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The Principles and Methods of Phylogenetic Systematics and Its THE PRINCIPLES AND METHODS OF PHYLOGENETIC SYSTEMATICS AND ITS APPLICATION TO THE TAXONOMY OF THE PRONOCEPHALIDAE LOOSS, 1902 (pLATYHELMINTHES: DIGENEA) A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy in Zoology in the University of Canterbury, Christchurch, New Zealand, by AlIen Gerard ?-odrigo ~./ ' University of Canterbury 1990 [515 L PREFACE 11 A Personal Introduction "~I , {, a' ",10 /LP If I were asked to describe that period between 1987 and 1989 when I worked for my Ph.D., I would say that it was stimulating and exciting - in short, I would say that I enjoyed myself. Working in the area of theoretical and applied systematics has allowed me to combine three fields of study of which I am particular fond - mathematics, computing, and evolutionary biology. It is with this feeling of excitement in mind, that I have chosen to present not only the results of the 'systematic research I have carried out, but also the motivation for such research. More often than not, theses and journal articles, constrained as they are by tradition and editorial policy, are sterile reports of scientific work. They fail to reflect the strong personal component in all scientific enterprise which, to a large extent, determines its direction. While personal reflections, such as those which I have included in this thesis, may be considered irrelevant by some, they provide the backdrop against which this work is set, the context in which it can be understood. Aside from answering the scientific questions which I have attempted to solve, this thesis also addresses the personal questions, "Why did I do such-and-such 7", and, "What do I really believe in 7". A Ph.D. is almost a kind of Membership Card into a community of scientists, and I believe that it is as important to understand the person as it is to aCknowledge the work, before membership is granted. Although my work on the systematics of the Pronocephalidae began in 1987, my interest in phylogenetic reconstruction and cladistics was sparked off by the visit of Dr. Dan Brooks, in 1986. Dan is a vital and enthusiastic individual, and his enthusiasm is contagious. In 1987, then, when I began to work on revising the taxonomy of the pronocephalids, under the supervision of Dr. David Blair, I was sure that there was one and only one reasonable way to reconstruct evolutionary history - parsimony. I soon realised that there were gaps in the techniques available, gaps which I had to fill myself. As the work progressed, it also became apparent that the fundamental assertions of cladists - to a large extent, these are philosophical - are open to debate and subject to criticism. At this stage, I thought it necessary to review these claims, for my own satisfaction. I was loath to doggedly follow a course of action until I was satisfied that its principles rested on firm foundations. Hence, my brief sojourn into philosophical realms. The three parts of this thesis is a reflection of these three periods of my research, although the order in which the first two parts are presented is the reverse of the chronological order of the work. Most of my results have been written up as manuscripts and submitted to various journals for publication, or presented at conferences. I have treated these as chapters of my dissertation. Although each chapter has a different emphasis, there is often some overlap between chapters. I ask the reader to bear with this. In each chapter, I have also included, when necessary, footnotes, and addenda. AlIen Roddgo April, 1990 ABSTRACT Biological systematics has developed according to the Kuhnian model of science: there have been paradigm shifts in systematic practices, the consequence of changing perceptions of what is required of scientists, theories, and classifications. Under the current paradigm of phylogenetic systematics, there are two sub­ disciplines which can be ,broadly categorised as Methodological Procedures and Modelling Tools. The former include the techniques of Parsimony and Compatibility, while the latter consists of the recently developed techniques of Maximum­ Likelihood Estimation (MLE). Parsimony and Compatibility, while intuitively appealing, can lead to incorrect hypotheses of phylogeny when characters of taxa change at unequal rates. MLE takes account of unequal rates of change, but is mathematically demanding. In this thesis, a number of methods are derived which retains the simplicity of Parsimony and the efficiency of MLE. These techniques are applied to uncovering the relationships of the Pronocephalidae Looss, 1902 (Platyhelminthes:Digenea) a family of monostomatous parasites of reptiles. The analsysis revealed that certain genera of the Pronocephalidae are polyphyletic. In revising the taxonomy of the group it was necessary to erect a paraphyletic genus because of the insufficiency of good character-taxon information. Under the revised classification, the Pronocephalid~e consists of seven genera: Notocotyloides Dollfus, 1966, Pyelosomum Looss,. 