Inferring explicit weighted consensus networks to represent alternative evolutionary histories

Background: The advent of molecular biology techniques and constant increase in availability of genetic material have triggered the development of many phylogenetic tree inference methods. However, several reticulate evolution processes, such as horizontal gene transfer and hybridization, have been shown to blur the species\ud evolutionary history by causing discordance among phylogenies inferred from different genes.\ud Methods: To tackle this problem, we hereby describe a new method for inferring and representing alternative(reticulate) evolutionary histories of species as an explicit weighted consensus network which can be constructed from a collection of gene trees with or without prior knowledge of the species phylogeny.\ud Results: We provide a way of building a weighted phylogenetic network for each of the following reticulation\ud mechanisms: diploid hybridization, intragenic recombination and complete or partial horizontal gene transfer. We successfully tested our method on some synthetic and real datasets to infer the above-mentioned evolutionary events which may have influenced the evolution of many species.\ud Conclusions: Our weighted consensus network inference method allows one to infer, visualize and validate statistically major conflicting signals induced by the mechanisms of reticulate evolution. The results provided by the new method can be used to represent the inferred conflicting signals by means of explicit and easy-to-interpret phylogenetic networks

UMA ESTRATÉGIA UNIFICADA PARA A ESTIMATIVA DE COMPONENTES ESPACIAIS, TEMPORAIS E FILOGENÉTICOS EM MODELOS ECOLÓGICOS

The goals of this paper are to expose ecologists to the problem related to statistical inference when testing the association between data sets that are autocorrelated and to introduce a relatively new method for controlling the bias introduced by autocorrelation that can be easily incorporated in any statistical approach. In addition, I show the flexibility of this class of methods to the types of data that ecologists are currently most interested, namely temporal, spatial and phylogenetic data. In this contribution, I also stress the point that is not all variation due to autocorrelation that affects statistical inference and is important to control only the component that biases inference. Thus, statistical frameworks should attempt to separate the autocorrelation component that biases inference from the one that may prove interesting for understanding important ecological processes, such as contagious processes, driving spatial patterns in species distributions.O objetivo deste trabalho é de expor aos ecólogos o problema relacionado aos testes de inferência estatística quando os dados são autocorrelacionados e apresentar uma técnica relativamente nova que pode ser facilmente incorporada em análises estatísticas para controlar os erros causados pela autocorrelação. Além disso, eu demonstro a flexibilidade deste método utilizando três tipos de dados que são importantes em análises ecológicas: dados temporais, espaciais e filogenéticos. Neste trabalho, eu reitero que não é toda a variação autocorrelacionada que afeta as inferências estatísticas e que é importante controlar apenas o componente de variação reponsável. Assim, análises estatísticas devem ser realizadas com o objetivo de separar o componente de variação autocorrelacionada -- que causa erros em testes de hipóteses -- do componente que pode ser importante para a compreensão de processos ecológicos, como processos contagiosos (e.g., dispersão), estruturando padrões de distribuição espacial em espécies

The Interaction of Phylogeny and Community Structure: Linking the Community Composition and Trait Evolution of Clades

Aim Community phylogenetic studies use information about the evolutionary relationships of species to understand the ecological processes of community assembly. A central premise of the field is that the evolution of species maps onto ecological patterns, and phylogeny reveals something more than species traits alone about the ecological mechanisms structuring communities, such as environmental filtering, competition, and facilitation. We argue, therefore, that there is a need for better understanding and modelling of the interaction of phylogeny with species traits and community composition. Innovation We outline a new approach that identifies clades that are ecophylogenetically clustered or overdispersed and assesses whether those clades have different rates of trait evolution. Ecophylogenetic theory would predict that the traits of clustered or overdispersed clades might have evolved differently, in terms of either tempo (fast or slow) or mode (e.g., under constraint or neutrally). We suggest that modelling the evolution of independent trait data in these clades represents a strong test of whether there is an association between the ecological co‐occurrence patterns of a species and its evolutionary history. Main conclusions Using an empirical dataset of mammals from around the world, we identify two clades of rodents whose species tend not to co‐occur in the same local assemblages (are phylogenetically overdispersed) and find independent evidence of slower rates of body mass evolution in these clades. Our approach, which assumes nothing about the mode of species trait evolution but instead seeks to explain it using ecological information, presents a new way to examine ecophylogenetic structure

Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees

<p>Abstract</p> <p>Background</p> <p>Non-parametric bootstrapping is a widely-used statistical procedure for assessing confidence of model parameters based on the empirical distribution of the observed data <abbrgrp><abbr bid="B1">1</abbr></abbrgrp> and, as such, it has become a common method for assessing tree confidence in phylogenetics <abbrgrp><abbr bid="B2">2</abbr></abbrgrp>. Traditional non-parametric bootstrapping does not weigh each tree inferred from resampled (i.e., pseudo-replicated) sequences. Hence, the <it>quality </it>of these trees is not taken into account when computing bootstrap scores associated with the clades of the original phylogeny. As a consequence, traditionally, the trees with different bootstrap support or those providing a different fit to the corresponding pseudo-replicated sequences (the fit quality can be expressed through the LS, ML or parsimony score) contribute in the same way to the computation of the bootstrap support of the original phylogeny.</p> <p>Results</p> <p>In this article, we discuss the idea of applying weighted bootstrapping to phylogenetic reconstruction by weighting each phylogeny inferred from resampled sequences. Tree weights can be based either on the least-squares (LS) tree estimate or on the average secondary bootstrap score (SBS) associated with each resampled tree. <it>Secondary bootstrapping </it>consists of the estimation of bootstrap scores of the trees inferred from resampled data. The LS and SBS-based bootstrapping procedures were designed to take into account the quality of each "pseudo-replicated" phylogeny in the final tree estimation. A simulation study was carried out to evaluate the performances of the five weighting strategies which are as follows: LS and SBS-based bootstrapping, LS and SBS-based bootstrapping with data normalization and the traditional unweighted bootstrapping.</p> <p>Conclusions</p> <p>The simulations conducted with two real data sets and the five weighting strategies suggest that the SBS-based bootstrapping with the data normalization usually exhibits larger bootstrap scores and a higher robustness compared to the four other competing strategies, including the traditional bootstrapping. The high robustness of the normalized SBS could be particularly useful in situations where observed sequences have been affected by noise or have undergone massive insertion or deletion events. The results provided by the four other strategies were very similar regardless the noise level, thus also demonstrating the stability of the traditional bootstrapping method.</p

Diversity from genes to ecosystems : a unifying framework to study variation across biological metrics and scales

This work was assisted through participation in “Next Generation Genetic Monitoring” Investigative Workshop at the National Institute for Mathematical and Biological Synthesis, sponsored by the National Science Foundation through NSF Award #DBI-1300426, with additional support from The University of Tennessee, Knoxville. Hawaiian fish community data were provided by the NOAA Pacific Islands Fisheries Science Center's Coral Reef Ecosystem Division (CRED) with funding from NOAA Coral Reef Conservation Program. O.E.G. was supported by the Marine Alliance for Science and Technology for Scotland (MASTS). A. C. and C. H. C. were supported by the Ministry of Science and Technology, Taiwan. P.P.-N. was supported by a Canada Research Chair in Spatial Modelling and Biodiversity. K.A.S. was supported by National Science Foundation (BioOCE Award Number 1260169) and the National Center for Ecological Analysis and Synthesis. All data used in this manuscript are available in DRYAD (https://doi.org/dx.doi.org/10.5061/dryad.qm288) and BCO-DMO (http://www.bco-dmo.org/project/552879).Biological diversity is a key concept in the life sciences and plays a fundamental role in many ecological and evolutionary processes. Although biodiversity is inherently a hierarchical concept covering different levels of organisation (genes, population, species, ecological communities and ecosystems), a diversity index that behaves consistently across these different levels has so far been lacking, hindering the development of truly integrative biodiversity studies. To fill this important knowledge gap we present a unifying framework for the measurement of biodiversity across hierarchical levels of organisation. Our weighted, information-based decomposition framework is based on a Hill number of order q = 1, which weights all elements in proportion to their frequency and leads to diversity measures based on Shannon’s entropy. We investigated the numerical behaviour of our approach with simulations and showed that it can accurately describe complex spatial hierarchical structures. To demonstrate the intuitive and straightforward interpretation of our diversity measures in terms of effective number of components (alleles, species, etc.) we applied the framework to a real dataset on coral reef biodiversity. We expect our framework will have multiple applications covering the fields of conservation biology, community genetics, and eco-evolutionary dynamics.Publisher PDFPeer reviewe

Brazilian cerrado species: wood characteristics

The characterization of wood anatomy and proprieties can provide subsidies for rational use of tree species. Enables, oftentimes, the definition of technological potential of wood - and wood products -   through the assessment of quality information and also allows it´s correct identification, contributing to the timber production chain.  The objective of this study was to contribute to the knowledge about wood properties of the Cerrado biome (Brazilian savanna) species trough the anatomical characterization and determination of density profile. Twenty trees species belonging to thirteen families occurring in Pirenópolis, Goiás and Brasília, Federal District, Brazil, was selected and radial samples were removed from the tree trunks at the DBH (1.30 m) in a non-destructive way using an incremental probe and a motorized extractor. The qualitative and quantitative anatomical parameters of vessels and fibers and the wood density were determined in the collected samples. Species presented fibers with mean values between 900.5 and 2052.9 µm for the length; 18.1 and 27.7 µm for the diameter; and 4.4 to 9.4 µm for the wall thickness. The species presented a variation in the vessel dimensions from 29.2 to 155.6 µm for the diameter; 17.7 to 32.5% for occupied area; and 2.6 to 165 to vessels.mm-2. The apparent density presented mean values between 0.36 and 1.21 g cm-3. The specie that presented the highest variation of wood density was A. fraxinifolium. According to the radial profiles two patterns of increasing and stable variation in the apparent density of the pith to bark were defined as a function of the wood anatomical characteristics

