Estimating evolutionary rates using discrete morphological characters: a case study with birds Luke Barrett Harrison Department of Biology McGill University, Montreal April 2013 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Doctor of Philosophy © Luke Harrison 2013 DEDICATION I dedicate this thesis to my wife, Soo Bin Chun. I would not have been able to do it without you nor would I have wanted to. semper fidelis & love always TABLE OF CONTENTS ABSTRACT / RÉSUMÉ 1 ACKNOWLEDGEMENTS 5 PREFACE 7 GENERAL INTRODUCTION 10 CHAPTER 1: Estimating Evolutionary Rates of Discrete Morphological Characters Introduction 14 Rates of Phenotypic Evolution 15 Traits, Characters, and Discrete Morphological Characters 16 Heterogeneity in Rates Between Discrete Morphological Characters in Phylogenetic Analysis 18 Absolute Rates of Evolution of Discrete Morphological Characters 20 Westoll (1949) 22 Forey (1988) 22 Cloutier (1991) 23 Wagner (1997) 23 Bromham et al. (2002) 24 Ruta et al. (2006) 24 Brusatte et al. (2008) 25 Roelants et al. (2011) 25 Lloyd et al. (2012) 27 Summary of Previous Methods and Future Directions 28 Appropriate Null Models 28 Likelihood-based Methods for Estimating Morphological Evolutionary Rates: Potential Advantages 29 An Ideal Model-based Framework for Estimating Absolute Rates of Evolution of Discrete Morphological Characters 30 Conclusions 31 CONNECTING TEXT 32 CHAPTER 2: Among-Character Rate Variation in Phylogenetic Analysis of Discrete Morphological Characters: Prevalence and Bayesian Model Selection Introduction 33 Materials and Methods Data Sets 35 Bayesian Analysis 36 Topology Comparisons 40 Parsimony-based Estimation of Rate Distributions 40 Optimal Number of Discrete Rate Categories 41 Focal Phylogenetic Analysis 42 Results Equal Rates Models and Unequal Rates Models 43 Gamma and Lognormal Rate Distributions 43 Parsimony Analysis 45 Optimal Number of Discrete Rate Categories 45 Effect on Phylogenetic Topology and Branch Lengths: Sidlauskas and Vari (2008) 46 Discussion Rate Heterogeneity in Data Sets of Discrete Morphological Characters 46 Gamma and Lognormal Rate Distributions 47 Optimal Number of Discrete Rate Categories 49 Effects on Estimations of Phylogenetic Topology 51 Alternative Approaches to Model ACRV 53 Conclusions 54 Figures 56 Tables 70 Appendices 73 CONNECTING TEXT 86 CHAPTER 3: Embracing Uncertainty: A Distribution of Evolutionary Timescales for Modern Bird Lineages Introduction 87 Materials and Methods 90 Sequence Data 91 Phylogenetic Analysis 92 Divergence Time Analysis 93 Comparisons with the Jetz et al. (2012) Distribution of Chronograms 94 Results and Discussion Phylogenetic Analysis 95 Divergence Time Analysis 96 Comparisons to Other Divergence Time Studies – Higher-Level Divergences 99 Comparison to Jetz et al. (2012) – Lower Level Divergences 100 Implications for Avian Evolution 101 Conclusions 102 Figures 104 Tables 108 Supplementary Methodology 122 Supplementary Figures 150 Appendices 156 CONNECTING TEXT 220 CHAPTER 4: Estimating Absolute Rates of Evolution using Discrete Morphological Characters across an Uncertain Phylogeny: Rates of Anatomical Evolution in Modern Birds Introduction 221 Materials and Methods 225 Morphological Data 225 Chronogram Distributions 226 Reconstruction of Morphological Evolution 226 Estimating Rates of Evolution: MCC Chronograms 227 Estimating Rates of Evolution: Chronogram Distributions 228 Rates of Evolution of Monophyletic Clades 229 Visualizing and Testing Absolute Rates of Evolution Through Time 231 Aggregate Morphological and Molecular Rates Through Time 232 Results Among-character Rate Heterogeneity and Partition Testing 233 Rates of Evolutionary Change on MCC Trees 233 Rates of Evolution of Focal Clades 235 Absolute Rates of Evolutionary Change Through Time 236 Correlation Test for the Early-Burst Hypothesis 238 Discussion Modular Evolution in the Livezey and Zusi (2007) Data Set 239 Estimating Rates of Evolution of Discrete Morphological Characters 241 Implications for the Evolution of Modern Birds 242 Limitations of the Present Analysis 244 Broad-scale Patterns of Molecular and Morphological Evolutionary Rates 246 Future Research 246 Conclusions 248 Figures 250 Tables 262 Supplementary Methodology 268 Supplementary Figures 276 Appendix 298 SUMMARY AND CONCLUSIONS 304 BIBLIOGRAPHY 309 ABSTRACT The rate of evolution is a fundamental unifying concept in evolutionary biology and sets the stage for the investigation of genotypic, phenotypic and taxonomic biodiversity. This thesis specifically examined the rate of phenotypic evolution using discrete morphological characters, which are relatively understudied for this purpose compared to continuously-valued characters and traits. I first focused on heterogeneity