1899, Charaxicephalus Looss, 1901, Pronocephalus Looss, 1899, Cetiosaccus Gilbert, 1938, Macravestibulum Mackim, 1930, and Neopronocephalus Mehra, 1932. TABLE OF CONTENTS PART I THE PHILOSOPHY OF SYSTEMATICS CHAPTER 1. The Kuhnian Structure of Biological 3 Systematics Addendum 1.1 A brief reyiew of systematic techniques 15 Addendum 1.2 A further note on incommensurability 18 CHAPTER 2. What is the Real difference between 20 numerical Taxonomies ? Addendum 2.1 A note on justifiability 27 Addendum 2.2 Methodological Tools versus Modelling 28 Procedures Addendum 2.3 A critique of Cladistics 29 PART 11 TECHNIQUES IN PHYLOGENETIC SYSTEMATICS CHAPTER 3. Two optimality criteria for selecting 39 subsets of most-parsimonious trees CHAPTER 4. Aninformation-richcharacterweighting 48 procedure for parsimony analysis Addendum 4.1 A priori character analyses 55 Addendum 4.2 A possible method for comparing an 59 alternative phylogenetic tree against a set of most-parsimonious trees CHAPTER 5. A family of heu'tistic methoids for 62 approximating solutions to maximum­ likelihood estimates of evolutionary trees PART III THE PHYLOGENY AND TAXONOMY OF THE PRONOCEPHALIDAE LOOSS, 1902 (PLATYHELMINTHES: DIGENEA) CHAPTER 6. The phylogeny of the Pronocephalidae 76 Looss, 1902 (Platyhelminthes: Digenea) CHAPTER 7. Translating the phylogeny of the 91 Pronocephalidae into a classification: two criteria for generating acceptable classifications CHAPTER 8. A taxonomic revision of the 97 Pronocephalidae Looss, 1902 (Platyhelminthes: Digenea) ACKNOWLEDGEMENTS APPENDIX The derivation of the Optimal Likelihood Index REFERENCES FLATWORMS, by M.C. Escher PART I THE PHILOSOPHY OF SYSTEMATICS "Philosophy ... is not a presumptious effort to explain the mysteries of the world by means of any superhuman insight or extraordinary cunning, but has its origins and value in an attempt to give a reasonable account of our own personal attitude towards the more serious business of life." Josiah R6yce The Spirit of Philosophy "Every genuine scientist must be ... a metaphysician" George Bernard Shaw Back to Methuselah INTRODUCTION As a group, scientists are reticent a bou t engaging 10 philosophical debate. Science, after all, is 10 the business of finding out empirical truths. The point and counterpoint arguments of philosophers, the endless dialogues on metaphysical abstractions and semantic minutiae, have no place in scientific enterprise, for they cannot be resolved objectively by recourse to Hard Fact. Many scientists would go further and say that the converse is equally true: science has little or nothing to gain from philosophical soul-searching. This is patently false. Logic is the yardstick by which we measure the quality of our hypotheses and theories, inferences, and experiments. Theories about knowledge and the acquisition of knowledge -the domain of epistemology - allow us to evaluate the soundness of our scientific methods. We cannot reasonably expect to explore the boundaries of our concepts, and the adequacy of their definitions, without recourse to some form of metaphysical discourse. The disputes that currently rage in the diverse field of evolutionary biology typify our reliance on ideas philosophical. The debates between Creation "Scientists" and Evolutionists, Structuralists and Functionalists, Pheneticists and Phylogeneticists, are, in essence, philosophical dialogues. I have' always had a passion for philosophy, particularly the philosophy of science. However, this section of my work owes more to my bewilderment at the level of disagreement between systematists over fundamental issues, than any self -indulgence. As I mention in the Preface, I began this project believing strongly that cladistics was the panacea for all the ills of biological systematics. It was only after I had applied parsimony techniques to real data sets, that I began to see some of the shortcomings of the method. In the next section, I will review these problems and offer some solutions. However, more often than not, the solutions that I had developed altered cladistic methodology to such an extent. that it was "parsimony" in name only. It was this fact that led me to a closer inspection of the aims, and foundations of parsimony as a technique of phylogenetic systematics. (A note on terminology: I use the term cladistics to refer specifically to the method of constructing phylogenetic hypotheses using parsimony. Phy/ogenetic systematics. on the other hand, is a generic term referring to all methods that are designed
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