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 licensety ofgranted Cape to UCTTown by the author. si Univer DEMOGRAPHIC AND GENETIC VARIABILITY IN CAPE DWARF CHAMELEONS, Bradypodion pumilum, WITHIN A FRAGMENTED, URBAN HABITAT MASTER OF SCIENCE CANDIDATE: Eric Michael Katz [email protected] SUPERVISORS: Dr.y K. of A. Tolley Cape Town South African tNational Biodiversity Institute si Dr. J. M. Bishop Department of Zoology, University of Cape Town Univer & Dr. R. Altwegg South African National Biodiversity Institute Thesis presented for the degree of Master of Science Within the Department of Zoology University of Cape Town, South Africa June, 2012 (2nd Submission) PLAGIARISM DECLARATION 1. I know that plagiarism is wrong. Plagiarism is to use another’s work and pretend that it is one’s own. 2. Each contribution to, and quotation in, this thesis from the work(s) of other people has been attributed, and has been cited and referenced. 3. This thesis is my own work. 4. I have not allowed, and will not allow, anyone to copy my work with the intention of passing it off as his or her own work. 5. I acknowledge that copying someone else’s assignment or essay, or part of it, is wrong, and declare that this is my own work. _________________________ Signature Removedty of Cape Town Eric M. Katz si Univer II ACKNOWLEDGEMENTS A special thanks to Krystal Tolley for her support and guidance throughout my research and the completion of my Masters of Science (MSc) degree. Thanks to Jacqueline Bishop and Res Altwegg for their input and expertise, and to John Hoffmann for approving my candidacy for the MSc degree through the University of Cape Town (UCT). Thanks to all of the students and staff from the South African National Biodiversity Institute (SANBI) and UCT whom contributed towards my research and the completion of my MSc degree. A special thanks to Stephen Doucette-Riise for his friendship and continual assistance in the completion of my field work. Thanks to the many others whom also assisted me with my field work. Thanks to SANBI for logistical and financial support and to SANParks for permitting access to my field site. Thanks to UCT for logistical support and again for my candidacy for the MSc degree. All research was conducted under permits from CapeNature (0035-AAA007-00056 and AAA004-00322- 0035) and SANParks, with SANBI (002/10) and UCT ethical clearance. Lastly, endless thanks to my family, particularlyy my of older Cape sister, Stephanie, Town whom spurred my initial travels to the city of Cape Town and my eventualt return for my Masters degree. She is my daily inspiration, without her love and continuedsi support none of this would have been possible. Univer III ABSTRACT Habitat fragmentation is recognized as a primary cause of biodiversity loss. To maximize biodiversity maintenance, researchers in the field of conservation biology often investigate population demography and genetic variability for species inhabiting fragmented landscapes. Findings from such work enable effective conservation management, maximizing viability for potentially imperiled populations. Previous research has relied predominately on spatial analysis when investigating population demography and genetic variability; however, temporal analysis is also important to species conservation. As of 2006, reptiles and amphibians had the highest threat status among small, terrestrial vertebrates, warranting continual investigation of herpetofaunal species inhabiting fragmented landscapes. Of the two, reptiles are the more poorly studied, though are suggested to be equally or more threatened than amphibians. The Cape Dwarf Chameleon, Bradypodion pumilum, exemplifies one potentially threatened reptile species which has suffered habitat loss, due to urbanization, inducing fragmentation and transformation among much of its habitat. As a result, many B. pumilum populations currently exist as a collection of isolated groups inhabiting critically endangered ecosystems. Continued habitat alteration may prove detrimental to B. pumilum’s continued existence. This study investigated temporal dynamicsy of in the Cape local demographic Town and genetic characteristics of a group of Cape Dwarf Chameleons; the populationt inhabits a patch of transformed, fragmented habitat within the Noordhoek Wetlands siNature Reserve, Cape Town, South Africa. One year of capture-mark-recapture data indicated the study site typically supports a fluctuating abundance of adult individuals, ranging from 25-100 adult chameleons. Chameleons experienced annual survival similar to other small-bodied lizardsUniver as well as size-dependent survival, where