Reconstructing (super)trees from data sets with missing distances: Not all is lost

The wealth of phylogenetic information accumulated over many decades of biological research, coupled with recent technological advances in molecular sequence generation, present significant opportunities for researchers to investigate relationships across and within the kingdoms of life. However, to make best use of this data wealth, several problems must first be overcome. One key problem is finding effective strategies to deal with missing data. Here, we introduce Lasso, a novel heuristic approach for reconstructing rooted phylogenetic trees from distance matrices with missing values, for datasets where a molecular clock may be assumed. Contrary to other phylogenetic methods on partial datasets, Lasso possesses desirable properties such as its reconstructed trees being both unique and edge-weighted. These properties are achieved by Lasso restricting its leaf set to a large subset of all possible taxa, which in many practical situations is the entire taxa set. Furthermore, the Lasso approach is distance-based, rendering it very fast to run and suitable for datasets of all sizes, including large datasets such as those generated by modern Next Generation Sequencing technologies. To better understand the performance of Lasso, we assessed it by means of artificial and real biological datasets, showing its effectiveness in the presence of missing data. Furthermore, by formulating the supermatrix problem as a particular case of the missing data problem, we assessed Lasso's ability to reconstruct supertrees. We demonstrate that, although not specifically designed for such a purpose, Lasso performs better than or comparably with five leading supertree algorithms on a challenging biological data set. Finally, we make freely available a software implementation of Lasso so that researchers may, for the first time, perform both rooted tree and supertree reconstruction with branch lengths on their own partial datasets

THREaD Mapper Studio: a novel, visual web server for the estimation of genetic linkage maps

The estimation of genetic linkage maps is a key component in plant and animal research, providing both an indication of the genetic structure of an organism and a mechanism for identifying candidate genes associated with traits of interest. Because of this importance, several computational solutions to genetic map estimation exist, mostly implemented as stand-alone software packages. However, the estimation process is often largely hidden from the user. Consequently, problems such as a program crashing may occur that leave a user baffled. THREaD Mapper Studio (http://cbr.jic.ac.uk/threadmapper) is a new web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers. The rationale behind the web site is to make the estimation process as transparent and robust as possible, while also allowing users to use their expert knowledge during analysis. Indeed, the 3D visual nature of the tool allows users to spot features in a data set, such as outlying markers and potential structural rearrangements that could cause problems with the estimation procedure and to account for them in their analysis. Furthermore, THREaD Mapper Studio facilitates the visual comparison of genetic map solutions from third party software, aiding users in developing robust solutions for their data sets

Comparing groups versus individuals in decision making: A systematic review protocol

Background Biodiversity management requires effective decision making at various stages. However decision making in the real world is complex, driven by multiple factors and involves a range of stakeholders. Understanding the factors that influence decision making is crucial to addressing the conflicts that arise in conservation. Decisions can be made either by individuals or by groups. This precise context has been studied extensively for several decades by behavioural economists, social psychologists and intelligence analysts. The observations from these disciplines can offer useful insights for biodiversity conservation. A systematic review on group versus individual decision making is currently lacking. This systematic review would enable us to synthesize the key insights from these disciplines for a range of scenarios useful for conservation. Methods The review will document studies that have investigated differences between group and individual decision making. The focus will be on empirical studies; the comparators in this case are decisions made by individuals while the intervention is group decision making. Outcomes include level of bias in decision outcomes or group performance. The search terms will include various combinations of the words “group”, “individual” and “decision-making”. The searches will be conducted in major publication databases, google scholar and specialist databases. Articles will be screened at the title and abstract and full text level by two reviewers. After checking for internal validity, the articles will be synthesized into subsets of decision contexts in which decision making by groups and individuals have been compared. The review process, all extracted data, original studies identified in the systematic review process and inclusion and exclusion decisions will be freely available as Additional file 1 in the final review.NM is funded by the Fondation Weiner Anspach in Belgium. WJS is funded by Arcadia. LVD was supported under the Biodiversity and Ecosystem Service Sustainability (BESS) Programme, grant code NE/K015419/1. GES is funded by The Nature Conservancy.This is the final version of the article. It first appeared from BioMed Central via http://dx.doi.org/10.1186/s13750-016-0066-

Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species

The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the internal transcribed spacer region, frequently used in plant phylogenetics, is now recognized as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analyzed data sets from the Saccharomyces Genome Resequencing Project, characterizing rDNA sequence variation within multiple strains of the baker's yeast Saccharomyces cerevisiae and its nearest wild relative Saccharomyces paradoxus in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterization of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intraspecies phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridization events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of closely related organisms, and discuss how it could be extended to future studies of multilocus rDNA systems. [concerted evolution; genome hydridisation; phylogenetic analysis; ribosomal DNA; whole genome sequencing; yeast]

