Cardinalfish (Apogonidae)
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Colour vision diversity in coral reef fishes: Cardinalfish (Apogonidae) Martin Luhrmann M.Sc., B.Sc. A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2018 The Queensland Brain Institute Abstract Colour vision is important for numerous behavioural tasks in animals, but the selective forces underlying the evolutionary diversification of colour vision remain poorly understood. The visual systems of fish are broadly tuned to environmental light conditions, yet this concept alone does not explain the full extent of variability found in their opsin proteins, the molecular building blocks of photopigments, and their corresponding photoreceptor spectral sensitivities. However, what other selective forces, environmental or behavioural, impact the evolution of colour vision variability in this group is unclear. Coral reef fishes, which boast stunningly diverse body colours and patterns, fascinating researchers for decades, are no exception to this. Thus, considering their great species, colour, and ecological diversity, these animals are ideal to study the many facetted nature of colour vision diversification. The objective of this thesis was to elucidate the mechanisms influencing colour vision diversification in one of the most abundant and diverse fish families found on tropical coral reefs world-wide: cardinalfishes (Apogonidae). These small fish are predominantly nocturnal foragers and aggregate in multispecies assemblages at refuge sites in and around coral heads during the day. Using molecular, physiological, anatomical and behavioural methods, I discovered that cardinalfish visual systems, specifically their colour vision, are remarkably diverse. Despite their nocturnal habits, cardinalfish express a broad palette of opsin genes, translating into cone photoreceptor spectral sensitivities ranging from violet (420 nm) to green/yellow (537 nm). Opsin expression and photoreceptor sensitivities furthermore showed potentially functional differentiation, and I identified microhabitat partitioning as a factor that contributes to this. Finally, I showed that opsin gene expression changes in response to altered light conditions in adult reef fish, and that these changes likely differ between distinct reef fish families. These findings expand our understanding of colour vision diversification among reef fishes by highlighting that even among predominantly nocturnally active species, colour vision appears to be vital. Furthermore, demonstrating the dynamic nature of reef fish opsin gene expression over short time spans and in response to environmental changes, as well as identifying microhabitat partitioning behaviour as a likely candidate for a factor contributing to colour vision diversification in cardinalfishes, revealed some aspects involved in the diversification of reef fish visual systems, while adding to the complexity of the system. ii Declaration by author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, financial support and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my higher degree by research candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis and have sought permission from co-authors for any jointly authored works included in the thesis. iii Publications during candidature Luehrmann, M.; Stieb, S. M.; Carleton, K. L.; Pietzger, A.; Cheney, K. L.; Marshall, N. J. (2018) Short term colour vision plasticity on the reef: Changes in opsin expression under varying light conditions differ between ecologically distinct reef fish species. Journal of Experimental Biology. doi:10.1242/jeb.175281 Publications included in this thesis Data from chapter 3 has been published as: Luehrmann, M.; Stieb, S. M.; Carleton, K. L.; Pietzger, A.; Cheney, K. L.; Marshall, N. J. (2018) Short term colour vision plasticity on the reef: Changes in opsin expression under varying light conditions differ between ecologically distinct reef fish species. Journal of Experimental Biology. doi:10.1242/jeb.175281 iv Submitted manuscripts included in this thesis Data from chapter 2 has been submitted for publication (02 Sep 2018, in review) as: Luehrmann, M.; Carleton, K. L.; Cortesi, F.; Cheney, K. L.; Marshall, N. J. Surprising visual pigment diversity in nocturnal reef fishes: the cardinalfish (Apogonidae). Molecular Ecology v Contributions by others to the thesis SM Stieb contributed to conception, experimentation, and manuscript editing of Chapter 3. F Cortesi helped during fieldwork with fish catching (Chapter 2 & 4), and microhabitat counts for Chapter 4. KL Carleton helped with λmax sequence calculations for Chapter 2. NJ Marshall and KL Cheney provided feedback and suggestions for drafts of the entire thesis. KL Carleton provided additional feedback and suggestions for drafts of Chapters two and three. F Cortesi provided feedback for drafts of Chapters two and four. Statement of parts of the thesis submitted to qualify for the award of another degree None. Research Involving Human or Animal Subjects Research was carried out with permission of the University of Queensland Animal Ethics Committee (AEC approval numbers: QBI/236/13/ARC/US AIRFORCE and QBI/304/16. vi Acknowledgements First of all, I want to express my gratitude to The University of Queensland and the Queensland Brain Institute for enabling me to conduct my PhD studies here in beautiful Australia. Thank you also to my supervisors, Justin Marshall and Karen Cheney, for putting trust in me by giving me the opportunity to join their research groups, and in doing so, allowing me to visit wonderful Lizard Island for fieldwork, travel to international conferences, and meet many fantastic people. I particularly want to thank Sara Stieb, who has been a wonderful mentor, colleague, office mate, and friend. Sara, I don’t think I would have lasted until the end if it hadn’t been for your encouragement and peace of mind. Equally big hugs and thanks I owe to Fabio Cortesi and Fanny de Busserolles, for being great teachers, office mates and friends. Thank you guys! Thank you Marshall and Cheney lab for having been a fantastic group of people to get to know and work with. Specifically, I want to express my gratitude to Wen-Sung Chung, who introduced me to the world of microspectrophotometry and managed to never be annoyed when I came running to ask for technical assistance. I am particularly grateful to have met Karen Carleton. It was a pleasure getting to know you, and I am especially thankful for you always having a friendly ear, as well as being inspirational. Thank you Janette Edson, manager of the QBI sequencing facility, for handling all my RNA sequencing needs, and providing troubleshoot expertise whenever needed. I also want to express my gratitude to my PhD committee members, Ian Tibbetts, Massimo Hilliard, Stephen Williams, and Bruno van Swinderen who kindly stepped in as backup committee Chair for my M2 milestone, and whose critical but extremely constructive feedback was instrumental in getting to the finish line. Thank you to all staff, present and past, at Lizard Island Research Station, you are doing a fantastic job, and I hope I will have opportunities to come and visit in the future. Thanks to Steve Doo and Alexia Landry, without whom months of unsuccessful fish training probably would have had a much heavier toll on me than it had in the end. vii Thank you Justin, Karen, Karen (Carleton), Fabio and Sara for all the time and effort put into providing feedback to my draft manuscripts. Thank you also to my thesis examiners. Finally, I want thank my friends and family for putting up with my grumpiness, and to the most important of you, for tolerating my being on the other side of the world… A special thanks to Tino, for keeping me sane, grounded, and making fur ensuring I did not starve during the last few months of writing. You are fantastic! viii Financial support This research was supported by a University of Queensland International living allowance stipend and a University of Queensland International tuition fee waiver stipend. Research was also funded by the Australian Research Council. Keywords cardinalfish, coral reef fish, colour vision, opsin, spectral tuning, niche partitioning,