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Large Trees, Supertrees and the Grass Phylogeny

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Large Trees, Supertrees and the Grass Phylogeny LARGE TREES, SUPERTREES AND THE GRASS PHYLOGENY Thesis submitted to the University of Dublin, Trinity College for the Degree of Doctor of Philosophy (Ph.D.) by Nicolas Salamin Department of Botany University of Dublin, Trinity College 2002 Research conducted under the supervision of Dr. Trevor R. Hodkinson Department of Botany, University of Dublin, Trinity College Dr. Vincent Savolainen Jodrell Laboratory, Molecular Systematics Section, Royal Botanic Gardens, Kew, London DECLARATION I thereby certify that this thesis has not been submitted as an exercise for a degree at any other University. This thesis contains research based on my own work, except where otherwise stated. I grant full permission to the Library of Trinity College to lend or copy this thesis upon request. SIGNED: ACKNOWLEDGMENTS I wish to thank Trevor Hodkinson and Vincent Savolainen for all the encouragement they gave me during the last three years. They provided very useful advice on scientific papers, presentation lectures and all aspects of the supervision of this thesis. It has been a great experience to work in Ireland, and I am especially grateful to Trevor for the warm welcome and all the help he gave me, at work or outside work, since the beginning of this Ph.D. in the Botany Department. I will always remember his patience and kindness to me at this time. I am also grateful to Vincent for his help and warm welcome during the different periods of time I stayed in London, but especially for all he did for me since my B.Sc. at the University of Lausanne. I wish also to thank Prof. Mark Chase for his comments and advice on different manuscripts taken from this thesis. Thanks to Jonathan Davis for being an interested beta tester for my programs, and the members of the Molecular Systematic Section from the Jodrell Laboratory for their welcome. Thanks finally to all members of the Botany Department from Trinity College. I will not forget Ireland! Finally, I could not imagine having spent the last three years in Dublin without Karine. This project was funded by the Irish Higher Education Authority, the Roche Research Foundation, the Agassiz Foundation and a University of Lausanne Research Grant. Large Trees, Supertrees and the Grass Phylogeny TABLE OF CONTENT Table of Content ......................................................................................................i List of Figures........................................................................................................vi List of Appendices ................................................................................................ix List of Appendices ................................................................................................ix List of Abbreviations..............................................................................................x List of Abbreviations..............................................................................................x Phylogenetic inference .................................................................................... x DNA sequencing ............................................................................................. x Grass systematics .......................................................................................... xi Abstract.................................................................................................................xii Chapter 1. Introduction ........................................................................................1 1.1 Historical overview of phylogenetics ........................................................1 1.2 Beyond classification purposes................................................................5 1.2.1 Ancestral character states ................................................................5 1.2.2 Timing of evolutionary events ...........................................................6 1.2.3 Tempo and mode of evolution...........................................................7 1.2.4 Comparative methods.......................................................................7 1.2.5 Genomics and evolution of development ..........................................8 1.3 Phylogenetic inference ..........................................................................10 1.3.1 Choosing an optimality criterion......................................................10 1.3.2 Searching the tree space ................................................................11 1.3.3 Meta-analysis approaches ..............................................................12 1.3.4 Confidence intervals .......................................................................12 1.3.5 Networks.........................................................................................13 i Large Trees, Supertrees and the Grass Phylogeny 1.3.6 Coalescent process ........................................................................14 1.4 Angiosperm and grass phylogeny..........................................................14 1.4.1 Angiosperms...................................................................................15 1.4.2 Poaceae .........................................................................................15 1.5 Aims of this thesis..................................................................................16 1.6 Structure of the thesis............................................................................18 Chapter 2. Towards the Reconstruction of Complete Generic-Level Angiosperm Phylogenies: Are the Big Indeed Easy? ............................20 2.1 Introduction............................................................................................20 2.1.1 Pitfalls of phylogenetics ..................................................................20 2.1.2 Aims ...............................................................................................22 2.2 Material and Methods ............................................................................22 2.2.1 Data matrices and phylogenetic trees .............................................22 2.2.2 Simulations.....................................................................................24 2.2.3 A 13,000 taxa tree ..........................................................................25 2.3 Results ..................................................................................................26 2.3.1 Parameter estimation......................................................................26 2.3.2 Branch length and number of substitutions .....................................28 2.3.3 Simulations of 18S rDNA, atpB and rbcL ........................................31 2.3.4 Simulations based on three codon positions ...................................34 2.3.5 A 13,000 taxa tree ..........................................................................36 2.4 Discussion.............................................................................................38 2.5 Conclusion.............................................................................................42 Chapter 3. Assessing Internal Support with Large Phylogenetic DNA Matrices for the Angiosperms.................................................................................44 3.1 Introduction............................................................................................44 3.1.1 Searching the tree space................................................................44 3.1.2 Aims ...............................................................................................45 3.2 Material and Methods ............................................................................46 ii Large Trees, Supertrees and the Grass Phylogeny 3.2.1 Data and phylogenetic analyses .....................................................46 3.2.2 Statistical analyses .........................................................................46 3.3 Results ..................................................................................................47 3.4 Discussion.............................................................................................53 3.5 Conclusion.............................................................................................55 Chapter 4. Building Supertrees: an Empirical Assessment using the Grass Family ........................................................................................................57 4.1 Introduction............................................................................................57 4.1.1 Building large phylogenetic trees ....................................................57 4.1.2 Supertree reconstructions...............................................................58 4.1.3 Coding procedures .........................................................................59 4.1.4 Aims ...............................................................................................60 4.2 Material and Methods ............................................................................60 4.2.1 Combined phylogenetic tree ...........................................................60 4.2.2 MRP reconstructions ......................................................................61 4.2.3 Topological comparisons ................................................................64 4.3 Results ..................................................................................................64 4.3.1 GPWG combined tree.....................................................................64
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