Processes and drivers of Prosopis invasions in Eastern Africa By María Loreto Castillo1 December 2019 Thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy in the Faculty of Science at Stellenbosch University Principal supervisor: Prof. Jaco Le Roux1,2 Co-supervisor: Prof. Brian W. van Wilgen1, Dr. Urs Schaffner3 1DST-NRF Centre of Excellence for Invasion Biology, Department of Botany & Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa. 2Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia 3CABI, Rue de Grillons 1 , CH-2800 Delémont, Switzerland Stellenbosch University https://scholar.sun.ac.za CONTENTS CONTENTS ............................................................................................................................................... ii DECLARATION ......................................................................................................................................... v ABSTRACT ............................................................................................................................................... vi OPSOMMING ......................................................................................................................................... ix ACKNOWLEDGEMENTS ......................................................................................................................... xii LIST OF TABLES ......................................................................................................................................xiv LIST OF FIGURES ................................................................................................................................... xvii CHAPTER 1 General Introduction ....................................................................................................... 1 1.1 Introduction ............................................................................................................................. 1 1.2 Motivation, aims and thesis structure .................................................................................... 6 1.3 Study sites ............................................................................................................................... 7 1.4 Study species ........................................................................................................................... 8 CHAPTER 2 Taxonomic uncertainty and genetic insights into the globally invasive tree genus Prosopis ....................................................................................................................................... 16 2.1 Introduction ........................................................................................................................... 17 2.2 Materials and methods ......................................................................................................... 20 a) Sampling and DNA extraction ............................................................................................... 20 b) Phylogenetic analysis ............................................................................................................ 24 c) Microsatellite genotyping ..................................................................................................... 25 d) Genetic diversity .................................................................................................................... 25 e) Genetic structure and hybridization ...................................................................................... 26 f) Genetic differentiation .......................................................................................................... 28 2.3 Results ................................................................................................................................... 28 a) Phylogenetic analysis ............................................................................................................ 28 b) Genetic diversity .................................................................................................................... 29 c) Genetic structure and hybridization ...................................................................................... 31 d) Genetic differentiation .......................................................................................................... 35 2.4 Discussion .............................................................................................................................. 37 Uncertainty in Prosopis taxonomy ................................................................................................ 37 Hybridization, polyploidy and genetic diversity ............................................................................ 40 Invasion history of Prosopis .......................................................................................................... 43 Implications for management and regulation .............................................................................. 44 2.5 Supporting information ........................................................................................................ 47 ii Stellenbosch University https://scholar.sun.ac.za CHAPTER 3 The roles of rapid evolution and phenotypic plasticity in promoting invasiveness: insights from Prosopis invasions in Eastern Africa ................................................................................ 56 3.1 Introduction .......................................................................................................................... 57 3.2 Materials and Methods ......................................................................................................... 60 a) Study species and study site .................................................................................................. 60 b) Reciprocal transplant experiment ......................................................................................... 62 c) Greenhouse experiment ........................................................................................................ 65 d) Statistical analysis ................................................................................................................. 66 3.3 Results ................................................................................................................................... 68 a) Reproductive output of mother trees .................................................................................... 68 b) Reciprocal transplant experiment ......................................................................................... 68 c) Greenhouse experiment ........................................................................................................ 73 3.4 Discussion .............................................................................................................................. 79 Phenotypic plasticity and invasiveness ......................................................................................... 79 Evidence for rapid post-introduction evolution ............................................................................. 80 Coping with environmental variation in the invaded range ......................................................... 82 3.5 Conclusion ............................................................................................................................. 83 3.6 Supporting information ........................................................................................................ 84 CHAPTER 4 Following the footsteps of invasion: genetic comparisons between founder and invasive Prosopis trees in Eastern Africa .............................................................................................. 87 4.1 Introduction ........................................................................................................................... 88 4.2 Methods ................................................................................................................................ 91 a) Study sites and study species ................................................................................................ 91 b) Samples collection and DNA extraction ................................................................................ 94 c) Genotyping ............................................................................................................................ 95 d) Evaluating allopolyploidy or autopolyploidy origin of P. juliflora ......................................... 96 e) Polyploidy, hybridization and population genetic structure ................................................. 96 f) Genetic analysis of stages of invasion................................................................................... 98 g) Landscape genetic analysis ................................................................................................... 99 4.3 Results ................................................................................................................................. 101 a) Evaluating allopolyploidy or autopolyploidy origin of P. juliflora ....................................... 101 b) Polypoidy, hybridization and population genetic structure ................................................ 102 c) Genetic analysis of stages of invasion................................................................................