PROTOTYPE of a CLADISTICS EDUCATION 1 Cladogram
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Lecture Notes: the Mathematics of Phylogenetics
Lecture Notes: The Mathematics of Phylogenetics Elizabeth S. Allman, John A. Rhodes IAS/Park City Mathematics Institute June-July, 2005 University of Alaska Fairbanks Spring 2009, 2012, 2016 c 2005, Elizabeth S. Allman and John A. Rhodes ii Contents 1 Sequences and Molecular Evolution 3 1.1 DNA structure . .4 1.2 Mutations . .5 1.3 Aligned Orthologous Sequences . .7 2 Combinatorics of Trees I 9 2.1 Graphs and Trees . .9 2.2 Counting Binary Trees . 14 2.3 Metric Trees . 15 2.4 Ultrametric Trees and Molecular Clocks . 17 2.5 Rooting Trees with Outgroups . 18 2.6 Newick Notation . 19 2.7 Exercises . 20 3 Parsimony 25 3.1 The Parsimony Criterion . 25 3.2 The Fitch-Hartigan Algorithm . 28 3.3 Informative Characters . 33 3.4 Complexity . 35 3.5 Weighted Parsimony . 36 3.6 Recovering Minimal Extensions . 38 3.7 Further Issues . 39 3.8 Exercises . 40 4 Combinatorics of Trees II 45 4.1 Splits and Clades . 45 4.2 Refinements and Consensus Trees . 49 4.3 Quartets . 52 4.4 Supertrees . 53 4.5 Final Comments . 54 4.6 Exercises . 55 iii iv CONTENTS 5 Distance Methods 57 5.1 Dissimilarity Measures . 57 5.2 An Algorithmic Construction: UPGMA . 60 5.3 Unequal Branch Lengths . 62 5.4 The Four-point Condition . 66 5.5 The Neighbor Joining Algorithm . 70 5.6 Additional Comments . 72 5.7 Exercises . 73 6 Probabilistic Models of DNA Mutation 81 6.1 A first example . 81 6.2 Markov Models on Trees . 87 6.3 Jukes-Cantor and Kimura Models . -
Poaceae: Bambusoideae) Christopher Dean Tyrrell Iowa State University
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2008 Systematics of the neotropical woody bamboo genus Rhipidocladum (Poaceae: Bambusoideae) Christopher Dean Tyrrell Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Botany Commons Recommended Citation Tyrrell, Christopher Dean, "Systematics of the neotropical woody bamboo genus Rhipidocladum (Poaceae: Bambusoideae)" (2008). Retrospective Theses and Dissertations. 15419. https://lib.dr.iastate.edu/rtd/15419 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Systematics of the neotropical woody bamboo genus Rhipidocladum (Poaceae: Bambusoideae) by Christopher Dean Tyrrell A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Ecology and Evolutionary Biology Program of Study Committee: Lynn G. Clark, Major Professor Dennis V. Lavrov Robert S. Wallace Iowa State University Ames, Iowa 2008 Copyright © Christopher Dean Tyrrell, 2008. All rights reserved. 1457571 1457571 2008 ii In memory of Thomas D. Tyrrell Festum Asinorum iii TABLE OF CONTENTS ABSTRACT iv CHAPTER 1. GENERAL INTRODUCTION 1 Background and Significance 1 Research Objectives 5 Thesis Organization 6 Literature Cited 6 CHAPTER 2. PHYLOGENY OF THE BAMBOO SUBTRIBE 9 ARTHROSTYLIDIINAE WITH EMPHASIS ON RHIPIDOCLADUM Abstract 9 Introduction 10 Methods and Materials 13 Results 19 Discussion 25 Taxonomic Treatment 26 Literature Cited 31 CHAPTER 3. -
A Phylogenomic Analysis of Turtles ⇑ Nicholas G
Molecular Phylogenetics and Evolution 83 (2015) 250–257 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev A phylogenomic analysis of turtles ⇑ Nicholas G. Crawford a,b,1, James F. Parham c, ,1, Anna B. Sellas a, Brant C. Faircloth d, Travis C. Glenn e, Theodore J. Papenfuss f, James B. Henderson a, Madison H. Hansen a,g, W. Brian Simison a a Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA b Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA c John D. Cooper Archaeological and Paleontological Center, Department of Geological Sciences, California State University, Fullerton, CA 92834, USA d Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA e Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA f Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA g Mathematical and Computational Biology Department, Harvey Mudd College, 301 Platt Boulevard, Claremont, CA 9171, USA article info abstract Article history: Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and Received 11 July 2014 prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle Revised 16 October 2014 phylogeny. We sequenced 2381 ultraconserved element (UCE) loci representing a total of 1,718,154 bp of Accepted 28 October 2014 aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and Available online 4 November 2014 an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. -
Phylogenetic Comparative Methods: a User's Guide for Paleontologists
