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Diversity of Eukaryotes and Their Genomes

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Diversity of Eukaryotes and Their Genomes University of Massachusetts Amherst ScholarWorks@UMass Amherst Open Access Dissertations 2-2011 Diversity of Eukaryotes and Their Genomes Laura Ellen Wegener Parfrey University of Massachusetts Amherst Follow this and additional works at: https://scholarworks.umass.edu/open_access_dissertations Part of the Ecology and Evolutionary Biology Commons Recommended Citation Wegener Parfrey, Laura Ellen, "Diversity of Eukaryotes and Their Genomes" (2011). Open Access Dissertations. 345. https://scholarworks.umass.edu/open_access_dissertations/345 This Open Access Dissertation is brought to you for free and open access by ScholarWorks@UMass Amherst. It has been accepted for inclusion in Open Access Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. DIVERSITY OF EUKARYOTES AND THEIR GENOMES A Dissertation Presented by LAURA E. WEGENER PARFREY Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY February 2011 Program in Organismic and Evolutionary Biology © Copyright by Laura E. Wegener Parfrey 2011 All Rights Reserved DIVERSITY OF EUKARYOTES AND THEIR GENOMES A Dissertation Presented by LAURA E. WEGENER PARFREY Approved as to style and content by: ____________________________________________________ Laura A. Katz, Chair ____________________________________________________ Benjamin B. Normark, Member ____________________________________________________ Robert L. Dorit, Member ____________________________________________________ Samuel S. Bowser, Member ____________________________________ Elizabeth R. Dumont, Program Director Organismic and Evolutionary Biology DEDICATION To James for his continued respect and support, despite my persistent lack on interest in cute, furry research subjects. ACKNOWLEDGEMENTS I am extremely grateful to the numerous people who helped me complete my Dissertation. I want to thank Laura Katz for inviting me to her lab and providing guidance in all aspects of my academic development. I am indebted to her for all her advice and encouragement. I would like to thank the members of the lab that have provided assistance, insightful conversations, and good times through the years, especially Yonas Tekle, Maiko Tamura, Micah Dunthorn, Daniel Lahr, and Mary Doherty. Thanks to Jessica Grant for a tremendous amount of support in the through the years. I also acknowledge Judith Wopereis and Dick Briggs at Smith College for help in the microscopy facilities, and Tony Caldanaro for technical assistance. I would also like to thank many people who contributed their time and knowledge to my development as a scientist and as a person. I thank my Dissertation committee, Sam Bowser, Ben Normark, and Rob Dorit, for their helpful comments on manuscripts, career advice, and good conversations. Sue Goldstein, Sam, and Andrea Habura, and Paddy Patterson were instrumental in my development as a field biologist. Many in the OEB community made my graduate experience much more fulfilling, enlightening, and enjoyable, especially Dana Moseley, Susannah Lerman, and Sharlene Santana. Of course, thanks to Penny Jaques for much guidance and help navigating the ways of UMass, and more importantly actively seeking to improve the lives of all OEB students. I would like to thank my family for being supportive and stressing the importance of education, and especially James Parfrey. Finally, this research would not have been possible without the financial support from many sources. I thank the University of Massachusetts Amherst for teaching v assistantship support and a UMass Graduate School Fellowship. Support also came from a Sigma Xi Grant in aid of research, a Joseph A. Cushman award from the Cushman Foundation for Foraminiferal Research, and a miniPEET grant from the Society of Systematic Biologists. This work was presented at numerous meetings with travel support supplied by the International Society of Protistologists, American Society of Microbiology, Society for Integrative and Comparative Biology, Cushman Foundation for Foraminiferal Research, UMass Amherst, and the OEB program. Research was also supported by an NSF grant to Laura A Katz (NSF AToL 043115). vi ABSTRACT DIVERSITY OF EUKARYOTES AND THEIR GENOMES FEBRUARY 2011 LAURA E. WEGENER, B.S., UNIVERSITY AT ALBANY Ph.D., UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Laura A. Katz My dissertation addresses two aspects of eukaryotic evolution, 1) the organization of eukaryotic diversity and 2) genomic variation in Foraminifera. The bulk of eukaryotic diversity is microbial with plants and animals representing just two of the estimated 75 lineages of eukaryotes. Among these microbial lineages, there are many examples of dynamic genome processes. Elucidating the origin and evolution of genome features requires a robust phylogenetic framework for eukaryotes. Taxon-rich molecular analyses provide a mechanism to test hypothesized evolutionary relationships and enable placement of diverse taxa on the tree of life. These analyses result in a well-resolved eukaryotic tree of life. Relaxed molecular clock analyses of this taxon-rich dataset place the origin on eukaryotes in the Paleoproterozoic, and suggest that all of the major lineages of eukaryotes diverged before the Neoproterozoic. This robust scaffold of the tree of eukaryotes is also used to elucidate common themes in genome evolution across eukaryotes. Mapping dynamic genome features onto this tree demonstrates that they are widespread in eukaryotes, and suggests that a common mechanism underlies genome plasticity. Foraminifera, a diverse lineage of marine amoebae, provide a good model system for investigating genome dynamics because they amplify portions of their genome vii and go through ploidy cycles during their life cycle. Assessment of nuclear dynamics in one species of Foraminifera, Allogromia laticollaris strain CSH, reveals that genome content varies according the life cycle stage and food source, which may differentially impact organismal fitness. The inclusion of diverse microbial eukaryotes enables better resolution of eukaryotic relationships and improves our understanding the dynamic nature of eukaryotic genomes. viii TABLE OF CONTENTS ACKNOWLEDGEMENTS ............................................................................................. v ABSTRACT..................................................................................................................... vii LIST OF TABLES .......................................................................................................... xii LIST OF FIGURES .......................................................................................................xiii CHAPTER 1. EVALUATING SUPPORT FOR THE CURRENT CLASSIFICATION OF EUKARYOTIC DIVERSITY.......................................................................................... 1 1.1 Abstract.................................................................................................................................1 1.2 Introduction ..........................................................................................................................2 1.2.1 Eukaryotic Classification................................................................................................2 1.2.2 The Supergroups .............................................................................................................3 1.2.3 Our Approach..................................................................................................................7 1.3 Methods.................................................................................................................................8 1.3.1 Stability of Taxonomy ....................................................................................................8 1.3.2 Membership support .......................................................................................................8 1.3.3 Supergroup Monophyly ..................................................................................................9 1.4 Results .................................................................................................................................10 1.4.1 Taxonomic Instability ...................................................................................................10 1.4.2 Varying Support for Membership within and Monophyly of Targeted Supergroups ..11 1.4.3 Decreased Support for Monophyly of Supergroups as Outgroups in Other Studies ....12 1.5 Discussion............................................................................................................................14 1.5.1 Supergroup Robustness.................................................................................................14 1.5.2 Alternative hypotheses..................................................................................................15 1.5.3 Why is Eukaryotic Taxonomy so Difficult? .................................................................16 1.5.4 Towards a Robust Scaffold of the Eukaryotic Tree of Life..........................................20 1.6 Conclusion...........................................................................................................................23 2. THE DYNAMIC NATURE OF EUKARYOTIC GENOMES............................... 33 2.1 Abstract...............................................................................................................................33
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