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Seasonal Rainfall Regime Modulates Genetic Variation in the Moss Pseudocrossidium Crinitum

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Seasonal Rainfall Regime Modulates Genetic Variation in the Moss Pseudocrossidium Crinitum BOLUS LIBRAR Y C24 0008 5494 1111 II U 111111111 lll Seasonal rainfall regime modulates genetic variation in the moss Pseudocrossidium crinitum Nicholas Wilding UniversityOctober of 2009 Cape Town Honours degree Supervisor: Professor T.A.J. Hedderson The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town Acknowledgements I would like to thank Alastair Potts for his help and enthusiasm in collecting Pseudocrossidium crinitum in the Eastern Cape, his collections have proven invaluable for this study. Jeff Duckett and Howard Matcham provided the material from Lesotho and Chile, demonstrating the importance for bryologists to travel the world and make collections! Thanks to Tracey Nowell and Krystal Tolley for their willingness to tackle my issues with SAMOV A. You guys saved me hours of pulling my hair out! Many other people helped with running of analyses, thanks for your help (Terry, Yanis and Vera). Last but not least I would like to thank Terry Hedderson for his support and enthusiasm in this very cool project. This project made me realise how exciting and challenging science can be. 2 Abstract Patterns of genetic variation, resulting from Pliocene-Pleistocene climate shifts have been largely documented for species from Europe. However, little is known from Africa and especially South Africa, where climate shifts have often been invoked to explain the amazingly high diversity of the Cape Floristic Region. An analysis of cpDNA and nDNA sequence variation for 65 populations of the moss Pseudocrossidium crinitum across South Africa revealed the presence of a phylogeographic break corresponding to the split between the winter-rainfall zone (WRZ) and the all-year-(ARZ) and summer-rainfall zones (SRZ). Coalescent estimates of the time since these populations split (1.3 - 3.4 Mya) are highly consistent with the onset of winter-rainfall in the south-western Cape. Estimates of gene flow indicate much higher levels of gene flow into the WRZ, fitting the expected direction of gene flow based on wind patterns and differences in phenology. Haplotype diversity was observed to be highest in the WRZ, suggesting a number of genetic structuring factors in play within the WRZ. Additional analysis of populations from Chile and Lesotho suggest recent dispersal from Chile and possibly high levels of trans-continental gene flow between these populations. The study provides a first look at the genetic consequences of paleo-climate shifts on a moss species in South Africa. These results, in combination with other similar studies, may help to piece together the factors and processes responsible for the high diversity in the CFR today. 3 I Table of Contents ACKNOWLEDGEMENTS .................................................................................................................................. 2 ABSTRACT .......................................................................................................................................................... 3 TABLE OF CONTENTS ..................................................................................................................................... 4 TABLE OF FIGURES .......................................................................................................................................... 5 LIST OF TABLES ................................................................................................................................................ 6 INTRODUCTION ................................................................................................................................................ 7 MATERIAL AND METHODS ........................................................................................................................ 12 SAMPLING ....................... ................................................................................................................................................. 12 DNA EXTRACTION AND PCRAMPLIFICATION .......................................................................................................... 13 SEQUENCE DATA ANALYSIS ......................................... ................................................................. ......... ...................... 13 RESULTS ........................................................................................................................................................... 17 SEQUENCE DATA AND RECOMBINATION ................................................................ .. ................................................. 17 HAPLOTYPE NETWORKS .... .. ............ ............................................................................................................................. 17 I PHYLOGENETIC TREES ..................................................................................................................................... ............. 19 SPATIAL ANALYSIS OF MOLECULAR VARIANCE ........................................................................................................ 23 I ISOLATION WITH MIGRATION (IMA) ............................. ........... ....................................... ... .. ..................................... 23 DISCUSSION .................................................................................................................................................... 27 SEQUENCE VARIATION AND HAPLOTYPE DIVERSITY ................................................................................................ 27 RECOMBINATION .................................................................................. ......................................................................... 27 SPATIAL GENETIC STRUCTURE OF POPULATIONS ..................................................................................................... 28 WHITE AND YELLOW AWNED POPULATIONS ............................................................................................................ 28 ARZ AND SRZ ..................................................................................................................................... ........................... 29 WRZ ..................................... ................................................................. .......................................................................... 30 I GENE FLOW BETWEEN WRZ AND ARZ-SRZ ............. ......................................................... .. .................................... 31 RELATIONSHIP BETWEEN POPULATIONS FROM CHILE, LESOTHO AND SOUTH AFRICA .................................... 32 IMPLICATIONS FOR BRYOPHYTE SPECIATION AND EVOLUTION OF THE REGIONS FLORA ................................... 33 CONCLUSION ................................................................................................................................................... 34 REFERENCES ................................................................................................................................................... 35 APPENDIX 1 .................................................................................................................................................... 42 APPENDIX 2 .................................................................................................................................................... 43 I I 4 Table of Figures I Figure 1 : Distribution of Pseudocrossidium crinitum around the world. Frequency of occurrences is shaded in red ................................................................................................................................. 10 I Figure 2 : Rainfall seasonality in South Africa. The region shaded blue receives mostly winter rain (WRZ) while the orange receives the majority of its rain during summer months (SRZ) . The area shaded green is the all-year-round rainfall zone (ARZ). Map adapted from Chase and Thomas (2007) ............................................................................................................................................11 Figure 3 : Map of South Africa and Lesotho, indicating sampling localities of Pseudocrossidium crinitum. Numbers correspond to populations listed in Appendix 2. Black circles are populations with yellow hairpoints. White circles are populations with white hairpoints and half-black-half- white circles are localities with both forms present ..................................................................... 12 Figure 4 : Haplotype network for the /TS1 sequences of Pseudocrossidium crinitum. The size of the circle representing each haplotype is proportional to its frequency and numbers indicate the populations in which each haplotype is found. Black circles indicate 'missing' haplotypes, whilst haplotypes connected by single lines differ by a single mutational difference. The degree of blue shading, indicates the proportion of populations found in the WRZ, 0 shading = none; darkest I shading= all .................. ..................... .. ......... ................. ................................................................ 18 Figure 5 : Haplotype network for the trnl-F sequences of Pseudocrossidium crinitum. The size of the circle representing
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