FoundationsFoundations ofof PhylogeneticPhylogenetic SystematicsSystematics Johann-Wolfgang Wägele Verlag Dr. Friedrich Pfeil • München 1 Johann-Wolfgang Wägele Foundations of Phylogenetic Systematics 2 Bibliographic Information published by Die Deutschen Bibliothek Die Deutsche Bibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data is available in the Internet at http://dnb.ddb.de. Original Title: Grundlagen der Phylogenetischen Systematik, first published by Verlag Dr. Friedrich Pfeil, München, 2000 2nd, revised edition 2001. Copyright © 2005 by Verlag Dr. Friedrich Pfeil, München All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying or otherwise, without the prior permission of the copyright owner. Applications for such permission, with a statement of the purpose and extent of the reproduction, should be addressed to the Publisher, Verlag Dr. Friedrich Pfeil, Wolfratshauser Str. 27, D-81379 München. Druckvorstufe: Verlag Dr. Friedrich Pfeil, München CTP-Druck: grafik + druck GmbH Peter Pöllinger, München Buchbinder: Thomas, Augsburg ISBN 3-89937-056-2 Printed in Germany Verlag Dr. Friedrich Pfeil, Wolfratshauser Straße 27, D-81379 München, Germany Tel.: + 49 - (0)89 - 74 28 270 • Fax: + 49 - (0)89 - 72 42 772 • E-Mail: [email protected] www.pfeil-verlag.de J.-W. Wägele: Foundations of Phylogenetic Systematics 3 Foundations of Phylogenetic Systematics Johann-Wolfgang Wägele Translated from the German second edition by C. Stefen, J.-W. Wägele, and revised by B. Sinclair Verlag Dr. Friedrich Pfeil München, January 2005 ISBN 3-89937-056-2 4 J.-W. Wägele: Foundations of Phylogenetic Systematics 5 Contents Introduction ............................................................................................................................................................... 9 1. Metaphysical foundations of science ...................................................................................................... 11 1.1 What is knowledge? ................................................................................................................................. 11 1.2 Classification and the function of language .................................................................................... 12 1.3 What is there outside of our cognition apparatus? What is “really existing”? ..................... 16 1.3.1 Objects of nature, the “thing per se” ............................................................................................... 17 1.3.2 Systems ................................................................................................................................................ 18 1.3.3 Thing and system ............................................................................................................................... 19 1.3.4 What is a “system in the animal kingdom”? ................................................................................. 20 1.3.5 What is “information”? ...................................................................................................................... 21 1.3.6 Quantifying information ................................................................................................................... 24 1.3.7 What is a character? ........................................................................................................................... 25 1.4 Acquisition of knowledge in sciences .................................................................................................... 29 1.4.1 What is a “truth”? ...............................................................................................................................29 1.4.2 Deduction and induction .................................................................................................................. 30 1.4.3 The hypothetico-deductive method ................................................................................................ 32 1.4.4 Laws and theories .............................................................................................................................. 34 1.4.5 Probability and the principle of parsimony ................................................................................... 34 1.4.6 Phenomenology .................................................................................................................................. 40 1.4.7 The role of logic .................................................................................................................................. 41 1.4.8 Algorithms and gaining knowledge ............................................................................................... 41 1.5 Evolutionary epistemology .................................................................................................................... 42 2. The subject of phylogenetic systematics ............................................................................................... 44 2.1 Transfer of genetic information between organisms ..................................................................... 45 2.1.1 Horizontal gene transfer ................................................................................................................... 45 2.1.2 Clonal reproduction ........................................................................................................................... 45 2.1.3 Bisexual reproduction ........................................................................................................................ 46 2.1.4 The special case of endosymbionts which evolved to organelles (mitochondria and plastids) 47 2.2 The population ............................................................................................................................................. 48 2.3 The “biological species” ............................................................................................................................. 52 2.3.1 The species concept as a tool of phylogenetics .............................................................................56 2.3.2 Recognition of species ....................................................................................................................... 63 2.4 The transitional field between species ................................................................................................... 65 2.5 Speciation as a “key event” ....................................................................................................................... 68 2.5.1 Notions and real processes ............................................................................................................... 68 2.5.2 Dichotomy and polytomy ................................................................................................................. 68 2.6 Monophyla .................................................................................................................................................... 69 2.7 Evolutionary theory and models of evolution as basis for systematics .......................................... 73 2.7.1 Variability and evolution of morphological structures ................................................................ 75 2.7.2 Variability and evolution of molecules ........................................................................................... 81 2.7.2.1 Changes in populations .................................................................................................................. 81 2.7.2.2 The theory of neutral evolution .................................................................................................... 83 2.7.2.3 The molecular clock ......................................................................................................................... 85 2.7.2.4 Evolutionary rates ............................................................................................................................ 89 2.8 Summary: Constructs, processes and systems ................................................................................. 97 3. Phylogenetic graphs ........................................................................................................................................ 98 3.1 Ontology and terms .................................................................................................................................. 98 Contents 6 3.2 Topology ....................................................................................................................................................... 100 3.2.1 Visualization of compatible hypotheses of monophyly ............................................................... 100 3.2.2 Visualization of incompatible hypotheses of monophyly ........................................................... 103 3.2.3 Visualization of hypotheses of character polarity and of apomorphy ...................................... 103 3.3 Consensus dendrograms ......................................................................................................................... 104 3.3.1 Supertrees and “democratic voting” ............................................................................................... 106 3.4 Number of elements of a dendrogram and number of topologies ..........................................