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Guttera Pucherani Were Also Obtained from Rossouwof (1996) 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 Molecular systematics and phylogeography of the Helmeted Guineafowl (Numida me/eagris) by Jonathan van Alphen-Stahl Town Submitted in partial fulfilment of the requirements for theCape degree of of Master of Science in the UniversityFaculty of Science University of Cape Town Cape Town Supervisor: Prof. T. M. Crowe Co-supervisor: Assoc. Prof. P. Bloomer 2005 ACKNOWLEDGEMENTS I would like to thank my supervisors Tim Crowe and Paulette Bloomer. Tim, thank you for the opportunity to work on this project as well as your patience and perseverance. Paulette, thanks for your friendly advice and help throughout the project, particularly in the draft stages. Thanks must also go out to all the wingshooters who provided samples of guineafowl from across Africa. To all the members of lab MEEP thank you for accepting me into the lab and making me feel welcome. In particular: Lisel Solms for getting me started in the lab, Carel Oosthuizen for sorting out the admin. in the lab and with the university, as well as being roomy for a while, Wayne Oelport for help with analysis and computer related issues, as well as a golf buddy. A mention must also go to Michael Cunningham for project advice and late night games of hallway footy, Marina Alais and Isa-Rita Russo for the drinks we shared of an evening. Town To my other Pretoria 'maatjies', Minique de Castro, Vinet Coetzee, Tracey-Leigh Hatherell and Jason Pienaar, thanks for some great evenings and weekends away that kept me sane during the project. Cape of Finally, I would like to thank my parents for putting me up and putting up with me for the duration of the thesis, and especially for monetary, culinary and hydratory support throughout. Thanks for your support and dogged patience in a marathon struggle that seemed an ultra most of the time. I really appreciate everything that you have done for me through the years. University ii TABLE OF CONTENTS ACKNOWLEDGEMENTS ii TABLE OF CONTENTS iii LIST OF TABLES v LIST OF FIGURES vi Town CHAPTER 1: GENERAL INTRODUCTION General Introduction 1 Members of the family 3 Systematics of Numida meleagris Cape 6 General Background .................................................................................of . 8 Molecular systematics and phylogeography ................................................... 10 Aims 12 References 13 CHAPTER 2: MOLECULARUniversity DIFFERENTIATION AMONG THE SUBSPECIES OF HELMETED GUINEAFOWL (NUMIDA MELEAGRIS) Abstract 18 Introduction ...................................................................................... , ... ... 19 Materials and Methods ............ '" ..................................................... , . .. .. ... 22 Results 24 Discussion.................. ............ ............ ........................ ...... ... ...... ......... ... ...... 31 References . .. ............................................................................ 35 iii CHAPTER 3: PHYLOGEOGRAPHY OF THE HELMETED GUINEAFOWL IN SOUTHERN AFRICA Abstract . .. .. .. 42 Introduction ........ , .. , .. , ........ , ...... '" ...... '" .,. ... ... ... .. ... ... ... ... ... ... ... ... .. ... ... 43 Materials and Methods . .. .. .. 45 Results 49 Discussion 58 References 61 Conclusions 68 APPENDICES 69 Town Cape of University iv LIST OF TABLES Table 2.1 Subspecies of Helmeted Guineafowl and the localities of populations sampled. 22 Table 2.2 Pairwise estimates of nucleotide sequence divergence (% HKY85) for the control region below the diagonal and for cytochrome b above the diagonal for six subspecies of Helmeted Guineafowl. 27 Table 3.1 Geographic coordinates of all collecting localities of Numida meleagris in southern Africa analysed in the present study. The locality numbers correspond to those in Figure. 3.1 and the haplotypes numbers correspond with those in Table 3.2..... 48 Town Table 3.2 Distribution of 27 observed mtDNA control region haplotypes from a sample of 51 Helmeted Guineafowl from 18 sampling localities. The vertical numbers indicate the positions of variable nucleotides within the 321 Capebp sequence. Dots indicate the same nucleotide is present as in haplotype 1.of The number of individuals for each haplotype from a population are given, with the numbers in parentheses 0 following a population name corresponding to the locality numbers in Figure 3.1. Haplotypes in bold are N. m. damarensis, all other haplotypes are N. m. coronata .. 