Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2016 Molecular evolution of opsins, a gene responsible for sensing light, in scallops (Bivalvia: Pectinidae) Anita J. Porath-Krause Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Developmental Biology Commons, and the Evolution Commons Recommended Citation Porath-Krause, Anita J., "Molecular evolution of opsins, a gene responsible for sensing light, in scallops (Bivalvia: Pectinidae)" (2016). Graduate Theses and Dissertations. 16612. https://lib.dr.iastate.edu/etd/16612 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Molecular evolution of opsins, a gene responsible for sensing light, in scallops (Bivalvia: Pectinidae) by Anita J. Porath-Krause A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Ecology and Evolutionary Biology Program of Study Committee: Jeanne M. Serb, Major Professor Maura A. McGrail Dean C. Adams Anne M. Bronikowski Stephan Q. Schneider Iowa State University Ames, Iowa 2016 ii DEDICATION For my son iii TABLE OF CONTENTS TABLE OF CONTENTS ............................................................................................................... iii LIST OF FIGURES .........................................................................................................................v LIST OF TABLES ......................................................................................................................... vi ACKNOWLEDGEMENTS .......................................................................................................... vii ABSTRACT ................................................................................................................................. viii CHAPTER I. GENERAL INTRODUCTION ................................................................................1 Overview ................................................................................................................................................... 1 Gene duplications and their fate ............................................................................................................... 1 Opsin ......................................................................................................................................................... 3 Visually-mediated behaviors and scallops ................................................................................................ 5 Scallop eyes .............................................................................................................................................. 8 Dissertation outline ................................................................................................................................. 10 References ............................................................................................................................................... 11 CHAPTER II. STRUCTURAL DIFFERENCES AND DIFFERENTIAL EXPRESSION AMONG RHABDOMERIC OPSINS REVEAL FUNCTIONAL CHANGE AFTER GENE DUPLICATION IN THE BAY SCALLOP, ARGOPECTEN IRRADIANS (PECTINIDAE) ....... 20 Abstract ................................................................................................................................................... 21 Background ............................................................................................................................................. 22 Methods .................................................................................................................................................. 26 Results ..................................................................................................................................................... 33 Discussion ............................................................................................................................................... 39 Conclusions ............................................................................................................................................. 44 Acknowledgments .................................................................................................................................. 46 References ............................................................................................................................................... 46 CHAPTER III. DIFFERENT EVOLUTIONARY TRAJECTORIES BETWEEN GQ-OPSIN PARALOGS SAMPLED ACROSS SCALLOPS ......................................................................... 77 Abstract ................................................................................................................................................... 77 Introduction ............................................................................................................................................. 78 Methods .................................................................................................................................................. 82 Results ..................................................................................................................................................... 95 Discussion ............................................................................................................................................. 104 References ............................................................................................................................................. 109 iv CHAPTER IV. THE DISADVANTAGE OF IGNORING ALLELIC VARIATION WITH AN EMPHASIS ON SCALLOP PHOTOSENSORY ALLELES .............................................. 137 Abstract ................................................................................................................................................. 137 Introduction ........................................................................................................................................... 138 Methods ................................................................................................................................................ 144 Results ................................................................................................................................................... 147 Discussion ............................................................................................................................................. 149 References ............................................................................................................................................. 153 CHAPTER V. CONCLUSIONS ................................................................................................ 166 v LIST OF FIGURES Figure 1-1 Topographical model of Gq-opsin ........................................................................ 18 Figure 1-2 A sagittal cross-section of the scallop eye showing all ocular components present at the adult stage ...................................................................................... 19 Figure 2-1 Amino acid alignment of Gq-opsins from scallop (Air-OPNGq1-OPNGq4) and squid, Todarodes pacificus (Tpa-OPNGq1) ................................................. 66 Figure 2-2 Maximum likelihood (ML) topology of Gq-opsins .............................................. 67 Figure 2-3 38 amino acid sites predicted to interact with chromophore in Gq-opsins .......... 69 Figure 2-4 Expression profiles of scallop Gq-opsin genes across three tissues from a single light-treated animal .................................................................................... 70 Figure 2-5 An evolutionary hypothesis describing Gq-opsin duplications in Pectinioidea ... 71 Figure 2-S1 Bayesian inference phylogram of Gq-opsins ........................................................ 73 Figure 2-S2 Maximum likelihood phylogram of Gq-opsins………………………………….75 Figure 2-S3 Fifty base pair alignment of 5’- and 3’-UTRs from the four scallop Gq-opsins .. 76 Figure 3-1 Gq-opsin gene tree .............................................................................................. 128 Figure 3-2 Sequence variation of Gq-opsins ........................................................................ 129 Figure 3-S1 CODEML tests................................................................................................... 130 Figure 4-1 OPNGq1 and OPNGq2 amino acid sequence variation across scallops ............ 165 vi LIST OF TABLES Table 2-1 Percent similarity (below diagonal) and RMSD (above diagonal) of scallop (Air) and squid (Tpa) proteins ............................................................................. 57 Table 2-2 Sequence and structural motifs in scallop (Air) and squid (Tpa) Gq-opsins ........ 58 Table 2-S1 Primers used to amplify scallop Gq-opsins and intergenic region between Air-opnGq3 and Air-opnGq4 ............................................................................... 59 Table 2-S2 Gq-opsin sequences included in the phylogenetic analysis .................................. 60 Table 2-S3 Ramachandran