in rates among characters in phylogenetic analysis. I used Bayesian model selection tools and 77 matrices of discrete morphological characters to show that a) models incorporating rate-heterogeneity among characters in phylogenetic analysis were preferred over equal-rates models in 80–88% of matrices, suggesting rate heterogeneity is a common property of these data sets, and b) although most data sets were equivocal, there was some weak support for a recently formulated hypothesis that the lognormal distribution is more appropriate to model such variation relative to the commonly used gamma distribution. I then focused on estimating absolute rates of evolution of discrete morphological characters in a phylogenetic context. I extended previous methods to better incorporate phylogenetic and divergence time uncertainty using distributions of dated phylogenies derived from independent data. I used modern birds as a case study and performed a large Bayesian divergence time study of a comprehensive sample of 310 modern bird genera to provide a posterior sample of 10 000 dated trees to estimate absolute rates of evolution. This analysis, based on 23 fossil calibrations and a multigene molecular supermatrix of existing sequences, although qualified by uncertainty in estimated relationships and divergence times, estimated that the basal radiation of Neoaves occurred within a relatively short interval in the Late Cretaceous. Many lineages were estimated to cross the Cretaceous–Paleogene (K–Pg) boundary while within order diversification of crown groups was nearly exclusively in the Cenozoic. Finally, I employed this tree distribution along with another recently published tree distribution to estimate absolute rates of phenotypic evolution using both 1 maximum parsimony and likelihood-based methods using an existing comprehensive data set of discrete avian anatomical characters. Incorporating phylogenetic and divergence time uncertainty, estimated rates of evolution were found to be highly variable and had a complex multimodal distribution through time when visualized across 10 000 dated trees. Combined with an analysis of rates of evolution across clades, maximum clade credibility trees, and a correlation test of rates against time, the results were complex, but in aggregate, were consistent with the hypothesis of an early-burst of higher rates of phenotypic evolution in modern birds. 2 RÉSUMÉ Le taux d'évolution est un concept fondamental unificateur en biologie évolutive, et ouvre la voie à l'étude de la biodiversité génotypique, phénotypique et taxonomique. La présente thèse a examiné de manière spécifique le taux d'évolution phénotypique à l'aide de charactères morphologiques discrètes, qui sont relativement peu étudiés dans cette optique comparativement aux traits et charactèrs à valeur continue. Premièrement, je me suis penché sur l'hétérogénéité des taux dans les caractères d'analyse phylogénétique. Les outils de sélection du modèle Bayesien ainsi que 77 matrices de charactères morphologiques discrets ont été utilisé afin de démontrer que a) les modèles incorporant l'hétérogenéité des taux dans les charactères d'analyse phylogénétique étaient préférées des modèles à taux égaux dans 80 à 88% des matrices, ce qui suggère que l'hétérogénéité est une charactéristique commune dans les ensembles de données, et b) bien que la plupart des ensembles de données étaient équivoques, il y avait un faible appui pour l'hypothèse formulée récemment que la distribution log-normale est plus appropriée pour modéliser les variations relatives que la distribution gamma couramment utilisée. Ensuite, je me suis concentré sur l'esmination des taux absolus d'évolution des charactères morphologiques discrets dans un contexte phylogénétique. J'ai étendu des méthodes existantes afin de mieux incorporer les incertitudes phylogénétique et de divergence temporelle en utilisant des distributions de phylogénies datées extraits de données indépendantes. J'ai utilisé les oiseaux modernes comme étude de cas et j'ai effectué une grande étude Bayesien de divergence temporelle d'un échantillon exhaustif de 310 genera d'oiseaux modernes pour y extraire un échantillon postérieur de 10 000 arbres datées, dans le but d'arriver à une estimation absolue des taux d'évolution. Cette analyse, qui est basée sur vingt-trois étalonnages de fossils et une supermatrice multigène moléculaire de séquences existantes, bien que qualifié par une incertitude dans les relations estimées et divergences temporelles, estime que le rayonnement de base a eu lieu dans un laps de temps relativement court dans la 3 fin du Crétacé. De nombreuses lignées ont été estimés à traverser la frontière Crétacé-Paléogène (K–Pg) tandis que la diversification des groupes