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Phylogenics and Patterns of Molecular Evolution in Amoebozoa University of Massachusetts Amherst ScholarWorks@UMass Amherst Open Access Dissertations 9-1-2011 Phylogenics and Patterns of Molecular Evolution in Amoebozoa Daniel J.G. Lahr University of Massachusetts Amherst, [email protected] Follow this and additional works at: https://scholarworks.umass.edu/open_access_dissertations Part of the Ecology and Evolutionary Biology Commons Recommended Citation Lahr, Daniel J.G., "Phylogenics and Patterns of Molecular Evolution in Amoebozoa" (2011). Open Access Dissertations. 448. https://scholarworks.umass.edu/open_access_dissertations/448 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]. PHYLOGENETICS AND PATTERNS OF MOLECULAR EVOLUTION IN AMOEBOZOA A Dissertation Presented by DANIEL J. G. LAHR Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY September 2011 Program in Organismic and Evolutionary Biology © Copyright by Daniel J. G. Lahr 2011 All Rights Reserved PHYLOGENETICS AND PATTERNS OF MOLECULAR EVOLUTION IN AMOEBOZOA A Dissertation Presented by DANIEL J. G. LAHR Approved as to style and content by: ____________________________________________________ Laura A. Katz, Chair ____________________________________________________ Benjamin B. Normark, Member ____________________________________________________ Michael E. Hood, Member ____________________________________________________ O. Roger Anderson, Member _____________________________ Elizabeth R. Dumont, Director Organismic and Evolutionary Biology DEDICATION To Paula and my family. “Without trace of nerve elements, and without definite, fixed organs of any kind, internal or external, the Rhizopod,—simplest of all animals, a mere jelly-speck,—moves about with the apparent purposes of more complex creatures. It selects and swallows its appropriate food, digests it, and rejects the insoluble remains. It grows and reproduces its kind. It evolves a wonderful variety of distinctive forms, often of the utmost beauty, and, indeed, it altogether exhibits such marvelous attributes, that one is led to ask the question in what consists the superiority of animals usually regarded as much higher in the scale of life.” Joseph Leidy in Freshwater Rhizopods of North America, 1879, p. 5 ACKNOWLEDGEMENTS I am grateful to all the incredible people that supported me during the long years of crafting this dissertation. The many lessons I learned from Laura Katz while under her supervision cannot be easily tallied; above all she has been and will continue to be a great friend and inspiration. I am indebted to all the very talented colleagues and students with whom I had the pleasure of sharing the laboratory with: Laure Bellec, Mary Doherty, Micah Dunthorn, Jessica Grant, Allie Kovner, Jian Hua Lin, Truc Nguyen, Maiko Tamura and Yonas Tekle. They’ve all been fundamental since the training days up to the very end of my journey. I especially thank my long time office colleague Laura W. Parfrey with whom I had much fruitful discussions and collaborations. I am also indebted to my external collaborators, who helped expand my view of the world and understanding of different types of science: Edward Mitchell and Enrique Lara at the University of Neuchatel, Switzerland; Tanja Bosak at MIT; Francis MacDonald and Andrew Knoll at Harvard. David “Paddy” Patterson at MBL deserves special mention as he has been one of the most important influences on my scientific career. There are additionally many individuals at Smith College who were great colleagues and also helped me in many ways: Sara Pruss at the Geology Department; Rob Dorit at the Biological Sciences Department; Dick Briggs and Judith Wopereis at the Microscopy Center. A heartfelt thank you to my dissertation committee: Benjamin Normark, Michael Hood and O. Roger Anderson. These were incredibly smart and experienced people who had a great impact on the directions my research took. I would also like to thank the other great committee members I had while at the Organismic and Evolutionary Biology vi program: Joe Elkinton, Paul Sievert and Duncan Irschick have been helpful with literature suggestions and the like. The work of Betsy Dumont and Beth Jakobs as directors, and of Penny Jaques as program manager were equally extraordinary and very helpful to me. Finally I’d like to thank the friends and family who were supportive and put up with my often overly long conversations about evolutionary biology (and how everything else is meaningless). Firstly, the Americans who welcomed me into their country and lives: the Crand family (John, Sue, Gigi, Hannah and Mike) and the Reyda family (Florian, Laura, Sonja and Sam). Then, all the Brazilians who visited and supported us while in our “exile”: Felipão; Lamas; Vitão; Fernando; Tim; Ana Paula and Thomás; Fernanda and Fábio; Verônica. Alas, I could not have done this without the love and support from my family and especially Paula Turrini. vii ABSTRACT PHYLOGENETICS AND PATTERNS OF MOLECULAR EVOLUTION IN AMOEBOZOA SEPTEMBER 2011 DANIEL J. G. LAHR, B. Sc., UNIVERSITY OF SÃO PAULO, BRAZIL M. Sc., UNIVERSITY OF SÃO PAULO, BRAZIL Ph.D., UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Laura A. Katz My dissertation explores several aspects of the relationship between morphological and molecular evolution in amoeboid lineages: Chapter 1 – General Introduction: This chapter provides an overview of the most pressing issues in Amoebozoa phylogeny that are dealt with in the remainder of the thesis. Chapter 2 - Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new generation high fidelity DNA polymerase: This chapter addresses the methodological difficulty in the study of large gene families, the generation of artifactual sequences by recombination during PCR Chapter 3 - Evolution of the actin gene family in testate lobose amoebae (Arcellinida) is characterized by two distinct clades of paralogs and recent independent viii expansions: This chapter explores intriging patterns of evolution in the actin gene families of testate amoebae. Chapter 4 - Comprehensive phylogenetic reconstruction of Amoebozoa based on concatenated analysis of SSU-rDNA and actin genes: A deep phylogenetic analyses of the Amoebozoa, enables exploration of well supported taxonomic units within the group. Chapter 5 - Interpreting the evolutionary history of the Tubulinea (Amoebozoa), in light of a multigene phylogeny: This chapter explores a more restrict taxonomic unit within the Amoebozoa – the Tubulinea – based on an expanded sample of genes and taxa. Chapter 6 - The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms: This chapter asks whether the null-hypothesis that amoebae are asexual is consistent with current phylogenetic evidence. ix TABLE OF CONTENTS Page ACKNOWLEDGEMENTS.............................................................................................vi ABSTRACT ....................................................................................................................viii LIST OF TABLES .........................................................................................................xiv LIST OF FIGURES ........................................................................................................xv CHAPTER 1 GENERAL INTRODUCTION .....................................................................................1 2 REDUCING THE IMPACT OF PCR-MEDIATED RECOMBINATION IN MOLECULAR EVOLUTION AND ENVIRONMENTAL STUDIES USING A NEW GENERATION HIGH FIDELITY DNA POLYMERASE................................7 2.1 Abstract................................................................................................................................7 2.2 Introduction.........................................................................................................................8 2.3 Methods..............................................................................................................................10 2.3.1 Origin of templates .......................................................................................................10 2.3.2 Conditions.....................................................................................................................11 2.3.3 Cloning .........................................................................................................................13 2.3.4 Replicates and controls.................................................................................................14 2.3.5 Determining PCR recombination events ......................................................................15 2.3.6 Software recognition of the chimeras obtained ............................................................15 2.4 Results ................................................................................................................................16 2.4.1 PCR recombination events across different treatments ................................................16 x 2.4.2 Recovery of original haplotypes per treatment.............................................................17 2.4.3 Number of breakpoints in chimeric sequences.............................................................18
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