BUILDING THE TREE OF LIFE: RECONSTRUCTING THE EVOLUTION OF A RECENT AND MEGADIVERSE BRANCH (CALYPTRATAE: DIPTERA) SUJATHA NARAYANAN KUTTY (B.Tech) A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF BIOLOGICAL SCIENCES NATIONAL UNIVERSITY OF SINGAPORE 2008 The great tragedy of Science - the slaying of a beautiful hypothesis by an ugly fact. Thomas H. Huxley ii ACKNOWLEDGEMENTS We don't accomplish anything in this world alone . and whatever happens is the result of the whole tapestry of one's life and all the weavings of individual threads from one to another that creates something - Sandra Day O'Connor. The completion of this project would have been impossible without help from so many different quarters and the few lines of gratitude and acknowledgements written out in this section would no justice to the actual amount of support and encouragement that I have received and that has contributed to making this study a successful endeavor. I am indebted to Prof. Meier for motivating me to embark on my PhD (at a very confusing point for me) and giving me a chance to explore a field that was quite novel to me. I express my sincere gratitude to him for all the guidance, timely advice, pep talks, and support through all the stages of this project and for always being patient while dealing with my ignorance. He has also been very understanding during all my nonacademic distractions in the last two years. Thanks Prof.- your motivation and inspiration in the five years of my graduate study has given me the confidence to push the boundaries of my own capabilities. You should be acknowledged as the best supervisor one can have. I would also like to thank Dr. Thomas Pape for sending large amounts of specimens all of which have been invaluable for this study and for all his timely inputs, immaculate proof reading and important suggestions at various junctures of the project. I would also like to i thank Dr. Brian Wiegmann and his lab members especially Brain Cassel for my enriching stint at NCSU, Raleigh. Special thanks to Dr. Frederik Petersen, Dr. Adrian Pont, Dr. Marco Bernasconi and Dr. František Šifner for all their important and useful inputs in this study. I also thank all other collaborators who have directly and indirectly contributed to this study. I would like to thank Kathy, my first labbie along with whom I figured out the tricks of pcr-ing and Nalini for all the unwinding sessions and especially for her support and ‘motivation’ during the last phase of thesis writing. Thanks girls for not just being such wonderful colleagues but also lovely friends with whom I have spent some of the best times in evolab. Thanks to all the other members of the evolab (past and current) who have helped and supported me at different stages and many of whom I have seen begin and finish their projects during these years: Gaurav, Shiyang, Gwynne, Guanyang, Weisong, Yuchen, Farhan, Danwei, Denise, Dave, Nanthinee, Zeehan, Martin, Mirza, WaiKit and Huifung. Thanks Anu, Aparna, Nilofer and Rika for all the fun times, get-togethers and of course the brilliant dance sessions. Thanks to Suni for being my support system for almost a decade now, Janesh for always sticking by my side, Ettan, Chechi and Vishu for being my family away from home and my ii friends on the other side of the globe who have ‘virtually’ always supported me- Pavan and Venky. I have to thank Acha, Amma and Sumi, my ‘perfect’ family for pitching in whichever way they could, and my extended family especially my darling Meena and also my new family (in-law). Lastly and most importantly - Sunil, who switched roles from being the ‘crazy’ guy in my world to my fiancée and finally to my better half, all during the course of this dissertation. In your own quiet way, you have always been my pillar of strength and constant source of support over the years. Thank you so much for understanding and putting up with my daily crankiness, random cooking patterns and the late night writing sessions for the last couple of months. I owe you one! iii TABLE OF CONTENTS Acknowledgements i Table of contents iv Summary ix List of Tables xi List of Figures xii List of Publications xv Introduction Chapter 1: Phylogeny and evolution of host choice in the Hippoboscoidea (Diptera) as reconstructed using four molecular markers 1.1 Introduction 1.1.1 Family portraits: Biology and Systematics 1.1.2 Hippoboscoidea Phylogenetics 11 1.2 Materials and Methods 14 1.2.1 Taxon sampling, DNA extraction and sequencing 14 1.2.2 Phylogenetic Analysis 17 1.3 Results 19 1.4 Discussion 23 1.4.1 Classificatory implications 26 1.4.2 Host-shifts and diversification in Hippoboscoidea 28 1.4.3 Morphological and life history evolution in Hippoboscoidea 32 1.5 Conclusions 34 iv Chapter 2: Sensitivity analysis, molecular systematics, and natural history evolution of Scathophagidae (Diptera:Cyclorrhapha:Calyptratae) 2.1 Introduction 2.1.1 Comparing alignment techniques 36 38 through a sensitivity analysis 2.2 Materials and Methods 40 2.2.1 Taxa and DNA extractions 40 2.2.2 DNA amplification and sequencing 40 2.2.3 Tree search strategies 42 2.2.4 Sensitivity analysis 43 2.2.5 Natural history 44 2.3 Results 49 2.3.1 Alignment techniques, indel treatment, character 49 transformation weighting 2.4 Discussion 56 2.4.1 Sensitivity analyses and Choice of alignment 56 2.4.2 Node support and Node stability 60 2.4.3 Systematic conclusions 61 2.4.4 Natural history evolution 64 2.5 Conclusions 68 v Chapter 3: The Muscoidea (Diptera: Calyptratae) are paraphyletic: Evidence from four mitochondrial and four nuclear genes 3.1 Introduction 70 3.1.1 Fanniidae 71 3.1.2 Muscidae 72 3.1.3 Anthomyiidae 73 3.1.4 Scathophagidae 74 3.1.5 Interfamilial relationships 75 3.2 Materials and Methods 77 3.2.1 Taxa and DNA extractions 77 3.2.2 DNA amplification 77 3.2.3 Alignments 81 3.2.4 Tree search strategies 82 3.3 Results 83 3.3.1 Alignment techniques, indel treatment, character transformation weighting 3.4 Discussion 90 3.4.1 Comparison of tree hypotheses 91 3.4.2 Calyptrate monophyly 92 3.4.3 Superfamily monophyly and the relationships 92 between the calyptrate superfamilies 3.4.4 Interfamilial relationships within the muscoid grade 94 3.4.5 Family monophyly and relationships within families 95 3.4.6 Alignments of the ribosomal genes 98 3.5 Conclusions 108 vi Chapter 4: Molecular phylogeny of the Calyptratae (Diptera:Cyclorrhapha) with emphasis on the Oestroidea 4.1 Introduction 110 4.1.1 Oestroidea phylogenetics 111 4.1.2 Oestroidea family relationships 111 4.1.3 Oestroidea family portraits 113 4.1.4 Is the McAlpine’s fly a calyptrate? 