Evidence for Genetic Decline Within Afromontane Forest Fragments on the Mambilla Plateau, Nigeria A thesis submitted in partial fulfilment of the requirements for the Degree of Master of Science in Biological Sciences at the University of Canterbury Lily E. Brailsford University of Canterbury March 2018 1 Table of Contents Acknowledgements ....................................................................................................................................... 4 Equations, Figures, and Tables ...................................................................................................................... 5 CHAPTER 1. Introduction ............................................................................................... 7 1.1 The Value of Genetic Diversity ...................................................................................... 7 1.1.1 Genetic diversity as a component of biodiversity. ............................................................ 7 1.1.2 Conservation genetics beyond rare species. ..................................................................... 9 1.1.3 Microsatellites in population genetics ............................................................................ 11 1.2 Afromontane Forests ................................................................................................. 12 1.2.1 Biodiversity of the Afromontane archipelago ................................................................. 12 1.2.2 Ecosystem services .......................................................................................................... 14 1.2.3 Threats and conservation ................................................................................................ 14 1.2.4 Conservation genetics of African trees ........................................................................... 16 1.3 This Thesis ................................................................................................................. 17 1.3.1 Mambilla Plateau ............................................................................................................ 17 1.3.2 Sampling sites .................................................................................................................. 21 1.3.3 Thesis outline .................................................................................................................. 22 References: ................................................................................................................................................. 23 CHAPTER 2. Genetic Diversity and Population Structure of Albizia gummifera ............. 30 Abstract ....................................................................................................................................................... 30 2.1 Introduction .............................................................................................................. 30 2.1.1 Population genetics in ecological restoration ................................................................. 30 2.1.2 Ecological restoration at Ngel Nyaki ............................................................................... 31 2.1.3 Genetic rescue ................................................................................................................. 32 2.1.4 Study species ................................................................................................................... 33 2.1.5 Research goals ................................................................................................................. 34 2.2 Methods .................................................................................................................... 35 2.2.1 Study sites and sample collection ................................................................................... 35 2.2.2 DNA extraction ................................................................................................................ 35 2.2.3 Microsatellite optimisation. ............................................................................................ 35 2.2.4 Microsatellite amplification and genotyping .................................................................. 36 2.2.5 Data analysis.................................................................................................................... 36 2.3 Results ....................................................................................................................... 38 2.3.1 Chloroplast loci ................................................................................................................ 38 2.3.2 Nuclear loci ...................................................................................................................... 45 2.4 Discussion .................................................................................................................. 49 2.4.1 Identification of microsatellite loci ................................................................................. 49 2.4.2 Genetic diversity ............................................................................................................. 50 2.4.3 Genetic differentiation and population structure .......................................................... 51 2.4.4 Restoration implications ................................................................................................. 53 2.4.5 Conclusions ..................................................................................................................... 54 References: ................................................................................................................................................. 54 2 CHAPTER 3. Genetic Diversity and Population Structure of Clausena anisata ............... 60 Abstract ....................................................................................................................................................... 60 3.1 Introduction .............................................................................................................. 60 3.1.1 Biodiversity value of sacred forests ................................................................................ 60 3.1.2 Sacred forests of the Mambilla Plateau .......................................................................... 62 3.1.3 Study species ................................................................................................................... 62 3.1.4 Research goals ................................................................................................................. 64 3.2 Methods .................................................................................................................... 64 3.2.1 Study sites, sample collection and DNA extraction......................................................... 64 3.2.2 Microsatellite optimisation ............................................................................................. 64 3.2.3 Microsatellite amplification, genotyping, and data analysis .......................................... 64 3.3 Results ....................................................................................................................... 65 3.3.1 Chloroplast loci ................................................................................................................ 65 3.3.2 Nuclear loci ...................................................................................................................... 73 3.4 Discussion .................................................................................................................. 77 3.4.1 Identification of microsatellite loci ................................................................................. 77 3.4.2 Genetic diversity and population structure .................................................................... 78 3.4.3 Conservation implications ............................................................................................... 80 3.4.4 Conclusions ..................................................................................................................... 81 References: ................................................................................................................................................. 82 CHAPTER 4. Does Dispersal Mechanism Influence Genetic Structure in Two Common Tree Species? ................................................................................................................ 87 Abstract ....................................................................................................................................................... 87 4.1 Introduction .............................................................................................................. 87 4.1.1 Seed dispersal in fragmented landscapes ....................................................................... 87 4.1.2 Estimating gene flow ....................................................................................................... 88 4.1.3 Genetic comparisons between species ........................................................................... 90 4.2 Methods .................................................................................................................... 92 4.3 Results ....................................................................................................................... 92 4.4 Discussion .................................................................................................................