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University of Florida Thesis Or Dissertation Formatting PATTERNS OF COEVOLUTION BETWEEN SYMBIOTIC FUNGI, BACTERIA AND SCOLYTINE BEETLES By CRAIG C. BATEMAN A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2018 © 2018 Craig C. Bateman This dissertation is dedicated to Chris DiFonzo 3 ACKNOWLEDGMENTS I thank my committee members, Jiri Hulcr, Andrea Lucky, Kirsten Pelz-Stelinski, and Jason Smith for direction and instruction. I thank my senior Hulcr lab members Caroline Storer, Andrew Johnson, James Skelton, Michelle Jusino, Martin Kostovcik, and Adam Black for their advisement, moral support, and collaboration. I thank my many collaborators at other institutions for their invaluable help in collecting and sharing of specimens and information, including Wang Bo, Li Lili, Liu Guangyu, Wissut Sittichaya, Park Ji-Hyun, Kim Mee Sook, Park Sangwook, Kim Moo-Sung, Malena Martinez, Jessenia Rosanna Castro Olaya, Rachel Osborn, Sarah Smith, Matthew Kasson, Chase Mayers, Anthony Cognato, and Miroslav Kolarik. I thank my parents, siblings, and friends for moral support, including Lynna Durst, Bryan Tarbox, Ashley Chapman, Verity Salmon, Hans Goertz, Ash Albinson, Anand Roopsind, Kyle Kehus, Sami Rifai, and Camille Truong. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 7 LIST OF FIGURES .......................................................................................................... 8 ABSTRACT ..................................................................................................................... 9 CHAPTER 1 INTRODUCTION .................................................................................................... 11 2 AMBROSIA BEETLE PREMNOBIUS CAVIPENNIS (SCOLYTINAE: IPINI) CARRIES HIGHLY DIVERGENT ASCOMYCOTAN AMBROSIA FUNGUS, AFRORAFFAELEA AMBROSIAE GEN. NOV. SP. NOV. (OPHIOSTOMATALES) .......................................................................................... 18 Methods .................................................................................................................. 21 Quantitative Culturing of Fungi from Beetle Mycangia ..................................... 21 DNA Extraction, Amplification, Library Preparation, and Sequencing .............. 22 Phylogenetic Analyses ..................................................................................... 23 Mycangium Presence and Content .................................................................. 24 Fungal Morphology on Agar Medium ............................................................... 26 Results .................................................................................................................... 26 Culturing of Fungi from Beetle Mycangia.......................................................... 26 Sequencing and Phylogenetic Analysis ............................................................ 27 Fungal Community Amplicon Analysis ............................................................. 27 Examination of Mycangia ................................................................................. 28 Taxonomy ......................................................................................................... 28 Discussion .............................................................................................................. 30 3 PATTERNS IN FUNGAL SYMBIONT FIDELITY AND DIVERSITY ACROSS TEN EVOLUTIONARY ORIGINS OF THE AMBROSIA SYMBIOSIS IN BEETLES (COLEOPTERA, CURCULIONIDAE: SCOLYTINAE) ............................ 42 Methods .................................................................................................................. 46 Sampling and Dissection .................................................................................. 46 DNA Extraction, Amplification, Library Preparation, and Sequencing .............. 47 Data Processing ............................................................................................... 48 Statistical Analyses .......................................................................................... 49 Phylogenetic Analyses ..................................................................................... 50 Results .................................................................................................................... 51 Fungal Community Sequencing ....................................................................... 51 Quantitative Culturing ....................................................................................... 52 5 Beetle-fungus Associations .............................................................................. 52 Discussion .............................................................................................................. 54 Symbiont Evolution and Fidelity ....................................................................... 54 Predictors of Primary Symbiont Communities .................................................. 55 Considerations for Fungal Community Sequencing ......................................... 58 Final Remarks .................................................................................................. 59 4 INBREEDING AND HAPLODIPLOIDY IN BARK AND AMBROSIA BEETLES (COLEOPTERA: CUCRCULIONIDAE: SCOLYTINAE) IS NOT CORRELATED WITH THE PRESENCE OF INTRACELLULAR BACTERIA ................................... 71 Methods .................................................................................................................. 74 Taxon Sampling ............................................................................................... 74 DNA Extraction and PCR ................................................................................. 75 Sample Pooling and High-Throughput Sequencing .......................................... 76 Data Processing ............................................................................................... 77 Phylogenetic Analysis of the Beetles ................................................................ 78 Results .................................................................................................................... 79 Sequencing ...................................................................................................... 79 Potential Reproductive Manipulators ................................................................ 79 Discussion .............................................................................................................. 80 5 CONCLUSIONS ..................................................................................................... 92 LIST OF REFERENCES ............................................................................................... 95 BIOGRAPHICAL SKETCH .......................................................................................... 108 6 LIST OF TABLES Table page 2-1 Species of Sordariomycetidae and Xylariales from used for phylogenetic analyses ............................................................................................................. 38 3-1 Summary of collection information for beetles sampled. .................................... 64 3-2 Summary of associations between beetle species and OTUs with taxonomy assignment. The OTUs included were significantly associated (p<.02) by the Indicator Species Analysis. Beetles marked with * were only represented by a single specimen. .............................................................................................. 67 3-3 Prevalence (% of specimens) and abundance (mean colony forming units) of fungi isolated from ambrosia beetle mycangia.................................................... 69 3-4 Results of the permutations-based multivariate analysis of variance (PERMANOVA) showing the effect of fungal symbiont presence on host ecology. .............................................................................................................. 70 4-1 Taxon sampling with sex-determination systems and inbreeding character states. Pairs of phylogenetically related species differing in reproductive system are shown in alternating background colours. ........................................ 85 4-2 Collection localities and number of specimens included for all samples used in miseq community sequencing. ........................................................................ 86 4-3 Taxa used in the 28S phylogenetic analysis of the beetles, with accompanying GenBank accession codes ......................................................... 88 4-4 Results of the permutations-based multivariate analysis of variance (PERMANOVA) showing the effect of intracellular bacteria presence on inbreeding in scolytine beetles. ........................................................................... 89 7 LIST OF FIGURES Figure page 2-1 Best ML tree from GARLI analysis of 18S, 28S rDNA, and βT (introns 3/4/5 removed) data matrix of Sordariomycetidae with Xylariales outgroup. Values at nodes represent ML bootstrap percentages ................................................... 34 2-2 A-B. Colony on PDA at 8th day. C-D. Colony on PDA after 14 d. E-F. Aerial hyphae, showing intercalary melanization and denticulate distal hyphae. G-H. Immersed hyphae. I-J. Monillioid hyphae. .........................................................
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