Concerns raised by people treated for head and neck cancer : a secondary analysis of audiotaped consultations in a health services follow-up clinic

Purpose People treated for head and neck cancer (HNC) face various barriers in communicating concerns with consultants. Our aim was to investigate the number of concerns raised between patients using the Patient Concerns Inventory (PCI) and those who did not. The PCI is a 57-item prompt list used in routine HNC follow-up clinics. Additionally, we aimed to examine whether who initiated the concerns differed between groups and the factors that may predict this initiation. Methods   Secondary data analysis included 67 participants across 15 HNC consultants from specialist cancer centres in Liverpool and Leeds. Seven consultants utilised the PCI and eight did not, assigned by preferential and random assignment. Results   Patients in the PCI group raised on average 2.5 more concerns than patients in the non-PCI group (p < .001). There was no significant relationship between group and who initiated the first concern (p = .28). A mixed-effects logistic regression was found to significantly predict who initiated the first concern in consultations (p < .05). Discussion   The number of concerns raised by patients increased when the PCI was introduced pre-HNC consultation. A number of factors were shown to predict the number of concerns raised in consultations by both patient and consultant. As concerns may not be raised further following the concern mentioned, we propose that the discussion of concerns needs to be maintained by the clinician throughout the consultation and not solely at the start. Conclusion   The PCI promoted the sharing of concerns in follow-up consultations between patient and consultant.Publisher PDFPeer reviewe

Release of cell wall phenolic esters during hydrothermal pretreatment of rice husk and rice straw

Background: Rice husk and rice straw represent promising sources of biomass for production of renewable fuels and chemicals. For efficient utilisation, lignocellulosic components must first be pretreated to enable efficient enzymatic saccharification and subsequent fermentation. Existing pretreatments create breakdown products such as sugar-derived furans, and lignin-derived phenolics that inhibit enzymes and fermenting organisms. Alkali pretreatments have also been shown to release significant levels of simple, free phenolics such as ferulic acid that are normally esterified to cell wall polysaccharides in the intact plant. These phenolics have recently been found to have considerable inhibitory properties. The aim of this research has been to establish the extent to which such free phenolic acids are also released during hydrothermal pretreatment of rice straw (RS) and rice husk (RH). Results: RS and RH were subjected to hydrothermal pretreatments over a wide range of severities (1.57–5.45). FTIR analysis showed that the pretreatments hydrolysed and solubilised hemicellulosic moieties, leading to an enrichment of lignin and crystalline cellulose in the insoluble residue. The residues also lost the capacity for UV autofluorescence at pH 7 or pH 10, indicating the breakdown or release of cell wall phenolics. Saponification of raw RS and RH enabled identification and quantification of substantial levels of simple phenolics including ferulic acid (tFA), coumaric acid (pCA) and several diferulic acids (DiFAs) including 8-O-4′-DiFA, 8,5′-DiFA and 5,5′-DiFA. RH had higher levels of pCA and lower levels of tFA and DiFAs compared with RS. Assessment of the pretreatment liquors revealed that pretreatment-liberated phenolics present were not free but remained as phenolic esters (at mM concentrations) that could be readily freed by saponification. Many were lost, presumably through degradation, at the higher severities. Conclusion: Differences in lignin, tFA, DiFAs and pCA between RS and RH reflect differences in cell wall physiology, and probably contribute to the higher recalcitrance of RH compared with RS. Hydrothermal pretreatments, unlike alkali pretreatments, release cinnamic acid components as esters. The potential for pretreatment-liberated phenolic esters to be inhibitory to fermenting microorganisms is not known. However, the present study shows that they are found at concentrations that could be significantly inhibitory if released as free forms by enzyme activity

Ecosystem service valuations of mangrove ecosystems to inform decision making and future valuation exercises

