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 University of Cape Town Phylogenetic relationships of the African species of the genus Merxmuellera Conert (Poaceae: Danthonioideae) submitted in partial fulfilment the degree of TownMaster of Science in Systematics Biodiversity Science Cape of PASEKA MAFA UniversityDepartment Botany University March Supervisors: Professor H. P. Under (University of Cape Town), and Doctor N. P. Barker (Rhodes University) 1\ Y have written 0/ dawn} 0/ the moon) and the tree:J)' 0/ people} and the /lower:J) and the dontj 0/ bee:J, But over thede thintjd my mind would padd} ~nd come to redt amontj tjraddTown (iradd do humble) that all thintjd tread Yt:J tender bladed, (ira:HCape - the breacl Jhe dta//o/ Ale;of a con:Jtant need 0/ the man and beadt - a power indeed." (iod in .JJid wi:Jdom tjave many /riend:J Jo tjrace our way) a:J alo~ it wend:J ButUniversity the tjrandeur 0/ many} my mind would pad:J) ~nd come to re:Jt amontj tjra:M ... Note DNA sequences available at GenBank or on request from Dr. Nigel Barker at the Department of Botany, Rhodes University. Town Cape of University of Contents of co ntents ............... ,. '" ...... , ..................................................i Abstract .......................................................................................iv Acknowledgements .........................................................................vi CHAPTER ONE: INTRODUCTION ................................. 1 1.1 General introduction ....................................................... 1 1.2 Classification Subfamily Danthonioideae ................ 2 1.3 Merxmuellera Conert ....................................... 6 1.3.1 Distribution of Merxmuellera in southern ......... 7 1.3.2 Leaf ........................................... 10 1.3.3 Phylogenetic studies ............................................ 15 1 .4 Aims the current study ..............................................Town 1 8 CHAPTER TWO: MATERIALS ANDCape METHODS .............. 19 2.1 Morphology and anatomical .................................... 19 2.1.1 .............................................................of 19 2.1.2 Source Material ............................................... 19 2.1 Preparation and examination of materiaL. ............... 21 2.1.3.1 Morphology..................................... 1 2.1 .2 Anatomy .......................................... 21 2.1.4University Character coding ............................................... .. 2.1.5 Character descriptions ......................................... 2.2 Molecular data ............................................................. 36 2.2.1 Utility of rpoC2 ITS sequences data ................. 36 2.2.1.1 The grass insert in the chloroplast ribosomal subunit 2 (rpoC2) gene ......................................................... 36 2. 1 The Internal transcribed spacers region ...................................................... 2.2 DNA sampling strategy ...................................... 2.2.3 DNA extraction .................................................. 2 .4 DNA amplification ........... , ................................... .45 2.2.4.1 electrophoresis, DNA visualisation and 2.2.5 DNA sequencing ..................................................47 2 .6 Sequences alignment .......................................... .4 7 2 Phylogenetic analysis .................................................. 2.3.1 Searching for most parsimonious trees ................ 2.3.1.1 analysis .............................. 50 2.3.1 character weighting ........... 51 2 .1.3 Bootstrap and ............ 51 2 .1.4 Combined analyses ............................ 53 Town CHAPTER THREE: RESUlTS ................................ 3.1 Individual data sets ..........................................................Cape 56 3.1.1 Morphology ......................................................... 56 3.1.1.1 Unweightedof morphologica data .......... 56 3.1.1.2 weighted morphological data ................................................ 59 3.1.2 Molecular .................................................. 60 3.1.2.1 data ..................................... 60 University3.1.2 ITS .......................................... 64 3.2 Combined data sets ............................................. 65 3.1 Combined molecular (rpoC2 + ITS) .............. 65 3.2.2. Com molecular morphological data evidence). ........................................ 66 CHAPTER FOUR: DiSCUSSiON ........................... 69 1 Phylogenetic resolution and support: findings ..... 