50 Table 3.3 Pairwise estimatesUniversity of percentage Tamura-Nei + r (10.3658) + I (0.8553) sequence divergence among 27 haplotypes (below the diagonal) and percentage HKY85 sequence divergence (above the diagonal). Haplotype numbers correspond to Table 3.2 and those in Figure. 3.2. Within-group divergences are highlighted. The light grey block indicates group A and the dark grey block indicates group B in Figure. 3.2.... 51 Table 3.4 Inference chain on the results given in Figure 4. Only those clades that resulted in a rejection of the null hypothesis are included in this table... ......... ... ...... .... 57 v LIST OF FIGURES Figure 1.1 Helmeted Guineafowl subspecies and their distributions. A-Numida me/eagris galeata, B-N. m. me/eagris, C- N. m. somaliensis, D- N. m. reichenowi, E­ N. m. marungensis, F- N. m. mitrata, G- N. m. damarensis, H- N. m. coronata, X- N. m. sabyi. (Map modified from Crowe & Snow, 1978; guineafowl illustrations reproduced from Crowe, 1978). .............. '" ... ... ... ...... ... ... ... ... ......... ... .... ... 2 Figure 1.2 Distribution and morphology of A meleagrides (distribution from Crowe et al. 1986, guineafowl illustration taken from Crowe 1978). ... ... ... ... ... ... ... ... ... 3 Figure 1.3 Distribution and morphology of A niger (distribution from Crowe et al. 1986, guineafowl illustration taken from Crowe 1978). Town 4 Figure 1.4 Distribution and morphology of G. plumifera, a) G. p. plumifera b) G. p. schubotzi (distribution from Crowe et al. 1986, guineafowlCape illustrations taken from Crowe 1978) ................................................of '" ... .. .. ... ... ... ... .. ... .. .. 4 Figure 1.5 Distribution and morphology of G. pucherani, a) G. p. pucherani b) G. p. verreauxi c) G. p. sclateri d) G. p. barbata e) G. p. edouardi (distribution from Crowe et al. 1986, guineafowl illustrations taken from Crowe 1978). 5 University Figure 1.6 Distribution and morphology of A vu/turinum (distribution from Crowe et al. 1986, guineafowl illustration taken from Crowe 1978). 6 vi Figure 2.1 The distribution of nine subspecies of Helmeted Guineafowl (Numida meleagris) and the country where collected. A - N. m. galeata (Angola), B - N. m. meleagris (Central African Republic & Uganda), C - N. m. somaliensis, 0 - N. m. reichenowi (Kenya), E - N. m. marungensis, F - N. m. mitrata (Zambia & Malawi), G - N. m. damarensis (Namibia), H - N. m. coronala (South Africa), X - N. m sabyi (Modified from Crowe & Snow 1978) Intermediate forms are found in narrow hybrid zones between subspecies boundaries. • - Study sites -- limits of Brachystegia woodland (from Coe and Skinner 1993). 20 Figure 2.2 Phylogenetic reconstruction of the relationships among the six subspecies of guineafowl from control region sequences. (A) Distance analysis calculated with the neighbour-joining method using uncorrected distances, 1000 bootstrap replicates were calculated. (8) Parsimony analysis using a heuristic search with 1000 bootstrap replicates. Only bootstrap values Townabove 50% are indicated. [CAR - Central African Republic, S.A - South Africa, Harrods - a domesticated guineafowl used in comparative analysis with N. m. galeata] Numbered clades: 1 - northern clade, 2 - eastern clade, 3 - West African clade and 4 - southern clade. Cape 28 of Figure 2.3 Phylogenetic reconstruction of the relationships among the six subspecies of guineafowl from cytochrome b sequences. (A) Distance analysis calculated with the neighbour-joining method using uncorrected distances, 1000 bootstrap replicates were calculated. (8) Parsimony analysis using a heuristic search with 1000 bootstrapUniversity replicates. Only bootstrap values above 50% are indicated. [CAR - Central African Republic, S.A - South Africa, Harrods - a domesticated guineafowl used in comparative analysis with N. m. galeata]. 29 Figure 2.4 Phylogenetic reconstruction of the relationships among six subspecies of Helmeted Guineafowl (Numida me/eagris) from combined analysis of control region and cytochrome b sequences. [CAR - Central African Republic, S.A. - South Africa, Harrods - a domesticated guineafowl used in comparative analysis with N. m. galeata] Numbered clades: 1 - northern clade, 2 - eastern clade, 3 - West African clade and 4 - southern clade. 30 vii Figure 3.1 Collecting localities of Numida meleagris from southern Africa. The top left inset shows the distribution of Numida meleagris throughout Africa, A=N. m. damarensis B=N. m. coronata. The numbers correspond to the locality numbers in Table 3.1. 1-Etosha; 2-Waterberg; 3-Bulawayo; 4-Marico; 5-Dullstroom; 6-Mafikeng; 7 -Setlagoli; 8-Petrus Steyn; 9-Reitz; 10-Utrecht; 11-Dundee; 12-Colenso; 13- Winterton; 14-Elandslaagte; 15-Spioenkop; 16-Underberg; 17-Rooipoort; 18- Groblershoop. c=J
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