Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life Ross Callum Parker Mounce http://orcid.org/0000-0002-3520-2046 A thesis submitted for the degree of Doctor of Philosophy University of Bath Department of Biology and Biochemistry October 2013 Copyright: © 2014 Ross Mounce. This is an open-access thesis distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Signature: 1 Table of Contents Table of Contents ................................................................................................................. 2 Acknowledgements .............................................................................................................. 5 Publications ......................................................................................................................... 6 Media ................................................................................................................................... 76 List of Abbreviations ............................................................................................................. 7 List of Figures ...................................................................................................................... 9 List of Tables ...................................................................................................................... 10 Summary ........................................................................................................................... 11 Chapter 1: Introduction ...................................................................................................... 12 1.1 Overview of Inferring Evolutionary Relationships in Palaeontology ...................... 13 1.2 Why not just use molecular data? ......................................................................... 16 1.3 Is Morphology Actually Useful for Reconstructing Phylogeny? ............................. 16 1.4 Aims of this thesis ................................................................................................. 19 The Congruence of Cranial & Postcranial Characters in Vertebrate Phylogeny ................ 21 2.1 Abstract ................................................................................................................. 21 2.2 Introduction ........................................................................................................... 23 2.2.1 Congruence between Partitions of Morphological Data ..................................... 24 2.2.2 Previous Quantitative Studies ............................................................................ 25 2.2.3 Why Examine the Congruence of Cranial and Postcranial Partitions? .............. 27 2.3 MATERIALS AND METHODS ....................................................................................... 28 2.3.1 Do Cranial and Postcranial Characters Imply Different Levels of Homoplasy? .. 29 2.3.2 Is there More Conflict Between Cranial and Postcranial Characters than we Might Expect? ............................................................................................................. 34 2.4 Results .................................................................................................................. 42 2.4.1 Homoplasy and Resolution in Cranial and Postcranial Data Partitions .............. 43 2.4.2 Congruence between Cranial and Postcranial Signals (ILD tests) ..................... 44 2.5 Discussion ................................................................................................................ 46 2.5.1 A Significant Minority of Cranial and Postcranial Partitions have Incongruent Signals ........................................................................................................................ 48 2.5.2 Cranial and Postcranial Partitions Imply Significantly Different Relationships in a Significant Minority of Cases ...................................................................................... 50 2.5.3 What do these Results Imply for Cladistic Analyses of Morphology? ................. 51 2.6 Conclusions .......................................................................................................... 53 2 Chapter 3: An Updated Examination of the Impact of the Fossil Taxa in Parsimony Analyses of Morphology ..................................................................................................... 55 3.1 Abstract ................................................................................................................. 55 3.2 Introduction .............................................................................................................. 56 3.3 Methods ................................................................................................................ 57 3.3.2 A new taxon-jackknifing analytical pipeline ........................................................ 58 3.4 Results ..................................................................................................................... 62 3.4.1 On average Fossil and Extant Taxa have remarkably similar Topological Impact as judged by single-taxon deletions ............................................................................ 64 3.4.2 Fossil Taxa on average do not increase the number of MPTs any more than Extant Taxa ................................................................................................................. 65 3.4.3 Leaf Stability ...................................................................................................... 67 3.4.4 Extreme Taxa ..................................................................................................... 67 3.5 Discussion ................................................................................................................ 67 3.6 Conclusion ............................................................................................................... 68 Chapter 4: A review of the ILD randomisation test: uses and abuses ................................ 69 4.1 Abstract .................................................................................................................... 70 4.2 Introduction .............................................................................................................. 70 4.2.1 Historical Importance and Context ..................................................................... 71 4.2.2 Inappropriate usages of the ILD test .................................................................. 72 4.2.3 Additional developments .................................................................................... 74 4.2.4 Raison d'etre for this review of ILD test usage ................................................... 75 4.3 Methods ................................................................................................................... 76 4.4 Results ..................................................................................................................... 77 4.5 Discussion ................................................................................................................ 78 4.6 Conclusion ............................................................................................................... 80 Chapter 5: A modification of Archie's Homoplasy Excess Ratio in the presence of missing data .................................................................................................................................... 82 5.1 Abstract .................................................................................................................... 82 5.2 Introduction .............................................................................................................. 82 5.2.1 The Problem of Permuting Missing / Inapplicable Data in Matrices ................... 84 5.2.2 Time-Efficient Computational Implementation .................................................... 87 5.2.3 How many replications are needed for a robust MEANNS estimate? ................ 87 5.2.4 Is the HER missing data problem significant in real matrices? .......................... 88 5.3 Method ..................................................................................................................... 88 5.4 Results ..................................................................................................................... 88 5.5 Discussion ................................................................................................................ 91 5.5.1 Why has HER seemingly been ignored for so long? .......................................... 91 3 Chapter 6: Optimal search strategies for finding phylogenetic data ................................... 93 6.1 Abstract .................................................................................................................... 93 6.2 Introduction .............................................................................................................. 94 6.2.1 Preliminary Investigation .................................................................................... 95 6.2.2 Scirus does not cover many important natural history journals .......................... 97 6.2.3 The long-tail of phylogenetic content ................................................................. 98 6.3 Methods