Systematics Systematics: A Course of Lectures Ward C. Wheeler A John Wiley & Sons, Ltd., Publication This edition first published 2012 c 2012 by Ward C. Wheeler Wiley-Blackwell is an imprint of John Wiley & Sons, formed by the merger of Wiley’s global Scientific, Technical and Medical business with Blackwell Publishing. Registered office: John Wiley & Sons, Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK Editorial offices: 9600 Garsington Road, Oxford, OX4 2DQ, UK The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK 111 River Street, Hoboken, NJ 07030-5774, USA For details of our global editorial offices, for customer services and for information about how to apply for permission to reuse the copyright material in this book please see our website at www.wiley.com/wiley-blackwell. The right of the author to be identified as the author of this work has been asserted in accordance with the UK Copyright, Designs and Patents Act 1988. All rights reserved. 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Set in Computer Modern 10/12pt by Laserwords Private Limited, Chennai, India 1 2012 For Kurt Milton Pickett (1972–2011) Ave atque vale Contents Preface xv Usingthesenotes............................. xv Acknowledgments............................. xvi List of algorithms xix I Fundamentals 1 1History 2 1.1Aristotle................................ 2 1.2Theophrastus............................. 3 1.3PierreBelon.............................. 4 1.4CarolusLinnaeus........................... 4 1.5GeorgesLouisLeclerc,ComtedeBuffon.............. 6 1.6Jean-BaptisteLamarck........................ 7 1.7GeorgesCuvier............................ 8 1.8 EtienneGeoffroySaint-Hilaire....................´ 8 1.9JohannWolfgangvonGoethe.................... 8 1.10LorenzOken............................. 9 1.11RichardOwen............................. 9 1.12CharlesDarwin............................ 9 1.13 Stammb¨aume............................. 12 1.14EvolutionaryTaxonomy....................... 14 1.15Phenetics............................... 15 1.16PhylogeneticSystematics...................... 16 1.16.1Hennig’sThreeQuestions.................. 16 1.17MoleculesandMorphology..................... 18 1.18WeareallCladists.......................... 18 1.19Exercises............................... 19 2 Fundamental Concepts 20 2.1Characters............................... 20 2.1.1 Classes of Characters and Total Evidence ......... 22 2.1.2 Ontogeny, Tokogeny, and Phylogeny ............ 23 2.1.3 CharactersandCharacterStates.............. 23 2.2Taxa.................................. 26 viii CONTENTS 2.3Graphs,Trees,andNetworks.................... 28 2.3.1 GraphsandTrees....................... 30 2.3.2 Enumeration......................... 31 2.3.3 Networks........................... 33 2.3.4 Mono-,Para-,andPolyphyly................ 33 2.3.5 SplitsandConvexity..................... 38 2.3.6 Apomorphy,Plesiomorphy,andHomoplasy........ 39 2.3.7 GeneTreesandSpeciesTrees................ 41 2.4PolarityandRooting......................... 43 2.4.1 Stratigraphy......................... 43 2.4.2 Ontogeny ........................... 43 2.4.3 Outgroups........................... 45 2.5Optimality.............................. 49 2.6Homology............................... 49 2.7Exercises............................... 50 3 Species Concepts, Definitions, and Issues 53 3.1TypologicalorTaxonomicSpeciesConcept............ 54 3.2BiologicalSpeciesConcept...................... 54 3.2.1 CriticismsoftheBSC.................... 55 3.3PhylogeneticSpeciesConcept(s).................. 56 3.3.1 Autapomorphic/MonophyleticSpeciesConcept...... 56 3.3.2 Diagnostic/PhylogeneticSpeciesConcept......... 58 3.4LineageSpeciesConcepts...................... 59 3.4.1 HennigianSpecies...................... 59 3.4.2 EvolutionarySpecies..................... 60 3.4.3 Criticisms of Lineage-Based Species ............ 61 3.5SpeciesasIndividualsorClasses.................. 62 3.6MonoismandPluralism....................... 63 3.7PatternandProcess......................... 63 3.8SpeciesNominalism......................... 64 3.9DoSpeciesConceptsMatter?.................... 65 3.10Exercises............................... 