Evolution of the Caecilian Skull A thesis submitted to The University of Manchester for the degree of Doctor of Philosophy (PhD) in Animal Biology in the Faculty of Life Sciences. 2011 Emma Sherratt List of Contents List of Tables 5 List of Figures 5 Abstract 7 Declaration 8 Copyright Statement 9 Acknowledgements 10 Preface 11 Chapter 1 ­ Introduction to the Evolution of the Caecilian Skull 13 Background............................................................................................................................................. 13 The skull: a model system for morphological evolution...................................................... 16 Enter caecilians: the study organisms ........................................................................................ 17 Bibliography...........................................................................................................................................25 Chapter 2 ­ Evolution of Cranial Shape in Caecilian Amphibians 30 Abstract .................................................................................................................................................... 31 Introduction............................................................................................................................................32 Materials and Methods ...................................................................................................................... 34 Study Taxon...................................................................................................................................34 X‐Ray Computed Tomography..............................................................................................37 Skull Models and Measurement ...........................................................................................38 Preliminary Shape Analysis ...................................................................................................40 Evolutionary Allometry Correction ....................................................................................41 Morphospace and Phylogeny ................................................................................................42 Phylogenetic Signal....................................................................................................................43 Disparity .........................................................................................................................................44 Correlation analyses..................................................................................................................45 Results ....................................................................................................................................................... 46 Evolution of shape variation..................................................................................................46 Phylogenetic Signal....................................................................................................................49 Differentiation among clades ................................................................................................49 Disparity .........................................................................................................................................50 2 Dynamics of Shape Variation.................................................................................................52 Ecological patterns.....................................................................................................................55 Discussion ................................................................................................................................................ 58 Large‐scale patterns of diversification..............................................................................58 Factors influencing clade disparity.....................................................................................61 Acknowledgements.............................................................................................................................. 67 References................................................................................................................................................ 67 Chapter 3 ­ Evolution of Cranial Modularity in Caecilians 76 Abstract .................................................................................................................................................... 77 Introduction............................................................................................................................................78 Materials and Methods ...................................................................................................................... 82 Preliminary shape analysis ....................................................................................................82 Integration and modularity analyses.................................................................................83 Patterns of shape variation in modules ............................................................................87 Results ....................................................................................................................................................... 88 Integration and modularity....................................................................................................88 Comparing shape variation in each module....................................................................90 Discussion ................................................................................................................................................ 93 Evolutionary implications of modularity .........................................................................97 Acknowledgements........................................................................................................................... 100 Chapter 4 ­ Morphological Integration in the Cranium, Mandible and Atlas of Caecilians 105 Abstract ................................................................................................................................................. 106 Introduction......................................................................................................................................... 107 Materials and Methods ................................................................................................................... 112 Samples ........................................................................................................................................112 Shape analysis...........................................................................................................................112 Levels of morphological variation....................................................................................114 Measuring allometry ..............................................................................................................114 Comparing covariance matrices........................................................................................116 Measuring integration ...........................................................................................................117 Results .................................................................................................................................................... 119 Allometry.....................................................................................................................................119 3 Similarity of covariance matrices .....................................................................................121 Covariation of the cranium and mandible ....................................................................123 Covariation of the cranium and atlas..............................................................................126 Discussion ............................................................................................................................................. 128 Patterns of integration in the cranium, mandible and atlas..................................128 The caecilian head and neck as an integrated complex ..........................................130 References............................................................................................................................................. 134 Chapter 5 ­ Discussion on the Evolution of the Caecilian Skull 138 Chapter synopsis and future outlook........................................................................................ 138 Conclusions........................................................................................................................................... 143 Bibliography........................................................................................................................................ 144 Appendix 1 ­ High Resolution X­ray Computed Tomography 146 Background.......................................................................................................................................... 146 Methods ................................................................................................................................................. 146 Scan Data.............................................................................................................................................. 148 Appendix