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The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgementTown of the source. The thesis is to be used for private study or non- commercial research purposes only. Cape Published by the University ofof Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University The spatial and temporal dynamics of diversification in Tylecodon, Cotyledon and Adromischus (Crassulaceae) in southern Africa. Town by Cape Tracey Lof Nowell University Thesis presented for the degree of Doctor of Philosophy in the Department of Botany, Faculty of Science, University of Cape Town February 2008 The spatial and temporal dynamics of diversification in Tylecodon, Cotyledon and Adromischus (Crassulaceae) in southern Africa. Town by Cape Tracey L.of Nowell University Thesis presented for the degree of Doctor of Philosophy in the Department of Botany, Faculty of Science, University of Cape Town February 2008 DECLARATION I confirm that this is my own work and the use of all material from other sources has been properly and fully acknowledged below or in the appropriate section of this thesis. • The majority of plant material used for DNA work was suppliedTown by Peter V. Bruyns. All such material is indicated by collector number in Table 1.1 of Chapter 1. • A large amount of the geographic data was supplied by Peter V. Bruyns in the form of an edited and supplemented version of data available on the PRECIS database. • Geo-referencing of all accession data used in CapeChapter 4 was carried out by Matthew Lewis. of • Awot Kiflu helped with measurements for sympatry calculations used in Chapter 4. University Tracey L. Nowell ABSTRACT A molecular phylogenetic hypothesis was generated for Tylecodon, Cotyledon and Adromischus in order to estimate the timing and spatial dynamics of diversification across these three southern African genera. These data were used to investigate the correlates and consequences of adaptations to extreme aridity and summer drought in members of the group. Molecular sequence data from three plastid regions (trnL-F, psbA-trnH and rpoB-trnC), together with nuclear ITS1 and 2 were produced and used to estimate phylogenetic relationships among and within the three focal genera. Bayesian and parsimony-based analysesTown of combined data supported the monophyly of Cotyledon and Adromischus, however Tylecodon was found to be polyphyletic as T. racemosus was recovered as sister to Adromischus. The level of genetic divergence exhibited by T. racemosus necessitatedCape its elevation to a new genus, thus Toelkenocodon was erected to accommodate the lineage. Relationships within Cotyledon were resolved and well-supported, and some well-supportedof clades were recovered within Tylecodon and Adromischus. Broad patterns of flowering phenology and geographic distributions emerged across the genera. Resolution at the level of species was generally poor within Tylecodon and Adromischus due to low sequence divergence. Divergence time estimationUniversity was performed to test hypotheses of climate-driven diversification in the genera focal to this study. Four methods were used: NPRS and Multidivtime, both of which assume autocorrelation of rates between ancestor-descendent lineages, a global molecular clock, and a relaxed phylogenetics approach that Simultaneously estimates phylogeny and divergence times (BEAST). Topology based tests for significant shifts in diversification rate were used, and parsimony and likelihood ancestral reconstruction of the transition to succulent karoo endemism across the group was performed. Diversity within the genera was found to be relatively young, although there was variation among the dating methods, with NPRS and Multidivtime returning older dates for events than either the molecular clock or BEAST. Diversification events among 11 and within Tylecodon, Cotyledon and Adromischus were coincident with major climatic events hypothesised to be drivers of speciation in the south-west of southern Africa during the late Miocene and early Pliocene. Tylecodon exhibits significantly higher rates of diversification than either Cotyledon or Adromischus. No significant shifts in diversification rates were detected across the phylogeny of the group and species accumulation appears to have been more or less linear throughout the separate histories of the genera. A clade of succulent karoo endemic species was identified in Tylecodon and the timing of the transition to this vegetation type occurred between 5.5 and 3.2 Myr, consistent with the establishment of the winter rainfall regime in the region. Data from a related study which involved estimating the timing of shifts to succulent karoo endemism in distantly related angiosperm groups corroborated this pattern. The majority of instances of endemism emerged during the last 5 Myr suggesting thatTown the succulent karoo is considerably younger than the neighbouring fynbos biome. Analyses of range size characteristics of Tylecodon andCape Cotyledon demonstrated that species of Tylecodon have significantly smaller ranges thanof species of Cotyledon. The hypothesis that range size is determined by plant size and the height at which seeds are released (the sum of vegetative height and inflorescence height) was tested and a positive relationship was found in Tylecodon, but not in Cotyledon. Further correlation-regression analyses revealed significant associations between the height of vegetative organs, inflorescences and the size of flowers in Tylecodon. Thus it was proposed that the proclivity of species with small ranges in Tylecodon is the result of limited Universitydispersal. The expectation for the geographical mode of speciation under such a scenario is one of allopatry. Age-range correlations revealed that the predominant mode of speciation in both Tylecodon and Cotyledon is allopatric. The hypothesis that Cotyledon and Tylecodon occupy different climatic niches was tested using using discriminant function analysis. The genera could be distinguished along an axis of increasing summer drought and potential evaporation. Species of Tylecodon occupy niches concentrated at the arid extremes of conditions where summer drought prevails: Cotyledon is III largely absent from these areas. The shift into arid environments in Tylecodon coincides with the evolution of putative morphological adaptations, including leaf deciduousness and vegetative diminution which likely represent evolutionary innovations that enabled ancestral forms of Tylecodon to colonise new habitats created during the formation of the winter rainfall desert of the succulent karoo. Passive dispersal coupled with the morphological adaptations exhibited by species of Tylecodon have led to the strong association observed between range size and plant size, such that small plants are effectively isolated in microhabitats; a factor which is likely to enable differentiation as a result of highly restricted gene flow. The increased stature of plants of Cotyledon and the fact that inflorescence height is uncoupled from vegetative height, may lead to the relative mobility of propagules of members of the genus. Species can disperse more broadly, gene flow sustains the genetic integrity of species, and they are able toTown colonise new areas. Cape of University IV ACKNOWLEDGEMENTS I am extremely indebted to my supervisor Tony Verboom. He has been a tremendous source of ideas during the course of this work and has been on hand throughout to provide me with advice, support, and feedback. I gained considerable knowledge and learned many new skills through my interactions with Tony, and it is under his guidance that this project grew into something coherent. This project was co-supervised by Jeremy Midgley. I am very grateful for his wise words, encouragement and pragmatism. Most of this research was funded by NRF grants awarded to Terry Hedderson. My thanks to Terry for supporting my research generously, and for the many stimulating discussions we had and ideas that he gave me during the 'early years' of this work. I received funds from the University of Cape Town in the form of the JW Jagger Award for international students and from the Dorothy Cameron Fund held by the Department of Botany, UCT. These funds were greatly appreciated and kept me fed and watered for a good part of my PhD. The thorough species sampling in this project is the result of extensive field collection by Peter Bruyns. I would like to thank him for sharing this material with me, and Townfor useful comments on an earlier version of Chapter 1. My thanks to Krystal Tolley and John Donaldson at the Kirstenbosch Research Centre for their generosity in providing me with space and resources during the final year of my PhD. This contributed enormously to the progress of my work during this time. The KRC is a great environment to work in, and I thank everyone there for Capemaking me feel so welcome. I look forward to the opportunity of working with you all in the nearof future. I am grateful to Nick Lindenberg at UCT and Granville van Ross at SANBI, Kirstenbosch for lots of help and advice with the GIS work, and to Matthew Lewis and Awot Kiflu for their input. Thanks to everyone in the Department of Botany at UCT for making it a vibrant and friendly place to work. I would particularly like to thank Sandy Smuts for lots of support and resourcefulness over the years. Mike, Judy and Fred, I am completely overwhelmed by your generosity and patience. I
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