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A Framework for Post-Phylogenetic Systematics

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A Framework for Post-Phylogenetic Systematics A FRAMEWORK FOR POST-PHYLOGENETIC SYSTEMATICS Richard H. Zander Zetetic Publications, St. Louis Richard H. Zander Missouri Botanical Garden P.O. Box 299 St. Louis, MO 63166 [email protected] Zetetic Publications in St. Louis produces but does not sell this book. Any book dealer can obtain a copy for you through the usual channels. Resellers please contact CreateSpace Independent Publishing Platform of Amazon. ISBN-13: 978-1492220404 ISBN-10: 149222040X © Copyright 2013, all rights reserved. The image on the cover and title page is a stylized dendrogram of paraphyly (see Plate 1.1). This is, in macroevolutionary terms, an ancestral taxon of two (or more) species or of molecular strains of one taxon giving rise to a descendant taxon (unconnected comma) from one ancestral branch. The image on the back cover is a stylized dendrogram of two, genus-level speciational bursts or dis- silience. Here, the dissilient genus is the basic evolutionary unit (see Plate 13.1). This evolutionary model is evident in analysis of the moss Didymodon (Chapter 8) through superoptimization. A super- generative core species with a set of radiative, specialized descendant species in the stylized tree com- promises one genus. In this exemplary image; another genus of similar complexity is generated by the core supergenerative species of the first. TABLE OF CONTENTS Preface..................................................................................................................................................... 1 Acknowledgments................................................................................................................................... 3 Chapter 1. Introduction ......................................................................................................................... 5 Chapter 2. Pluralism versus Structuralism in Phylogenetic Systematics ............................................ 19 Chapter 3. A Framework ..................................................................................................................... 25 Chapter 4. Element 1 - Contributions of Classical Systematics ......................................................... 27 Chapter 5. Element 2 - Contributions of Morphological Cladistics .................................................... 35 Chapter 6. Element 3 - Contributions of Molecular Systematics ........................................................ 51 Chapter 7. Element 4 - Contributions from Cross-Tree Heterophyly .................................................. 67 Chapter 8. Element 5 - Superoptimization and Consolidation ............................................................. 75 Chapter 9. Element 6 - Linnaean Classification ............................................................................... 107 Chapter 10. Systematics Reviewed and Recast ................................................................................. 109 Chapter 11. Conservation and Biodiversity ....................................................................................... 117 Chapter 12. Scientific Intuition and the Hard Sciences ..................................................................... 125 Chapter 13. The Macroevolutionary Taxon Concept ........................................................................ 145 Chapter 14. Support Measures for Macroevolutionary Transformations ........................................... 159 Chapter 15. Multiple Tests and “Discovering” Morphological Support ........................................... 167 Chapter 16. Summary of Framework ................................................................................................ 173 Glossary ............................................................................................................................................. 179 Bibliography ..................................................................................................................................... 183 Index ................................................................................................................................................. 205 Preface PREFACE This book is an attempt to find common principles other, which is the nut of macroevolutionary theory. and intellectual continuity in addressing today’s This book rejects classification informing evolu- problems in systematics. Certain difficulties endemic tion rather than the other way around. “The map is in human thought, and often faced in the past in other not the territory.” Given that historical reconstruction fields, are now evident in systematics. This has been cannot be directly verified, and will remain forever perceived by many workers and science is self- notional not actual, mere precision will never make correcting, however tardily. This book suggests a up for natural limits on accuracy, particularly if pre- needed correction that deals with several problems at cision is obtained at the sacrifice of a total evidence once, and its particular solution will be accepted or approach involving discursive logic and macroevolu- fail as weighed in the marketplace of reason. tionary theory. Phylogenetic attempts at “reconstruc- A new paradigm should present an acceptable so- tion” try to reconstruct evolutionary nesting, not a lution to a problem by addressing it in a new way. process in nature. Yet, with application of a pluralist Phylogenetics has redefined the problem of devising approach involving classical techniques, morphologi- an evolution-based classification by presenting evolu- cal cladistics, and phylogenetic analyses, satisfying tionary relationships not as descent with modification advances can be made within such natural limits. of taxa but as descent with modification of traits. Ac- The proposed Framework will probably not cording to the Web home page of the phylogeneti- change the methods of career phylogeneticists who cally oriented Society for Systematic Botany (De- may feel loyal or responsible to sunk-cost profes- cember 2012): “Systematics is the study of biological sional investments. The story goes that the Buddha, diversity and its origins. It focuses on understanding after enlightenment, went into the world to teach. The evolutionary relationships among organisms, species, first person he came upon was a holy man, a fellow higher taxa, or other biological entities, such as seeker of enlightenment. The Buddha cried, “Wait! genes, and the evolution of the properties of taxa in- Listen! I have found enlightenment!” The holy man cluding intrinsic traits, ecological interactions, and paused and looked at the Buddha a moment. He said geographic distributions. An important part of sys- “Maybe so...,” and walked on. If I can obtain a tematics is the development of methods for various “maybe so” from the phylogenetic establishment, I aspects of phylogenetic inference and biological no- will be well satisfied. menclature/classification.” [Italics mine.] This book is largely intended for students and un- Phylogenetics eliminates any hint of progenitor- committed professionals in systematics and evolu- descendant relationships in evolutionary analysis, and tion, and for those in other fields, such as philosophy, relies on algorithmic clustering data from descrip- physics and psychology, that deal with scientific and tions or specimens to provide a “hard science,” decision theory. The basic ideas and methods pre- mathematically non-trivial, statistically based, inte- sented here are a pluralistic means to correct the dif- grable (fully calculable) solution that has the appear- ficulties in which modern systematics has found it- ance of an evolutionary tree but lacks identification self. The reader will find the same basic concepts of the nodes of the tree as being any extant taxon be- presented often in this book, but this is defensible yond the name of that taxon including all specimens because the concepts are sometimes difficult, relate or descriptions used as data distal to that node. That to other fields, and require a familiarity with both all nodes are treated as pseudoextinction events never classical and modern methods in systematics. In addi- budding evolution totally vitiates any responsible tion, judging from reviewers’ comments of previous macroevolutionary inferences in sister-group analy- manuscripts, I have decided it is necessary to present sis. certain novel concepts each in several ways and in Phylogenetics imposes a classification on the re- different contexts to (1) clarify what is meant, (2) sults of cladistic analysis without a process-based hammer past intransigent preconceptions, and (3) explanation of those results. The sister-group struc- dispel through reasoned discourse and perhaps a little ture is taken to be a classification itself. Evolution is humor the fog now shrouding classical systematics. not clustering, classification is. Evolution is not nest- Repetition of logical argument is often the only way ing, classification is. Phylogenetics leaps from the to break through or reprogram hard-set mental view- clustering and nesting of cladistic analysis straight to points. classification without explanation of the analysis in Practitioners of evolutionary systematics are terms of serial transformations of one taxon into an- methodologically diverse, and this book does not try – 1 – A Framework for Post-Phylogenetic Systematics to represent the field. Instead, presented here are my remonstrated over my occasional reference to matters ideas on how systematics as a whole
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