120 4.1.5 Calyptratae phylogenetics 121 4.2 Materials and Methods 126 4.2.1 Taxa 126 4.2.2 DNA extractions 127 4.2.3 DNA amplification and sequencing 134 4.2.4 Alignments 135 4.2.5 Taxa selection strategy for analysis 136 4.2.6 Tree search strategies 137 4.3 Results 138 4.4 Discussion 147 4.4.1 Oestroidea monophyly 148 4.4.2 Placement of the McAlpine’s fly and M. zelandica in the 148 Oestroidea 4.4.3 Oestroidea family relationships 149 4.4.4 Higher-level systematics of the Calyptratae 152 4.5 Conclusions 155 vii Overall conclusions 156 References 159 viii Kloet, G. 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Increased Taxon Sampling Greatly Reduces Phylogenetic Error. Syst. Biol. 51, 588 - 598. 184 [...]... representation with parsimony) technique in the supertree approach The trees obtained by both approaches were poorly resolved in conflict and it became clear that new data were needed Since the data overlap of both genes and taxa in the available datasets was poor, adding more data into a supermatrix of taxa from across the calyptrate group was regarded as the most appropriate approach This is the technique... elaborate and discover the details of fly relationships and diversity with the ultimate goal of providing a newly resolved phylogeny for this major branch of the Tree of Life (FLYTREE 2006) The most effective way of transmitting new phylogenetic evidence is via a published data matrix analyzed in a quantitative framework (Yeates and Wiegmann, 1999) and the FLYTREE project is an ambitious endeavor that... markers Chapter 2: Sensitivity analysis, molecular systematics, and natural history evolution of Scathophagidae (Diptera:Calyptrate: Musocidea) Chapter 3: The Muscoidea (Diptera:Calyptratae) are paraphyletic: Evidence from four mitochondrial and four nuclear genes Chapter 4: Molecular phylogeny of the Calyptratae (Diptera:Cyclorrhapha) with emphasis on the Oestroidea The sequence of the chapters in the dissertation... information has to be collected and new analytic tools are needed to reconstruct the relationships based on these data This is the main goal of the US National Science Foundation funded project ‘Assembling the Tree of Life which involves many international teams that concentrate on different subsets of taxa Obtaining an accurate and universal Tree of Life has enormous research potentials and benefits... Fanniidae, Musciidae, Oestridae, Tachinidae, Rhinophoridae, Sarcophagidae, Mystaciinobiidae) iii position of the enigmatic species referred to as “McAlpine’s fly” 3 iv evolution of life history strategies like host choice and larval breeding habits within the group v the performance of various alignment and test various analyses techniques using the calyptrate dataset I approached this large and ambitious... within the calyptrates are very poorly understood and most literature on the phylogeny of the group (Hennig, 1973; McAlpine, 1989; Pape, 1992; Nirmala, 2001; etc.) is often controversial The Calyptratae are morphologically and biologically very diverse and have invaded a large variety of habitats They show an exceptional range of natural history traits However, despite all this diversity, the clade appears... free-living and only come into close contact with their host during feeding The other three families, Hippoboscidae, Nycteribiidae, and Streblidae, are all genuine ectoparasites (i.e species with a trophic and a spatial association to a host) spending all or most of their adult life within the fur or among the feathers of their mammal and bird hosts These families exhibit a large number of unique and striking... for at least part of their life An exception is Ascodipteron Adensamer 1896 in which females, after mating, embed themselves in the tissue of the host Wings and legs are shed and the fly attains a sack- or flask like appearance while the males retain their wings throughout life The morphology of the remaining Streblidae is also unusually variable For example, some species are dorsoventrally flattened,... like the Calyptratae can be approached by either using the supermatrix method or the supertree method (Sanderson et al., 1998) I combined all the available data for species under study into a single matrix and used the information from each character directly in the supermatrix analysis The trees from the different published studies are recoded in a matrix format and then combined using the MRP (Matrix... morphological and physiological adaptations, most of which are specifically associated with their ectoparasitic lifestyle One of the most remarkable of these is adenotrophic viviparity (Meier et al., 1999) The larvae develop individually, in the female oviduct, where they are fed by secretions from accessory glands The fully mature 3rd instar larva is deposited either as a motile larva, which quickly pupates . BUILDING THE TREE OF LIFE: RECONSTRUCTING THE EVOLUTION OF A RECENT AND MEGADIVERSE BRANCH (CALYPTRATAE: DIPTERA) SUJATHA NARAYANAN KUTTY (B.Tech) A THESIS. is often controversial. The Calyptratae are morphologically and biologically very diverse and have invaded a large variety of habitats. They show an exceptional range of natural history traits approaches were poorly resolved in conflict and it became clear that new data were needed. Since the data overlap of both genes and taxa in the available datasets was poor, adding more data