Phylogeography and population biology of Chrysoporthe austroafricana and allied species by NICOLAAS ALBERTUS VAN DER MERWE A thesis submitted in partial fulfilment 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 2012 © University of Pretoria Declaration I, the undersigned, hereby declare that the thesis submitted herewith for the degree Philosophiae Doctor to the University of Pretoria, contains my own independent work and has not been submitted for any degree at any other University. ______________________________ Nicolaas A. van der Merwe © University of Pretoria Table of Contents Acknowledgements .......................................................................................................... 7 Preface ................................................................................................................................. 9 CHAPTER 1 What is a fungal species?................................................................................................ 12 Introduction............................................................................................................................................................................... 13 A unified species concept................................................................................................................................................. 15 Species recognition criteria in the Ascomycota................................................................................................... 17 Recognizing species using phenotype...................................................................................................................................17 Biological species recognition......................................................................................................................................................20 Phylogenetic species recognition..............................................................................................................................................22 Evolutionary factors that confound species boundaries and their recognition............................. 23 Sex and hybridization .........................................................................................................................................................................24 Horizontal gene transfer ...................................................................................................................................................................26 Incomplete lineage sorting and cryptic speciation complicates recognition ...............................................27 What is the best definition of a species? ................................................................................................................. 28 Criterion – A pragmatic approach to species.....................................................................................................................28 Concept – A philosophical approach to species..............................................................................................................29 Prospects..................................................................................................................................................................................... 31 Tables............................................................................................................................................................................................. 34 Figures........................................................................................................................................................................................... 37 Bibliography............................................................................................................................................................................... 45 CHAPTER 2 Primers for the amplification of sequence-characterized loci in Cryphonectria cubensis populations....................................................................................................... 66 Abstract ........................................................................................................................................................................................ 67 Introduction............................................................................................................................................................................... 68 Materials and Methods....................................................................................................................................................... 68 3 © University of Pretoria Results ........................................................................................................................................................................................... 69 Discussion................................................................................................................................................................................... 70 Acknowledgements ............................................................................................................................................................. 71 Tables............................................................................................................................................................................................. 72 Bibliography............................................................................................................................................................................... 75 CHAPTER 3 Multigene phylogenetic and population differentiation data confirm the existence of a cryptic species within Chrysoporthe cubensis................................... 77 Abstract ........................................................................................................................................................................................ 78 Introduction............................................................................................................................................................................... 79 Materials & Methods............................................................................................................................................................. 81 Isolates and DNA extraction...........................................................................................................................................................81 Phylogenetic analyses .......................................................................................................................................................................82 Population genetic analyses..........................................................................................................................................................83 Morphology .............................................................................................................................................................................................84 Results ........................................................................................................................................................................................... 85 Phylogenetic analyses .......................................................................................................................................................................85 Population differentiation analysis ............................................................................................................................................86 Taxonomy..................................................................................................................................................................................................87 Restriction enzyme-based DNA diagnostic........................................................................................................... 90 Discussion................................................................................................................................................................................... 90 Acknowledgements ............................................................................................................................................................. 94 Tables............................................................................................................................................................................................. 95 Figures........................................................................................................................................................................................... 99 Bibliography.............................................................................................................................................................................126 CHAPTER 4 Continental drift fails to explain allopatric speciation patterns of Diaporthalean tree pathogens...............................................................................................................133 Abstract ......................................................................................................................................................................................134