REWEAVING THE TAPESTRY: A SUPERTREE OF BIRDS Katie E. Davis Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy to the University of Glasgow, Division of Environmental and Evolutionary Biology, January 2008 © K. E. Davis 2008 Declaration I attest that: All material presented in this document was compiled and written by myself unless otherwise acknowledged. Part of the material included in this thesis is being prepared for submission in co-authorship with others: • Chapter 2: Davis, K. E. and Dyke, G. J. In Prep for Neues Jahrbuch für Geologie und Paläontologie . “Two new specimens of Primobucco (Aves: Coraciiformes) from the Eocene of North America”. K. E. D. carried out the descriptive work, phylogenetic analyses and wrote the manuscript. G. J. D. provided the specimens and advised on description and writing of the manuscript. • Chapter 6: Lloyd, G. T., Davis, K. E., Pisani, D., Tarver, J. E., Ruta, M., Sakamoto, M., Hone, D. W. E., Jennings, J., Benton, M. J. In Prep for Proceedings of the National Academy of Sciences. “Dinosaurs and the Cretaceous Terrestrial Revolution”. KED and GTL designed the data collection protocols. GTL, JET, MS, DWEH and RJ performed data collection and entry. KED and DP created the MRP matrices. DP ran tree searches, performed post hoc taxon pruning and produced support values. MJB and GTL collected the stratigraphic data and GTL performed the subsampling tests and calculated diversification rates. JET, MR and GTL performed the time-slicing and diversification shift analyses. MJB, GTL, JET, DP, MR and KED wrote the paper. GTL and JET produced the Supporting Information and Figures. KATIE E. DAVIS, 2008 i Acknowledgements I would like to thank first of all my supervisor, Rod Page, for his help and assistance over the years and also the other members of the Page Lab for help, encouragement and, at times, much hilarity. Thanks go to Matt Yoder, Peter Foster and George Sangster for contributing to the work in Chapter 4 by joining in with the Bird Supertree Project. Matt Yoder uploaded trees, while Peter Foster and George Sangster helpfully pointed out data errors and synonyms. The results of that chapter are much improved for their input. I would also like to thank Gareth Dyke for his collaboration and advice on Chapter 2, and Graeme Lloyd, a friend and colleague with whom I worked on Chapter 6. Thanks, of course, also to the other collaborators on the dinosaur supertree project. I would also like to thank NERC for almost giving me enough money to survive on for the last four years. My colleagues and friends Nadia Anwar, Helen Ablitt and Heather Forbes also deserve many thanks for their support and friendship over the last four years. Heather in particular has made the hard times so much more bearable and the good times really good. Finally, thanks go to my husband Jon. On a practical note he wrote the Perl scripts utilised so many times in this thesis, but more importantly has always been there for me and never complained once even when asked on numerous occasions to proofread chapters at unsociable hours of the morning (and still turned up to the wedding). Katie Davis, 2008. ii Abstract Supertrees are a useful method of constructing large-scale phylogenies by assembling numerous smaller phylogenies that have some, but not necessarily all, taxa in common. Birds are an obvious candidate for supertree construction as they are the most abundant land vertebrates on the planet and no comprehensive phylogeny of both extinct and extant species currently exists. In order to construct supertrees, primary analysis of characters is required. One such study, presented here, describes two new partial specimens belonging to the Primobucconidae from the Green River Formation of Wyoming (USA), which were assigned to the species Primobucco mcgrewi . Although incomplete, these specimens had preserved anatomical features not seen in other material. An attempt to further constrain their phylogenetic position was inconclusive, showing only that the Primobucconidae belong in a clade containing the extant Coraciiformes and related taxa. Over 700 such studies were used to construct a species-level supertree of Aves containing over 5000 taxa. The resulting tree shows the relationships between the main avian groups, with only a few novel clades, some of which can be explained by a lack of information regarding those taxa. The tree was constructed using a strict protocol which ensures robust, accurate and efficient data collection and processing; extending previous work by other authors. Before creating the species-level supertree the protocol was tested on the order Galliformes in order to determine the most efficient method of removing non-independent data. It was found that combining non-independent source trees via a “mini-supertree” analysis produced results more consistent with the input source data and, in addition, significantly reduced computational load. Another method for constructing large-scale trees is via a supermatrix, which is constructed from primary data collated into a single, large matrix. A molecular-only tree was constructed using both supertree and supermatrix methods, from the same data, again of the order Galliformes. Both methods performed equally as well in producing trees that fit the source data. The two methods could be considered complementary rather than conflicting as the supertree took a long time to construct but was very quick to calculate, but the supermatrix took longer to calculate, but was quicker to construct. Dependent upon the data at hand and the other factors involved, the choice of which method to use appears, from this small study, to be of little consequence. Finally an updated species-level supertree of the Dinosauria was also constructed and used to look at diversification rates in order to elucidate the “Cretaceous explosion of terrestrial life”. Results from this study show that this apparent burst in diversity at the end of the Cretaceous is a sampling artefact and in fact, dinosaurs show most of their major diversification shifts in the first third of their history. iii Table of Contents DECLARATION ..................................................................................................................................... I ACKNOWLEDGEMENTS ....................................................................................................................... II ABSTRACT ......................................................................................................................................... III LIST OF FIGURES ............................................................................................................................... VI LIST OF TABLES ................................................................................................................................ IX CHAPTER 1 .........................................................................................................................................1 1.1 INTRODUCTION .............................................................................................................................1 1.2 CONSTRUCTING LARGE -SCALE PHYLOGENIES ...............................................................................3 1.3 SUPERTREE METHODS ...................................................................................................................5 1.4 CURRENT ESTIMATES OF AVIAN PHYLOGENY ............................................................................10 1.5 THIS THESIS ................................................................................................................................19 1.6 THESIS SUMMARY .......................................................................................................................20 CHAPTER 2 .......................................................................................................................................22 2.1 ABSTRACT ..................................................................................................................................22 2.2 INTRODUCTION ...........................................................................................................................22 2.3 SYSTEMATIC PALAEONTOLOGY ..................................................................................................24 2.4 PHYLOGENETIC ANALYSIS .........................................................................................................30 2.5 RESULTS .....................................................................................................................................30 2.6 DISCUSSION ................................................................................................................................32 CHAPTER 3 .......................................................................................................................................34 3.1 ABSTRACT ..................................................................................................................................34 3.2 INTRODUCTION ...........................................................................................................................34 3.3 CURRENT SUPERTREE BUILDING PROTOCOL ..............................................................................35 3.4 METHODS ...................................................................................................................................41 3.5 ANALYSIS ...................................................................................................................................55