Blog
About

9
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: not found
      • Article: not found

      Ecological constraints from incumbent clades drive trait evolution across the tree-of-life of freshwater macroinvertebrates

      Read this article at

      ScienceOpenPublisher
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Related collections

          Most cited references 53

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          BEAST: Bayesian evolutionary analysis by sampling trees

          Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. Results BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at under the GNU LGPL license. Conclusion BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            APE: Analyses of Phylogenetics and Evolution in R language.

            Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              jModelTest: phylogenetic model averaging.

              jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.). It implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion," the "Bayesian information criterion," and a "decision-theoretic performance-based" approach. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es.
                Bookmark

                Author and article information

                Affiliations
                [1 ]Grup de Recerca Freshwater Ecology and Management (FEM), Dept Biologia Evolutiva, Ecologia i Ciències Ambientals Facultat de Biologia, Univ. de Barcelona, Barcelona, Catalonia, Spain and Inst. de Recerca de la Biodiversitat (IRBio), Univ. de Barcelona, Barcelona; Catalonia Spain
                [2 ]Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Univ. Lyon 1; Villeurbanne Cedex France
                [3 ]Dept of Integrative Ecology; Estación Biológica de Doñana (CSIC); Seville Spain
                [4 ]Dept of Life Sciences; Natural History Museum; London UK
                [5 ]Dept of Life Sciences; Imperial College London, Silwood Park Campus; Ascot UK
                Journal
                Ecography
                Ecography
                Wiley
                09067590
                July 2018
                July 2018
                December 04 2017
                : 41
                : 7
                : 1049-1063
                10.1111/ecog.02886
                © 2017

                http://doi.wiley.com/10.1002/tdm_license_1.1

                http://onlinelibrary.wiley.com/termsAndConditions#vor

                Comments

                Comment on this article