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Molecular Diversity, Phylogeny, and Biogeographic Patterns of Crustacean Copepods Associated with Scleractinian Corals of the Indo-Pacific

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Molecular Diversity, Phylogeny, and Biogeographic Patterns of Crustacean Copepods Associated with Scleractinian Corals of the Indo-Pacific Molecular Diversity, Phylogeny, and Biogeographic Patterns of Crustacean Copepods Associated with Scleractinian Corals of the Indo-Pacific Dissertation by Sofya Mudrova In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy of Science King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia November, 2018 2 EXAMINATION COMMITTEE PAGE The dissertation of Sofya Mudrova is approved by the examination committee. Committee Chairperson: Dr. Michael Lee Berumen Committee Co-Chair: Dr. Viatcheslav Ivanenko Committee Members: Dr. James Davis Reimer, Dr. Takashi Gojobori, Dr. Manuel Aranda Lastra 3 COPYRIGHT PAGE © November, 2018 Sofya Mudrova All rights reserved 4 ABSTRACT Molecular diversity, phylogeny and biogeographic patterns of crustacean copepods associated with scleractinian corals of the Indo-Pacific Sofya Mudrova Biodiversity of coral reefs is higher than in any other marine ecosystem, and significant research has focused on studying coral taxonomy, physiology, ecology, and coral-associated fauna. Yet little is known about symbiotic copepods, abundant and numerous microscopic crustaceans inhabiting almost every living coral colony. In this thesis, I investigate the genetic diversity of different groups of copepods associated with reef-building corals in distinct parts of the Indo-Pacific; determine species boundaries; and reveal patterns of biogeography, endemism, and host-specificity in these symbiotic systems. A non-destructive method of DNA extraction allowed me to use an integrated approach to conduct a diversity assessment of different groups of copepods and to determine species boundaries using molecular and taxonomical methods. Overall, for this thesis, I processed and analyzed 1850 copepod specimens, representing 269 MOTUs collected from 125 colonies of 43 species of scleractinian corals from 11 locations in the Indo-Pacific. The genetic assessment of the most abundant copepod morphotypes associated with hermatypic corals in Lizard Island (Great Barrier Reef) revealed a large number of species previously unknown for this region. Analyses of diversity and patterns of biogeographical distribution of copepods associated with Galaxea corals throughout the Indo-Pacific showed that the species diversity of this group is high and appears to be 5 regionally specific, an uncommon pattern in most coral reef-associated invertebrates. Results for the symbiotic copepod fauna of Red Sea pocilloporid corals, a family of corals with a high level of morphological variability within and among its members, showed that the majority of the discovered poecilostomatoid copepods belong to the genus Spaniomolgus, which demonstrated a significant genetic diversity of morphologically-similar species. Assessment of the diversity of copepods associated with the Red Sea mushroom corals revealed several undescribed species and showed no evidence of specificity to the hosts neither on species nor on the family level, which contradicts a modern assumption of high host-specificity of copepods. Overall, this dissertation is a first study of genetic diversity of copepods associated with invertebrates, and it provides substantial insight into the diversity of coral-associated microcrustaceans and insight to patterns of their host-specificity as well as distribution around the Indo- Pacific. 6 ACKNOWLEDGMENTS I would like to express my sincere gratitude to my supervisor Dr. Michael Berumen for funding this project and providing guidance, help, and support throughout the course of this research. Very special thanks to my co-supervisor Dr. Slava Ivanenko for his academic and moral support, for sharing his collection of symbiotic copepods and his taxonomic expertise. Many thanks to my committee members Dr. Manuel Aranda Lastra, Dr. Takashi Gojobori, and Dr. James Davis Reimer for their feedback on the project and the dissertation. My special appreciation goes to Mikhail Nikitin, Dr. Diego Fontaneto, and Alejandro Martínez García for their assistance, feedback, and advice. I am very grateful to my friends and colleagues, the department faculty and staff for making my time at King Abdullah University of Science and Technology a great experience. Above all, I would like to express my gratitude to my husband and my parents for their support, faith, and confidence in me. 7 TABLE OF CONTENTS EXAMINATION COMMITTEE PAGE ........................................................................ 2 COPYRIGHT PAGE ........................................................................................................ 3 ABSTRACT ....................................................................................................................... 4 ACKNOWLEDGMENTS ................................................................................................ 6 TABLE OF CONTENTS ................................................................................................. 7 LIST OF ABBREVIATIONS .......................................................................................... 9 LIST OF FIGURES ........................................................................................................ 10 LIST OF TABLES .......................................................................................................... 13 Chapter 1: Background and literature review ............................................................. 15 1.1 Introduction ......................................................................................................................... 15 1.2 Symbiotic copepods ............................................................................................................. 17 1.3 Diversity of copepods associated with Scleractinia and their host-specificity .................... 21 1.4 Biogeography ...................................................................................................................... 25 1.5 Ecology and biology of the coral-associated copepods ....................................................... 27 1.5.1 Behavior, location on the host, and movement ........................................................ 27 1.5.2 Feeding preferences ................................................................................................. 32 1.5.3 Evolutionary traits and adaptations to symbiosis and parasitism on a coral ............ 33 1.5.4 Effect on coral hosts................................................................................................. 35 1.6 Molecular methods in the studies of diversity and taxonomy of copepods ......................... 37 1.7 Dissertation structure and objectives ................................................................................... 39 Chapter 2: General methodology .................................................................................. 41 2.1 Sampling procedures ........................................................................................................... 41 2.2 Morphological analyses ....................................................................................................... 42 2.2.1 Light microscopy ..................................................................................................... 42 2.2.2 Scanning electron microscopy ................................................................................. 43 2.2.3 Confocal microscopy ............................................................................................... 43 2.2.4 Coral identification .................................................................................................. 44 2.3 Molecular-phylogenetic analysis ......................................................................................... 44 2.3.1 DNA extraction ........................................................................................................ 44 2.3.2 Markers selection and DNA amplification .............................................................. 45 2.3.3 Sequence alignments and phylogenetic analyses ..................................................... 48 2.3.4 Species delimitation procedures .............................................................................. 50 Chapter 3: Genetic diversity of copepods associated with scleractinian corals in the Lizard Island (GBR) ....................................................................................................... 52 3.1 Introduction ......................................................................................................................... 52 3.2 Samples and study sites ....................................................................................................... 54 3.3 Results ................................................................................................................................. 57 3.3.1 PCR and sequencing ................................................................................................ 57 3.3.2 Genetic distances and species delimitation .............................................................. 58 8 3.3.3 Host specificity ........................................................................................................ 61 3.4 Discussion ............................................................................................................................ 62 3.5 Conclusion ........................................................................................................................... 67 Chapter 4: Biogeographic patterns, diversity,
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