65 4 Hypothesis Testing and the Philosophy of Science 67 4.1FormsofScientificReasoning.................... 67 4.1.1 TheAncients......................... 67 4.1.2 Ockham’s Razor ....................... 68 4.1.3 ModesofScientificInference................ 69 4.1.4 Induction ........................... 69 4.1.5 Deduction........................... 69 4.1.6 Abduction........................... 70 4.1.7 Hypothetico-Deduction................... 71 4.2OtherPhilosophicalIssues...................... 75 4.2.1 Minimization,Transformation,andWeighting....... 75 4.3QuotidianImportance........................ 76 4.4Exercises............................... 76 CONTENTS ix 5 Computational Concepts 77 5.1Problems,Algorithms,andComplexity............... 77 5.1.1 ComputerScienceBasics.................. 77 5.1.2 Algorithms.......................... 79 5.1.3 AsymptoticNotation..................... 79 5.1.4 Complexity.......................... 80 5.1.5 Non-DeterministicComplexity............... 82 5.1.6 Complexity Classes: P and NP ............... 82 5.2AnExample:TheTravelingSalesmanProblem.......... 84 5.3HeuristicSolutions.......................... 85 5.4Metricity,andUntrametricity.................... 86 5.5NP–CompleteProblemsinSystematics............... 87 5.6Exercises............................... 88 6 Statistical and Mathematical Basics 89 6.1TheoryofStatistics.......................... 89 6.1.1 Probability .......................... 89 6.1.2 Conditional Probability ................... 91 6.1.3 Distributions......................... 92 6.1.4 StatisticalInference..................... 98 6.1.5 PriorandPosteriorDistributions.............. 99 6.1.6 BayesEstimators.......................100 6.1.7 MaximumLikelihoodEstimators..............101 6.1.8 PropertiesofEstimators...................101 6.2 Matrix Algebra, Differential Equations, and Markov Models . 102 6.2.1 Basics.............................102 6.2.2 GaussianElimination....................102 6.2.3 DifferentialEquations....................104 6.2.4 DeterminingEigenvalues...................105 6.2.5 MarkovMatrices.......................106 6.3Exercises...............................107 II Homology 109 7 Homology 110 7.1Pre-EvolutionaryConcepts.....................110 7.1.1 Aristotle............................110 7.1.2 PierreBelon.........................110 7.1.3 EtienneGeoffroySaint-Hilaire................111´ 7.1.4 RichardOwen........................112 7.2CharlesDarwin............................113 7.3E.RayLankester...........................114 7.4AdolfRemane.............................114 7.5FourTypesofHomology.......................115 7.5.1 ClassicalView........................115 7.5.2 EvolutionaryTaxonomy...................115 x CONTENTS 7.5.3 PheneticHomology......................116 7.5.4 CladisticHomology.....................116 7.5.5 TypesofHomology......................117 7.6DynamicandStaticHomology...................118 7.7Exercises...............................120 8 Sequence Alignment 121 8.1Background..............................121 8.2“Informal”Alignment........................121 8.3Sequences...............................121 8.3.1 Alphabets...........................122 8.3.2 Transformations.......................123 8.3.3 Distances...........................123 8.4PairwiseStringMatching......................123 8.4.1 AnExample.........................127 8.4.2 ReducingComplexity....................129 8.4.3 OtherIndelWeights.....................130 8.5MultipleSequenceAlignment....................131 8.5.1 TheTreeAlignmentProblem................133 8.5.2 TreesandAlignment.....................133 8.5.3 ExactSolutions........................134 8.5.4 PolynomialTimeApproximateSchemes..........134 8.5.5 HeuristicMultipleSequenceAlignment..........134 8.5.6 Implementations.......................135 8.5.7 StructuralAlignment....................139 8.6Exercises...............................145 III Optimality Criteria 147 9 Optimality Criteria−Distance 148 9.1WhyDistance?............................148 9.1.1 Benefits............................149 9.1.2 Drawbacks..........................149 9.2DistanceFunctions..........................150