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The visual opsins of the starry flounder (Platichthys stellatus), a new model for studying the physiological and molecular basis of fish vision and light sensitivity. by Thomas Iwanicki BSc, University of Victoria, 2013 A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE in the Department of Biology Thomas Iwanicki, 2016 University of Victoria All rights reserved. This thesis may not be reproduced in whole or in part, by photocopy or other means, without the permission of the author. ii Supervisory Committee The visual opsins of the starry flounder (Platichthys stellatus), a new model for studying the physiological and molecular basis of fish vision and light sensitivity. by Thomas Iwanicki BSc, Univeristy of Victoria, 2013 Supervisory Committee Dr. John S. Taylor, the Department of Biology Supervisor Dr. Robert L. Chow, the Department of Biology Departmental Member Dr. John F. Dower, the Department of Biology Departmental Member Dr. Jürgen Ehlting, the Department of Biology Departmental Member iii Abstract Supervisory Committee Dr. John S. Taylor, the Department of Biology Supervisor Dr. Robert L. Chow, the Department of Biology Departmental Member Dr. John F. Dower, the Department of Biology Departmental Member Dr. Jürgen Ehlting, the Department of Biology Departmental Member Ray-finned fish from a diversity of distantly related lineages have remarkably large visual opsin repertoires. Starry flounder (Platichthys stellatus) development, morphology, life history, and behavior make this species especially suitable for experiments designed to determine why fish have so many opsins. Human and bird colour vision uses three and five opsins, respectively. Fish often have many more opsins. We sequenced an eye transcriptome to determine the starry flounder opsin repertoire, and used high performance liquid chromatography to determine the chromophore content of the retina. We found eight visual opsins that utilize only 11-cis-retinal (vitamin A1). This species’ entire visual opsin toolkit appears to be functional. The number of distinct cone and rod cell absorbance profiles determined using microspectrophotomery are consistent with the number of visual opsins in the transcriptome. RH2 transcripts were more abundant and SWS1 and SWS2 transcripts were less abundant in the dorsal retina, where cone density was highest, outer segments the longest, and where we observed double cones with outer segments that differed in their wavelength of maximum absorbance. Regions of fish iv retinas appear to be specialized and I predict that this fine-tuning is enhanced by photoreceptor plasticity and opsin gene duplication and divergence. Studies that compare opsin expression patterns among individuals, populations, or species typically assume that the differences observed influence vision. Direct connections between opsin expression and quantitative behaviours are rare. This thesis aimed to test whether varying opsin expression affects vision by modifying opsin expression and characterizing vision in starry flounder. We held starry flounder in aquaria exposed to either broad spectrum sunlight or green-filtered light. We tested vision by quantifying the visually-mediated camouflage response and we measured opsin expression using digital-PCR. Granularity analysis of photographs of the camouflage response revealed higher overall pattern energy at each of the seven spatial frequency bands in fish exposed to broad spectrum sunlight compared to the green-filtered fish. However, no statistical difference in typical measurements of pattern or contrast (e.g., maximum filter size, the standard deviation of pattern energy, and the proportional power) was observed between the two groups. Opsin expression was different between fish held in the green light environment compared to those exposed to broad spectrum light. SWS1 (UV sensitive) and SWS2B (blue sensitive) were significantly down regulated in response to the green light environment. Surprisingly, this difference was lost after only three hours under a white LED light, suggesting rapid changes in opsin expression in response to the light environment. We found tantalizing, albeit not statistically significant evidence that fish with higher expression of UV- and blue- wavelength sensitive opsins could see more contrast in colour on blue-green checkerboards. v Table of Contents Supervisory Committee ...................................................................................................... ii Abstract .............................................................................................................................. iii Table of Contents ................................................................................................................ v List of Tables .................................................................................................................... vii List of Figures .................................................................................................................. viii Acknowledgments............................................................................................................. xii Dedication ........................................................................................................................ xiii Chapter 1 – General introduction ........................................................................................ 1 Background ..................................................................................................................... 1 Motivation for this study ............................................................................................. 1 Spectral tuning of the retina ........................................................................................ 5 Starry flounder as a new model for visual ecology..................................................... 8 Research objectives ....................................................................................................... 11 Chapter 2 – Characterization of the starry flounder visual system: opsins, chromophores, and histology ..................................................................................................................... 13 Introduction ................................................................................................................... 13 Materials and Methods .................................................................................................. 14 Fish collection and preparation ................................................................................. 14 Histology ................................................................................................................... 14 RNA Isolation and RNA-Seq.................................................................................... 16 Phylogenetic analyses ............................................................................................... 18 High performance liquid chromatography ................................................................ 18 Microspectrophotometry ........................................................................................... 20 Digital PCR ............................................................................................................... 20 Results ........................................................................................................................... 22 Cone photoreceptor types and their distributions ..................................................... 22 Opsin repertoire ........................................................................................................ 29 Retinal chromophore content .................................................................................... 31 Visual pigments ........................................................................................................ 33 Opsin expression ....................................................................................................... 35 Discussion ..................................................................................................................... 38 Visual opsin repertoire and visual pigments ............................................................. 38 Retinal specializations for benthic existence in shallow waters ............................... 40 Contributions by collaborators ...................................................................................... 45 Chapter 3 – Light induced changes in opsin expression and its influence on visual ability estimated using a camouflage-based behavioural assay ................................................... 46 Introduction ................................................................................................................... 46 Methods......................................................................................................................... 51 Fish Collection and Light Environment .................................................................... 51 Behavioural Assay .................................................................................................... 54 Image Analysis.......................................................................................................... 56 RNA isolation and digital PCR ................................................................................. 58 vi Results ..........................................................................................................................
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