larger individuals showed higher survival rates. Sex and season, however, did not appear to have significant effects on chameleon survival within the study site as both sexes had similar thirty-day survival rates which remained constant throughout the study period . Results corroborate previous ten-day survival estimates for B. pumilum inhabiting the Noordhoek site, and suggest B. pumilum experiences similar short-term and extended survival. Demographic assessment also revealed that B. pumilum engaged in minimal movement between the core site and adjacent patch fragments during thirty-day periods, independent of time and/or sex, executed exclusively through the narrow corridors of continuous vegetation linking the core site to adjacent fragments. IV A three-year genetic assessment using eight microsatellite molecular markers was conducted to investigate temporal stability in allelic variation for B. pumilum inhabiting the field site. Specific focus was directed towards uncovering a potential relationship between allelic variation and stochastic events (e.g. temporary site-vacancy of adult chameleons). Quantitative genetic analysis (overall levels of polymorphism including number of alleles and observed heterozygosity) of B. pumilum samples indicated typical levels of genetic diversity within the Noordhoek population compared with other small-bodied lizards inhabiting more natural landscapes. Additionally, small, but detectable, differences in allele frequencies (RST = 0.017, 0.015, 0.015; P-value = 0.019, 0.046, 0.045) were observed between pre- versus post-vacancy periods for B. pumilum inhabiting the field site. Interestingly, despite these observed shifts, there are nonsignificant differences between pre- and post- vacancy periods for the FST statistics (as opposed to RST statistics) provided by the analysis of molecular variance (AMOVA). Cumulatively, results indicated a degree of genetic stability for B. pumilum inhabiting the Noordhoek site across the three-year period, particularly between years 2 and 3. Results support the initial hypotheses that B. pumilum inhabiting the Noordhoek site experience predominately stable allelic structure except following stochastic events such as the disappearance of the adults between years 1 and 2. This investigation of demographic and genetic variability provides important temporal data on local population dynamics and habitat use fory a potentially of Cape vulnerable Town species inhabiting primarily fragmented landscapes. Findings from this studyt benefit B. pumilum’s ongoing evaluation for IUCN Redlist status and provide empirical datasi useful to identifying and mitigating threats to chameleon viability through the implementation of effective conservation management strategy. Results suggest B. pumilum is capable of short-term occupation within fragmented landscapes with the potential for long-term viability, thoughUniver further study is required. Management strategy may be required to maintain quality habitat for chameleons inhabiting this fragmented landscape. This study exemplifies both the necessity and benefits of conducting species-specific investigations for small-vertebrate populations inhabiting fragmented landscapes. The combination of demographic and genetic approaches offers insight into local population dynamics likely unobtainable through their individual application. Results will likely aid in effective species conservation, maximizing the continual existence of potentially imperiled species inhabiting fragmented landscapes. V TABLE OF CONTENTS PLAGIARISM DECLARATION…………..…………………………………..…………………….II ACKNOWLEDGEMENTS…………………………………….……………………………………III ABSTRACT……………………………………………..………………………………………….…IV TABLE OF CONTENTS………………………………..…………………………………………....VI LIST OF FIGURES………………………………………………………………….……………….IX LIST OF TABLES………………………………………………………………..…….…………...…X LIST OF APPENDICES……..……………………...……………………………………………....XII CHAPTER ONE: AN INTRODUCTION TO (1) CHAMELEONS: WITH FOCUS ON DWARF CHAMELEONS (Bradypodion sp.) AND (2) THE EFFECTS OF HABITAT FRAGMENTATION ON SPECIES WITH ADDITIONAL FOCUS ON HERPETOFAUNA.......1 CHAMELEONS…………………..……………………………………….………………………2 Chameleons of Southern Africa……………………………………………………………..…..3 Dwarf Chameleons………………..……………………………………………………………...4 THE EFFECTS OF HABITAT FRAGMENTATION ON SPECIES…………………………7 The Effects of Habitat Fragmentation on Herpetofauna………………………………….....11 Study Aims……………………………………………………..……………………………..…12ty of Cape Town DESCRIPTION OF THE STUDYsi AREA………………………………………………...……14 CHAPTER TWO: MOVEMENT, ABUNDANCE, AND SURVIVAL OF Bradypodion pumilum WITHIN A FRAGMENTED, URBAN HABITAT………………………………...………….……18