68 4.2 Monophyly of Merxmuellera .......................................... 73 11 Generic limits .......................................................... CHAPTER FIVE: CONCLUSiONS ....................... 86 FUTURE PROSPECTS ...................................................... 88 REFERENCES .................................................................. 89 APPENDiCES ................................................................. 101 Town Cape of University ABSTRACT The subfamily Danthonioideae been the subject of many investigations at both and morphological . DNA contributed towards our understanding of both the composition of the subfamily I the relationships within and between the subfamily and other All previous, anatomical, embryological and molecular that within the the African· genus Merxmuellera Conert, highly polyphyletic and urgent taxonomic . This comprises 1 7 and two Madagascan species. study expands on existing molecular (rpoC2 ITS) and morphological data sets to further testTown of non-monophyly of Merxmuellera sensu The reveal that despite high levels resolution, the morphological data yield poorly supported phylogenies to high levelsCape of homoplasy in the dataset. Analyses of partitioned and combined molecular data sets provide topologies that are better supported ofand groups of in whole study group but their obscure. Topologies the total supported and that within Merxmuellera s.L are four lineages, of which are monophyletic: A monophyletic Merxmuellera s.s (M. drakensbergensis, M. stereophylla, M. Universityaureocephala, M. macowanii and type species M. davYI) basal to the rest the danthonioid monophyletic Cape Merxmuellera group (M. decora, M. rufa, M. lupulina I M. arundinacea and M. cincta); a monophyletic M. rangei - M. papposa group resolved the major clade containing the rest of the members the subfamily. Four of Merxmuellera including M. guillarmodiae; M. stricta, M. disticha M. dura are retrieved in a clade termed the I Rytidosperma which includes the Australasian Rytidosperma, Austrodanthonia, Notodanthonia and as well as the African Karroochloa, Schismus and Tribolium; study thus, supports the hypothesis that Merxmuellera s.1. is polyphyletic and concludes that two new genera are recognisable within this one comprising the Cape Merxmuellera species and the other comprising of M. rangei and M. papposa. Furthermore, this study corroborates exclusion of the latter group as a separate genus in Chloridoideae as hypothesised by studies. monophyletic Merxmuellera comprises of the Drakensberg species and possibly the Madagascan species. Taxonomy four Merxmuellera s.1. species in Rytidosperma clade remains uncertain and further work is needed in· this before any meaningful conclusions the interspecific can be Town Cape of University v Acknowledgements Financial towards this research study was made possible through support provided by Southern Botanical Diversity Network (SABONET) funded by the Global Environmental Facility (GEF) through the United Nations Development Programme (UNDP) and by Regional Center for southern Gaborone, Botswana, United Agency for International Development (USAID) (Plot no. 1481 Lebatlane Gaborone West, Extension 6, Botswana), under the terms grant No. 690-0283-A-OO-5950. opinions expressed are those of the author do not necessarily the of either the USAID, the World Conservation Union (iUCN), or the GEF/UNDP. Throughout the course of study at the University of Town, I many thanks to the following: Peter and Dr. Nigel Barker advices encouragement. Prof. Peter Under is commented for daily guidance and instruction and comments on various of the manuscript. Many thanks to Dr. Nigel Barker instruction TownDNA isolation, PCR amplification DNA purification, as well as allowing me to use many of his molecular sequences in my Tn"""",,,,, '" Ms Keletso Ntene, my brothers andCape my Moliehi Mafa for their motivation and moral support throughout the and the times of this study. of staff at the Department of Botany Department Biochemistry and Microbiology Rhodes University for use of facilities collecting DNA for research. All the staff, Postgraduate students as well as Post-doctoral fellows at Department of Botany at the University of Cape Town for never ending Universitysupport throughout the study. Ms Miranda Waldron of the Microscopy at the University of Town for assistance and use of digital microscopes for talking anatomical pictures. '" The at the Bolus Herbarium and the Roma Herbarium, National University of lesotho for usage Herbarium during this Ms Pia Eldans and Ms Cornelia Klak for translating for me, sections of some German