallels with other organisms.

Flavonols Mediate Root Phototropism and Growth through Regulation of Proliferation-to-Differentiation Transition.

Roots normally grow in darkness, but they may be exposed to light. After perceiving light, roots bend to escape from light (root light avoidance) and reduce their growth. How root light avoidance responses are regulated is not well understood. Here, we show that illumination induces the accumulation of flavonols in Arabidopsis thaliana roots. During root illumination, flavonols rapidly accumulate at the side closer to light in the transition zone. This accumulation promotes asymmetrical cell elongation and causes differential growth between the two sides, leading to root bending. Furthermore, roots illuminated for a long period of time accumulate high levels of flavonols. This high flavonol content decreases both auxin signaling and PLETHORA gradient as well as superoxide radical content, resulting in reduction of cell proliferation. In addition, cytokinin and hydrogen peroxide, which promote root differentiation, induce flavonol accumulation in the root transition zone. As an outcome of prolonged light exposure and flavonol accumulation, root growth is reduced and a different root developmental zonation is established. Finally, we observed that these differentiation-related pathways are required for root light avoidance. We propose that flavonols function as positional signals, integrating hormonal and reactive oxygen species pathways to regulate root growth direction and rate in response to light.

Selection on a genetic polymorphism counteracts ecological speciation in a stick insect.

The interplay between selection and aspects of the genetic architecture of traits (such as linkage, dominance, and epistasis) can either drive or constrain speciation [1-3]. Despite accumulating evidence that speciation can progress to "intermediate" stages-with populations evolving only partial reproductive isolation-studies describing selective mechanisms that impose constraints on speciation are more rare than those describing drivers. The stick insect Timema cristinae provides an example of a system in which partial reproductive isolation has evolved between populations adapted to different host plant environments, in part due to divergent selection acting on a pattern polymorphism [4, 5]. Here, we demonstrate how selection on a green/melanistic color polymorphism counteracts speciation in this system. Specifically, divergent selection between hosts does not occur on color phenotypes because melanistic T. cristinae are cryptic on the stems of both host species, are resistant to a fungal pathogen, and have a mating advantage. Using genetic crosses and genome-wide association mapping, we quantify the genetic architecture of both the pattern and color polymorphism, illustrating their simple genetic control. We use these empirical results to develop an individual-based model that shows how the melanistic phenotype acts as a "genetic bridge" that increases gene flow between populations living on different hosts. Our results demonstrate how variation in the nature of selection acting on traits, and aspects of trait genetic architecture, can impose constraints on both local adaptation and speciation.