Brigham Young University BYU ScholarsArchive Theses and Dissertations 2005-06-23 Crustacean phylogenetic systematics and opsin evolution Megan L. Porter Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Microbiology Commons BYU ScholarsArchive Citation Porter, Megan L., "Crustacean phylogenetic systematics and opsin evolution" (2005). Theses and Dissertations. 557. https://scholarsarchive.byu.edu/etd/557 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. CRUSTACEAN PHYLOGENETIC SYSTEMATICS AND OPSIN EVOLUTION by Megan L. Porter A dissertation submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Microbiology and Molecular Biology Brigham Young University August 2005 Copyright © 2005 Megan L. Porter All Rights Reserved BRIGHAM YOUNG UNIVERSITY GRADUATE COMMITTEE APPROVAL of a dissertation submitted by Megan L. Porter This dissertation has been read by each member of the following graduate committee and by majority vote has been found to be satisfactory. Date Keith A. Crandall, Chair Date David A. McClellan Date Dennis K. Shiozawa Date Jack W. Sites Date Michael F. Whiting Date Barry M. Willardson BRIGHAM YOUNG UNIVERSITY As chair of the candidate’s graduate committee, I have read the dissertation of Megan L. Porter in its final form and have found that (1) its format, citations, and bibliographical style are consistent and acceptable and fulfill university and department style requirements; (2) its illustrative materials including figures, tables, and charts are in place; and (3) the final manuscript is satisfactory to the graduate committee and is ready for submission to the university library. Date Keith A. Crandall Chair, Graduate Committee Accepted for the Department Alan R. Harker Department Chair Accepted for the College R. Kent Crookston Dean, College of Biology and Agriculture ABSTRACT CRUSTACEANS AND OPSIN EVOLUTION Megan L. Porter Department of Microbiology and Molecular Biology Doctor of Philosophy Composed of a chromophore bound to an integral membrane protein (opsin), visual pigments are phenotypically characterized by the wavelength of maximal absorption (λmax). The underlying molecular mechanism controlling λmax is the interaction between the opsin amino acid sequence and the chromophore. While a plethora of studies have looked at structure/function relationships in vertebrate opsins, fewer studies have investigated similar issues in invertebrates. Furthermore, those few studies undertaken in invertebrate systems suggest different mechanisms of spectral tuning and photoactivation compared to vertebrate systems. This dissertation research is focused on expanding our knowledge of opsin evolution in invertebrate systems, particularly from non-insect taxa. First, issues related to opsin evolution and the maintenance of supposedly ‘non- functional’ genes were explored in a review of regressive and reverse evolution. Second, in order to place studies of crustacean opsin evolution in context, phylogenetic studies of two crustacean groups (Mysidae and Decapoda) were completed. Studies of Mysidae utilized 16S mtDNA, and 18S and 28S rDNA to reconstruct phylogenetic relationships and assess newly developed Bayesian methods of assessing pattern heterogeneity. Using this suite of genetic markers, there are incongruencies between current taxonomy and inferred phylogenetic relationships. Studies of Decapoda assessed phylogenetic relationships and estimated divergence times using 16S mtDNA, H3 nDNA, and 18S and 28S rDNA sequence data in conjunction with a set of eight fossil calibrations. Reconstructed phylogenies show support for two well supported nodes corresponding to the Pleocyemata and the informal ‘Reptantia’ and place the emergence of the Decapod lineage in the early Devonian (407 MYA). Finally, opsin sequences and spectral sensitivity data from species within the Mysidae and Decapoda were combined with previously characterized invertebrate sequences to investigate opsin evolution. Standard dN/dS methods did not detect any evidence of selection. Methods investigating selection on amino acid properties, however, identified four properties (coil tendencies, compressibility, power to be at the middle of the alpha helix, and refractive index) to be under positive destabilizing selection. These properties occurred mostly at sites in transmembrane helices and included residues previously identified to affect spectral tuning as well as identifying novel sites. ACKNOWLEDGEMENTS I owe many people more thanks than I can express on these pages; to those who are too numerous to name who have given me support, encouragement, friendship, camaraderie, lively debate, and help with field work, analyses, or urgently needed specimens – thank you. Without you, the long days of my graduate career would not have been so productive, meaningful, and enjoyable. I am eternally indebted to my research advisor, Keith, for giving me the independence to find my own way (including making my own mistakes), but always being nearby to help me when I stumbled. Thank you for always believing in me. My appreciation goes to my graduate committee for their sage counsel and unyielding encouragement. I am also grateful for the guidance and support of Dr. Tom Cronin, who took me under his wing and gave an unknown graduate student his time and friendship. Many thanks to those organizations who saw fit to fund parts of this research, including the National Science Foundation, the Cave Conservancy Foundation, the Cave Research Foundation, the American Association of University Women, the Brigham Young University Doctoral Fellowship, and the Department of Integrative Biology, the Department of Microbiology & Molecular Biology, and the College of Biology and Agriculture, Brigham Young University. To my parents, I send all of my love and admiration for always believing in my quest to be an eternal student. Also many thanks are due to Dr. Horton H. Hobbs III, for sharing with me his love for science, setting me on this course of biological adventure, and for continuing to be my mentor and friend. Finally, special thanks are extended to Marcos Pérez-Losada and Katharina Dittmar, both of whom have traveled the world with me during my pursuit of this degree. If not for their devoted friendship and support through all of the best (and worst) times, I would not have survived to finish this research. You both have my unending adoration. To study history one must know in advance that one is attempting something fundamentally impossible, yet necessary and highly important. To study history means submitting to chaos and nevertheless retaining faith in order and meaning. It is a very serious task, young man, and possibly a tragic one. - Father Jacobus (from Hesse’s Magister Ludi) TABLE OF CONTENTS Abstract..........................................................................................................................v Acknowledgements..................................................................................................... vii Table of Contents......................................................................................................... ix List of Tables .................................................................................................................x List of Figures.............................................................................................................. xi Introduction....................................................................................................................1 Research Outline..........................................................................................................16 Chapter 2. Lost along the way: The significance of evolution in reverse....................36 Is evolution reversible?..........................................................................................38 The continuum of reversibility...............................................................................40 How does evolution back up?................................................................................44 The future of reversibility ......................................................................................46 Appendix 1. Glossary.............................................................................................48 Appendix 2. The debate over evolution in reverse ................................................49 Appendix 3. Experimental systems in reverse evolution.......................................51 Appendix 4. Regressive evolution in Astyanax mexicanus ...................................52 Appendix 5. Studies of genomics in reverse .........................................................54 Chapter 3. Phylogenetic relationships within the Mysidae..........................................59 Methods..................................................................................................................63 Results....................................................................................................................69 Discussion..............................................................................................................74