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Ecology and Genetic Diversity of Coryphodema Tristis on Eucalyptus Nitens in South Africa

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Ecology and Genetic Diversity of Coryphodema Tristis on Eucalyptus Nitens in South Africa Ecology and genetic diversity of Coryphodema tristis on Eucalyptus nitens in South Africa by DAWIT TESFAYE DEGEFU A thesis submitted in partial fulfillment of the degree Philosophiae Doctor in the Faculty of Natural and Agricultural Sciences Department of Genetics Forestry and Agricultural Biotechnology Institute University of Pretoria South Africa February 2014 Supervisor Prof. Bernard Slippers Co-Supervisors Prof. Michael J. Wingfield Dr. Brett Hurley Dr. Jeff Garnas © University of Pretoria DECLARATION I, Dawit Tesfaye Degefu declare that the thesis, which I hereby submit for the degree Philosophiae Doctor at the University of Pretoria, is my own work and has not previously been submitted by me for a degree at this or any other tertiary institution. Dawit Tesfaye Degefu February 2014 I © University of Pretoria DEDICATIONS This work is dedicated to my father Tesfaye Degefu Kassaye who passed away when I was in South Africa for my PhD study. It is also dedicated to all my family, my wife Frehiwot Aklilu and my lovely kids Henok Dawit and Bethelhem Dawit. II © University of Pretoria ACKNOWLEDGEMENTS First of all I would like to thank my God for giving me the patience and endurance for completing this thesis. And I would like to thank Him for all His help in my life. Without His help this thesis would not have been possible. I would like to express my deepest appreciation to my advisers Prof. Bernard Slippers, Dr. Brett Hurley, Dr. Jeff Garnas and Prof. Mike Wingfield for their support, guidance, encouragement and friendship throughout my post-graduate program. The lessons that I have learnt from them during this process of academic growth, especially in relation to my research, have fundamental value for my professional career. A sincere thank you also to my lab mates Alvaro Duran, Gudrun Dittrich-Schröder, Irene Barnes, Alisa Postma, Arista Fourie and Katrin Fitza for their friendship and making the Hearne-lab such a wonderful working environment. The financial support provided by the members of the Tree Protection Co-operative Programme (TPCP), the Department of Science and Technology (DST)/ National Research Foundation (NRF) Center of Excellence in Tree Health Biotechnology and the University of Pretoria are also gratefully acknowledged. Finally, I would like to thank my wife Frehiwot Aklilu, especially for her patience and understanding during my doctoral research years and for her immense contribution to the success of this process. Without her support and understanding it would have been immensely more difficult to commence and complete this post-graduate program. III © University of Pretoria Table of contents DECLARATION ............................................................................................................................. I ACKNOWLEDGEMENTS .......................................................................................................... III PREFACE ..................................................................................................................................... IX CHAPTER 1 .................................................................................................................................. 1 The threat of the cossidae to forest health with special reference to Coryphodema tristis and Chilecomadia valdiviana................................................................................................................ 1 ABSTRACT .................................................................................................................................... 1 INTRODUCTION .......................................................................................................................... 2 SYSTEMATICS AND CLASSIFICATION OF THE COSSIDAE ............................................... 4 BIOLOGY AND LIFE-CYCLE OF THE COSSIDAE ................................................................. 5 HOST ASSOCIATIONS OF THE COSSIDAE ............................................................................. 7 FACTORS CONTRIBUTING TO THE SUCCESS OF HOST PLANT SELECTION ................ 9 Pre-adaptation on closely related hosts ...................................................................................... 9 Plant secondary compounds...................................................................................................... 10 Escape from natural enemies .................................................................................................... 11 The role of symbiotic microbes ................................................................................................. 12 MANAGEMENT OF COSSIDAE ............................................................................................... 13 REFERENCES ............................................................................................................................. 19 TABLE .......................................................................................................................................... 38 IV © University of Pretoria FIGURES ...................................................................................................................................... 39 CHAPTER 2 ................................................................................................................................ 49 Parallel host range expansion in two unrelated cossid moths infesting Eucalyptus nitens on two continents .............................................................................................................................. 49 ABSTRACT .................................................................................................................................. 50 INTRODUCTION ........................................................................................................................ 51 MATERIALS AND METHODS .................................................................................................. 53 Sample collection and molecular procedures ........................................................................... 53 Molecular data analyses ........................................................................................................... 53 RESULTS AND DISCUSSION ................................................................................................... 54 REFERENCES ............................................................................................................................. 57 TABLES ....................................................................................................................................... 61 FIGURE ................................................................ ........................................................................ 63 CHAPTER 3 ................................................................................................................................ 64 Population genetics and origin of Coryphodema tristis recently colonizing non-native Eucalyptus nitens in South Africa .............................................................................................. 64 ABSTRACT .................................................................................................................................. 64 INTRODUCTION ........................................................................................................................ 65 MATERIALS AND METHODS .................................................................................................. 68 Sample collection ...................................................................................................................... 68 Cytochrome oxidase I sequence characterization ..................................................................... 68 Data analysis for COI mtDNA .................................................................................................. 71 V © University of Pretoria Amplified Fragment Length Polymorphism marker characterization ...................................... 71 Data analysis for AFLP markers .............................................................................................. 73 RESULTS ..................................................................................................................................... 75 Cytochrome Oxidase I sequence analysis ................................................................................. 75 Amplified fragment length polymorphism (AFLP) analysis ...................................................... 76 DISCUSSION ............................................................................................................................... 79 REFERENCES ............................................................................................................................. 84 TABLES ....................................................................................................................................... 91 FIGURES ...................................................................................................................................... 96 CHAPTER 4 .............................................................................................................................. 105 Yeast communities associated with Coryphodema tristis larvae and xylem tunnels in Eucalyptus nitens and Vitis vinifera ......................................................................................... 105 ABSTRACT ...............................................................
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