Phylogenetic Comparative Methods: A User’s Guide for Paleontologists Laura C. Soul - Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA David F. Wright - Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024, USA and Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA Abstract. Recent advances in statistical approaches called Phylogenetic Comparative Methods (PCMs) have provided paleontologists with a powerful set of analytical tools for investigating evolutionary tempo and mode in fossil lineages. However, attempts to integrate PCMs with fossil data often present workers with practical challenges or unfamiliar literature. In this paper, we present guides to the theory behind, and application of, PCMs with fossil taxa. Based on an empirical dataset of Paleozoic crinoids, we present example analyses to illustrate common applications of PCMs to fossil data, including investigating patterns of correlated trait evolution, and macroevolutionary models of morphological change. We emphasize the importance of accounting for sources of uncertainty, and discuss how to evaluate model fit and adequacy. Finally, we discuss several promising methods for modelling heterogenous evolutionary dynamics with fossil phylogenies. Integrating phylogeny-based approaches with the fossil record provides a rigorous, quantitative perspective to understanding key patterns in the history of life. 1. Introduction A fundamental prediction of biological evolution is that a species will most commonly share many characteristics with lineages from which it has recently diverged, and fewer characteristics with lineages from which it diverged further in the past. This principle, which results from descent with modification, is one of the most basic in biology (Darwin 1859). -
1 Integrative Biology 200 "PRINCIPLES OF
Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley B.D. Mishler March 14, 2018. Classification II: Phylogenetic taxonomy including incorporation of fossils; PhyloCode I. Phylogenetic Taxonomy - the argument for rank-free classification A number of recent calls have been made for the reformation of the Linnaean hierarchy (e.g., De Queiroz & Gauthier, 1992). These authors have emphasized that the existing system is based in a non-evolutionary world-view; the roots of the Linnaean hierarchy are in a specially- created world-view. Perhaps the idea of fixed, comparable ranks made some sense under that view, but under an evolutionary world view they don't make sense. There are several problems with the current nomenclatorial system: 1. The current system, with its single type for a name, cannot be used to precisely name a clade. E.g., you may name a family based on a certain type specimen, and even if you were clear about what node you meant to name in your original publication, the exact phylogenetic application of your name would not be clear subsequently, after new clades are added. 2. There are not nearly enough ranks to name the thousands of levels of monophyletic groups in the tree of life. Therefore people are increasingly using informal rank-free names for higher- level nodes, but without any clear, formal specification of what clade is meant. 3. Most aspects of the current code, including priority, revolve around the ranks, which leads to instability of usage. For example, when a change in relationships is discovered, several names often need to be changed to adjust, including those of groups whose circumscription has not changed. -
Evolutionary History of Floral Key Innovations in Angiosperms Elisabeth Reyes
Evolutionary history of floral key innovations in angiosperms Elisabeth Reyes To cite this version: Elisabeth Reyes. Evolutionary history of floral key innovations in angiosperms. Botanics. Université Paris Saclay (COmUE), 2016. English. NNT : 2016SACLS489. tel-01443353 HAL Id: tel-01443353 https://tel.archives-ouvertes.fr/tel-01443353 Submitted on 23 Jan 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. NNT : 2016SACLS489 THESE DE DOCTORAT DE L’UNIVERSITE PARIS-SACLAY, préparée à l’Université Paris-Sud ÉCOLE DOCTORALE N° 567 Sciences du Végétal : du Gène à l’Ecosystème Spécialité de Doctorat : Biologie Par Mme Elisabeth Reyes Evolutionary history of floral key innovations in angiosperms Thèse présentée et soutenue à Orsay, le 13 décembre 2016 : Composition du Jury : M. Ronse de Craene, Louis Directeur de recherche aux Jardins Rapporteur Botaniques Royaux d’Édimbourg M. Forest, Félix Directeur de recherche aux Jardins Rapporteur Botaniques Royaux de Kew Mme. Damerval, Catherine Directrice de recherche au Moulon Président du jury M. Lowry, Porter Curateur en chef aux Jardins Examinateur Botaniques du Missouri M. Haevermans, Thomas Maître de conférences au MNHN Examinateur Mme. Nadot, Sophie Professeur à l’Université Paris-Sud Directeur de thèse M. -
Phylocode: a Phylogenetic Code of Biological Nomenclature
