Niches, Distributions and Phylogenies A case study in Mosannona (Annonaceae) MSc-Thesis R.A. Wilschut Reg. nr. 890202960010 Supervisor: L.W. Chatrou Wageningen University and Research Centre October 2012 Contents Preface ....................................................................................................................................................... 3 Summary .................................................................................................................................................... 4 Introduction ............................................................................................................................................. 4 Methods ................................................................................................................................................... 4 Results and Discussion ............................................................................................................................... 4 Introduction ................................................................................................................................................ 5 Neotropical plant diversification ................................................................................................................... 5 Ecological niche conservatism ..................................................................................................................... 6 Ecological niche modelling .......................................................................................................................... 6 Phyloclimatic modelling .............................................................................................................................. 7 Mosannona ............................................................................................................................................... 7 Aim and hypotheses .................................................................................................................................. 8 Methods ..................................................................................................................................................... 9 Plant collections ........................................................................................................................................ 9 Morphological analyses............................................................................................................................... 9 Lab work .................................................................................................................................................. 9 DNA-Extraction ...................................................................................................................................... 9 Measuring DNA-concentrations ................................................................................................................. 9 DNA-amplification ................................................................................................................................... 9 Gel-electrophoresis ............................................................................................................................... 10 PCR-product cleaning ............................................................................................................................ 10 Cycle sequencing .................................................................................................................................. 10 Sequence editing and aligning ................................................................................................................ 11 Phylogenetic analyses .............................................................................................................................. 11 Species distribution modelling ................................................................................................................... 11 Data layers .......................................................................................................................................... 11 Modelling ............................................................................................................................................ 11 Niche overlap tests .................................................................................................................................. 12 Model performance tests .......................................................................................................................... 12 Data type ............................................................................................................................................ 12 Record number .................................................................................................................................... 12 Phyloclimatic modelling ............................................................................................................................ 12 Data extraction .................................................................................................................................... 12 Optimization ........................................................................................................................................ 13 Results ..................................................................................................................................................... 14 Morphological analyses............................................................................................................................. 14 Floral characters ................................................................................................................................... 14 Vegetative characters ............................................................................................................................ 14 Lab work ................................................................................................................................................ 14 1 Phylogenetic analyses .............................................................................................................................. 15 Topology ............................................................................................................................................. 15 Dating ................................................................................................................................................ 16 Species distribution modelling ................................................................................................................... 17 Niche overlap tests .................................................................................................................................. 17 Model performance tests .......................................................................................................................... 17 Record number .................................................................................................................................... 17 Data type ............................................................................................................................................ 20 Phyloclimatic modelling ............................................................................................................................ 21 Data ................................................................................................................................................... 21 Optimizations ....................................................................................................................................... 22 Discussion ................................................................................................................................................ 25 Sequence data ........................................................................................................................................ 25 Phylogeny & Dating ................................................................................................................................. 25 Phylogeny ........................................................................................................................................... 25 Dating ................................................................................................................................................ 25 Biogeography ......................................................................................................................................... 26 Morphology and taxonomy ........................................................................................................................ 27 M. costaricensis s.l. ............................................................................................................................... 27 M. hypoglauca ...................................................................................................................................... 27 Phyloclimatic modelling ............................................................................................................................ 27 Parameter selection .............................................................................................................................. 27 Optimizations and phylogenetic signal tests