Data Availability: The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files.Correction: 13 Oct 2014: The PLOS ONE Staff (2014) Correction: Ecosystem Service Valuations of Mangrove Ecosystems to Inform Decision Making and Future Valuation Exercises. PLOS ONE 9(10): e111386. https://doi.org/10.1371/journal.pone.0111386.Copyright © 2014 Mukherjee et al. The valuation of ecosystem services is a complex process as it includes several dimensions (ecological, socio-cultural and economic) and not all of these can be quantified in monetary units. The aim of this paper is to conduct an ecosystem services valuation study for mangroves ecosystems, the results of which can be used to inform governance and management of mangroves. We used an expert-based participatory approach (the Delphi technique) to identify, categorize and rank the various ecosystem services provided by mangrove ecosystems at a global scale. Subsequently we looked for evidence in the existing ecosystem services literature for monetary valuations of these ecosystem service categories throughout the biogeographic distribution of mangroves. We then compared the relative ranking of ecosystem service categories between the monetary valuations and the expert based analysis. The experts identified 16 ecosystem service categories, six of which are not adequately represented in the literature. There was no significant correlation between the expert based valuation (the Delphi technique) and the economic valuation, indicating that the scope of valuation of ecosystem services needs to be broadened. Acknowledging this diversity in different valuation approaches, and developing methodological frameworks that foster the pluralism of values in ecosystem services research, are crucial for maintaining the credibility of ecosystem services valuation. To conclude, we use the findings of our dual approach to valuation to make recommendations on how to assess and manage the ecosystem services provided by mangrove ecosystems.'Mandatd’ Impulsion Scientifique’ (MISID1765914) of the National Science Foundation (FNRS), Belgium and ‘‘CREC’’ (EUIRSES # 247514); British Ecological Society (Parkyn bursary); Arcadia; Natural Environment Research Council (Grant codes NE/K015419/1, NE/J500665/1)

Impacts of selected Ecological Focus Area options in European farmed landscapes on climate regulation and pollination services: a systematic map protocol

Background: This systematic map protocol responds to an urgent policy need to evaluate key environmental benefits of new compulsory greening measures in the European Union’s Common Agricultural Policy (CAP), with the aim of building a policy better linked to environmental performance. The systematic map will focus on Ecological Focus Areas (EFAs), in which larger arable farmers must dedicate 5% of their arable land to ecologically beneficial habitats, landscape features and land uses. The European Commission’s Joint Research Centre has used a software tool called the ‘EFA calculator’ to inform the European Commission about environmental benefits of EFA implementation. However, there are gaps in the EFA calculator’s coverage of ecosystem services, especially ‘global climate regulation’, and an opportunity to use systematic mapping methods to enhance its capture of evidence, in advance of forthcoming CAP reforms. We describe a method for assembling a database of relevant, peer-reviewed research conducted in all agricultural landscapes in Europe and neighbouring countries with similar biogeography, addressing the primary question: what are the impacts of selected EFA features in agricultural land on two policy-relevant ecosystem service outcomes—global climate regulation and pollination? The method is streamlined to allow results in good time for the current, time-limited opportunity to influence reforms of the CAP greening measures at European and Member State level. Methods: We will search four bibliographic databases in English, using a predefined and tested search string that focuses on a subset of EFA options and ecosystem service outcomes. The options and outcomes are selected as those with particular policy relevance and traction. Only articles in English will be included. We will screen search results at title, abstract and full text levels, recording the number of studies deemed non-relevant (with reasons at full text). A systematic map database that displays the meta-data (i.e. descriptive summary information about settings and methods) of relevant studies will be produced following full text assessment. The systematic map database will be published as a MS-Excel database. The nature and extent of the evidence base will be discussed, and the applicability of methods to convert the available evidence into EFA calculator scores will be assessed

Capturing and testing perceptual-cognitive expertise: A comparison of stationary and movement response methods

Numerous methods have been used to study expertise and performance. In the present article, we compare the cognitive thought processes of skilled soccer players when responding to film-based simulations of defensive situations involving two different experimental conditions. Participants either remained stationary in a seated position (n = 10) or were allowed to move (n = 10) in response to life-size film sequences of 11 versus 11 open-play soccer situations viewed from a player’s perspective. Response accuracy and retrospective verbal reports of thinking were collected across the two task conditions. In the movement-based response group, participants generated a greater number of verbal report statements, including a higher proportion of evaluation, prediction, and action planning statements, than did participants in the stationary group. Findings suggest that the processing strategies employed during performance differ depending on the nature of the response required of participants. Implications for behavioral methods and experimental design are discussed

Improving students’ ability at writing narrative text by using outline technique at the first grade of Mal Uin Su Medan in academic year 2016/2017

This research was aimed to know the students’ ability at writing narrative text by using outline technique. The research was conducted by using classroom action research. The subjects of this study were 36 of the tenth grade students of MAL UIN SU Medan in academic year 2016/2017. In doing this research, the technique of analyzing data was applied by using qualitative and quantitative approach. The qualitative data was taken from interview, observation, diary notes and documentation. The quantitative data was taken from the test. The result of the data analyzing showed that there was an improving on the students writing narrative text by using outline technique from each cycle. It was showed from mean of pre test was 51.41 and the mean of the students’ score for the post test I was 71.86, and the mean of the students’ score for post test II was 75.33. And based on interview, observation sheet, diary notes result and documentation showed that the students’ response at writing narrative text by using outline technique was good. It was found that teaching writing narrative text by using outline technique could improve the students’ ability