PhyloCode: A Phylogenetic Code of Biological Nomenclature Philip D. Cantino and Kevin de Queiroz (equal contributors; names listed alphabetically) Advisory Group: William S. Alverson, David A. Baum, Harold N. Bryant, David C. Cannatella, Peter R. Crane, Michael J. Donoghue, Torsten Eriksson*, Jacques Gauthier, Kenneth Halanych, David S. Hibbett, David M. Hillis, Kathleen A. Kron, Michael S. Y. Lee, Alessandro Minelli, Richard G. Olmstead, Fredrik Pleijel*, J. Mark Porter, Heidi E. Robeck, Greg W. Rouse, Timothy Rowe*, Christoffer Schander, Per Sundberg, Mikael Thollesson, and Andre R. Wyss. *Chaired a committee that authored a portion of the current draft. Most recent revision: April 8, 2000 1 Table of Contents Preface Preamble Division I. Principles Division II. Rules Chapter I. Taxa Article 1. The Nature of Taxa Article 2. Clades Article 3. Hierarchy and Rank Chapter II. Publication Article 4. Publication Requirements Article 5. Publication Date Chapter III. Names Section 1. Status Article 6 Section 2. Establishment Article 7. General Requirements Article 8. Registration Chapter IV. Clade Names Article 9. General Requirements for Establishment of Clade Names Article 10. Selection of Clade Names for Establishment Article 11. Specifiers and Qualifying Clauses Chapter V. Selection of Accepted Names Article 12. Precedence Article 13. Homonymy Article 14. Synonymy Article 15. Conservation Chapter VI. Provisions for Hybrids Article 16. Chapter VII. Orthography Article 17. Orthographic Requirements for Establishment Article 18. Subsequent Use and Correction of Established Names Chapter VIII. Authorship of Names Article 19. Chapter IX. Citation of Authors and Registration Numbers Article 20. Chapter X. Governance Article 21. Glossary Table 1. Equivalence of Nomenclatural Terms Appendix A. -
Zootaxa,Molecular Systematics of Serrasalmidae
Zootaxa 1484: 1–38 (2007) ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ ZOOTAXA Copyright © 2007 · Magnolia Press ISSN 1175-5334 (online edition) Molecular systematics of Serrasalmidae: Deciphering the identities of piranha species and unraveling their evolutionary histories BARBIE FREEMAN1, LEO G. NICO2, MATTHEW OSENTOSKI1, HOWARD L. JELKS2 & TIMOTHY M. COLLINS1,3 1Dept. of Biological Sciences, Florida International University, University Park, Miami, FL 33199, USA. 2United States Geological Survey, 7920 NW 71st St., Gainesville, FL 32653, USA. E-mail: [email protected] 3Corresponding author. E-mail: [email protected] Table of contents Abstract ...............................................................................................................................................................................1 Introduction ......................................................................................................................................................................... 2 Overview of piranha diversity and systematics .................................................................................................................. 3 Material and methods........................................................................................................................................................ 10 Results............................................................................................................................................................................... 16 Discussion -
Reconsidering Relationships Among Stem and Crown Group Pinaceae: Oldest Record of the Genus Pinus from the Early Cretaceous of Yorkshire, United Kingdom
Int. J. Plant Sci. 173(8):917–932. 2012. Ó 2012 by The University of Chicago. All rights reserved. 1058-5893/2012/17308-0006$15.00 DOI: 10.1086/667228 RECONSIDERING RELATIONSHIPS AMONG STEM AND CROWN GROUP PINACEAE: OLDEST RECORD OF THE GENUS PINUS FROM THE EARLY CRETACEOUS OF YORKSHIRE, UNITED KINGDOM Patricia E. Ryberg,* Gar W. Rothwell,1,y,z Ruth A. Stockey,y,§ Jason Hilton,k Gene Mapes,z and James B. Riding# *Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, U.S.A.; yDepartment of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331, U.S.A.; zDepartment of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701, U.S.A.; §Department of Biological Sciences, University of Alberta, Edmonton AB T6G 2E9, Canada; kSchool of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom; and #British Geological Survey, Kingsley Dunham Centre, Keyworth, Nottingham NG12 5GG, United Kingdom This study describes a specimen that extends the oldest fossil evidence of Pinus L. to the Early Cretaceous Wealden Formation of Yorkshire, UK (131–129 million years ago), and prompts a critical reevaluation of criteria that are employed to identify crown group genera of Pinaceae from anatomically preserved seed cones. The specimen, described as Pinus yorkshirensis sp. nov., is conical, 5 cm long, and 3.1 cm in maximum diameter. Bract/scale complexes are helically arranged and spreading. Vasculature of the axis forms a complete cylinder with few resin canals in the wood, and the inner cortex is dominated by large resin canals. -
Genomic Data Do Not Support Comb Jellies As the Sister Group to All Other Animals