Towards an applied metaecology

The complexity of ecological systems is a major challenge for practitioners and decision-makers who work to avoid, mitigate and manage environmental change. Here, we illustrate how metaecology – the study of spatial interdependencies among ecological systems through fluxes of organisms, energy, and matter – can enhance understanding and improve managing environmental change at multiple spatial scales. We present several case studies illustrating how the framework has leveraged decision-making in conservation, restoration and risk management. Nevertheless, an explicit incorporation of metaecology is still uncommon in the applied ecology literature, and in action guidelines addressing environmental change. This is unfortunate because the many facets of environmental change can be framed as modifying spatial context, connectedness and dominant regulating processes - the defining features of metaecological systems. Narrowing the gap between theory and practice will require incorporating system-specific realism in otherwise predominantly conceptual studies, as well as deliberately studying scenarios of environmental change.We thank FAPESP (grants 2014/10470-7 to AM, 2013/04585-3 to DL, 2013/50424-1 to TS and 2015/18790-3to LS), CNPq (Productivity Fellowships 301656/2011-8 to JAFDF,308205/2014-6 to RP, 306183/2014-5 to PIP and 307689/2014-0 to VDP), the National Science Foundation (DEB 1645137 toJGH), the Natural Sciences and Engineering Council of Canada (SJL,PPN), and the Academy of Finland (grants 257686 and 292765 toMC) for support. This work contributes to the Labex OT-Med (no.ANR-11-LABX-0061), funded by the French government throughthe A*MIDEX project (no. ANR-11-IDEX-0001-02)

Towards an applied metaecology

The complexity of ecological systems is a major challenge for practitioners and decision-makers who work to avoid, mitigate and manage environmental change. Here, we illustrate how metaecology - the study of spatial interdependencies among ecological systems through fluxes of organisms, energy, and matter - can enhance understanding and improve managing environmental change at multiple spatial scales. We present several case studies illustrating how the framework has leveraged decision-making in conservation, restoration and risk management. Nevertheless, an explicit incorporation of metaecology is still uncommon in the applied ecology literature, and in action guidelines addressing environmental change. This is unfortunate because the many facets of environmental change can be framed as modifying spatial context, connectedness and dominant regulating processes - the defining features of metaecological systems. Narrowing the gap between theory and practice will require incorporating system-specific realism in otherwise predominantly conceptual studies, as well as deliberately studying scenarios of environmental change. (C) 2019 Associacao Brasileira de Ciencia Ecologica e Conservacao. Published by Elsevier Editora Ltda.Peer reviewe

Consenso da Sociedade Brasileira de Cefaleia sobre o tratamento da migrânea crônica

Chronic migraine poses a significant personal, social and economic burden and is characterized by headache present on 15 or more days per month for at least three months, with at least eight days of migrainous headache per month. It is frequently associated with analgesic or acute migraine medication overuse and this should not be overlooked. The present consensus was elaborated upon by a group of members of the Brazilian Headache Society in order to describe current evidence and to provide recommendations related to chronic migraine pharmacological and nonpharmacological treatment. Withdrawal strategies in medication overuse headache are also described, as well as treatment risks during pregnancy and breastfeeding. Oral topiramate and onabotulinum toxin A injections are the only treatments granted Class A recommendation, while valproate, gabapentin, and tizanidine received Class B recommendation, along with acupuncture. biofeedback, and mindfulness. The anti-CGRP or anti-CGRPr monoclonal antibodies, still unavailable in Brazil, are promising new drugs already approved elsewhere for migraine prophylactic treatment, the efficacy of which in chronic migraine is still to be definitively proven777509520A migrânea (enxaqueca) crônica determina uma carga pessoal, social e econômica significativa e é caracterizada por dor de cabeça presente em quinze ou mais dias por mês por ao menos três meses, com no mínimo oito dias de cefaleia migranosa a cada mês. É frequentemente associada ao uso excessivo de medicação analgésica ou antimigranosa aguda e isso não deve ser negligenciado. Este consenso foi elaborado por um grupo de membros da Sociedade Brasileira de Cefaleia, para descrever as evidências atualmente disponíveis e fornecer recomendações relacionadas ao tratamento farmacológico e não farmacológico da migrânea crônica. Estratégias de retirada na cefaleia por uso excessivo de medicamentos também são descritas, assim como os riscos dos tratamentos durante a gravidez e a amamentação. O topiramato oral e as injeções de toxina onabotulínica A são os únicos tratamentos que receberam a recomendação classe A, enquanto que o valproato, a gabapentina e a tizanidina receberam recomendação classe B, juntamente com acupuntura, biofeedback e mindfulness. Os anticorpos monoclonais anti-CGRP ou anti-CGRPr, ainda não disponíveis no Brasil, são novos fármacos promissores, já aprovados em outros países para o tratamento profilático da migrânea, cuja eficácia na migrânea crônica ainda está por ser definitivamente comprovad