Genomic data do not support comb jellies as the sister group to all other animals Davide Pisania,b,1, Walker Pettc, Martin Dohrmannd, Roberto Feudae, Omar Rota-Stabellif, Hervé Philippeg,h, Nicolas Lartillotc, and Gert Wörheided,i,1 aSchool of Earth Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom; bSchool of Biological Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom; cLaboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, 69622 Villeurbanne cedex, France; dDepartment of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany; eDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125; fDepartment of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’ Adige 38010, Italy; gCentre for Biodiversity Theory and Modelling, USR CNRS 2936, Station d’Ecologie Expérimentale du CNRS, Moulis 09200, France; hDépartement de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montreal, QC, Canada H3C 3J7; and iBayerische Staatssammlung für Paläontologie und Geologie, Munich 80333, Germany Edited by Neil H. Shubin, The University of Chicago, Chicago, IL, and approved November 2, 2015 (received for review September 11, 2015) Understanding how complex traits, such as epithelia, nervous animal phylogeny separated ctenophores from all other ani- systems, muscles, or guts, originated depends on a well-supported mals (the “Ctenophora-sister” -
The Impact of Tree Topology on Neutrality Tests
| INVESTIGATION Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests Luca Ferretti,*,1 Alice Ledda,† Thomas Wiehe,‡ Guillaume Achaz,§,** and Sebastian E. Ramos-Onsins†† *The Pirbright Institute, Woking, GU24 0NF, United Kingdom, †Department of Infectious Disease Epidemiology, Imperial College, London, W2 1PG, United Kingdom, ‡Institute of Genetics, University of Cologne, D-50674, Germany, §Institut de Systématique, Evolution, Biodiversité, Unité Mixte de Recherche 7205, and **Centre Interdisciplinaire de Recherche en Biologie, Unité Mixte de Recherche 7241, Paris College de France, and ††Centre for Research in Agricultural Genomics (CRAG), Bellaterra, 08290 Barcelona, Spain ABSTRACT We investigate the dependence of the site frequency spectrum on the topological structure of genealogical trees. We show that basic population genetic statistics, for instance, estimators of u or neutrality tests such as Tajima’s D, can be decomposed into components of waiting times between coalescent events and of tree topology. Our results clarify the relative impact of the two components on these statistics. We provide a rigorous interpretation of positive or negative values of an important class of neutrality tests in terms of the underlying tree shape. In particular, we show that values of Tajima’s D and Fay and Wu’s H depend in a direct way on a peculiar measure of tree balance, which is mostly determined by the root balance of the tree. We present a new test for selection in the same class as Fay and Wu’s H and discuss its interpretation and power. Finally, we determine the trees corresponding to extreme expected values of these neutrality tests and present formulas for these extreme values as a function of sample size and number of segregating sites. -
Testing Hypotheses About the Sister Group of the Passeriformes Using an Independent 30-Locus Data Set Ning Wang,1,2 Edward L
Testing Hypotheses about the Sister Group of the Passeriformes Using an Independent 30-Locus Data Set Ning Wang,1,2 Edward L. Braun,1 and Rebecca T. Kimball*,1 1Department of Biology, University of Florida 2MOE Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China *Corresponding author: E-mail: rkimball@ufl.edu. Associate editor: Herve´ Philippe Abstract Although many phylogenetic studies have focused on developing hypotheses about relationships, advances in data collection Research article and computation have increased the feasibility of collecting large independent data sets to rigorously test controversial hypotheses or carefully assess artifacts that may be misleading. One such relationship in need of independent evaluation is the position of Passeriformes (perching birds) in avian phylogeny. This order comprises more than half of all extant birds, and it includes one of the most important avian model systems (the zebra finch). Recent large-scale studies using morphology, Downloaded from mitochondrial, and nuclear sequence data have generated very different hypotheses about the sister group of Passeriformes, and all conflict with an older hypothesis generated using DNA–DNA hybridization. We used novel data from 30 nuclear loci, primarily introns, for 28 taxa to evaluate five major a priori hypotheses regarding the phylogenetic position of Passeriformes. Although previous studies have suggested that nuclear introns are ideal for the resolution of ancient avian relationships, introns have also been criticized because of the potential for alignment ambiguities and the loss of signal due to saturation. To http://mbe.oxfordjournals.org/ examine these issues, we generated multiple alignments using several alignment programs, varying alignment parameters, and using guide trees that reflected the different a priori hypotheses.