Effects of Protected Areas and Climate Change on the Occupancy Dynamics of Common Bird Species in South Africa Greg Duckworth Doctor of Philosophy In the Department of Statistics University of Cape Town July 2018 Supervisor: Associate Professor Res Altwegg University of Cape Town 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 DECLARATIONS I, Gregory Duncan Duckworth hereby: (a) grant the University of Cape Town free license to reproduce the above thesis in whole or in part, for the purpose of research; (b) declare that: (i) the above thesis is my own unaided work, both in conception and execution, and that apart from the normal guidance of my supervisor, I have received no assistance apart from that stated below; (iii) neither the substance nor any part of the above thesis has been submitted in the past, or is being, or is to be submitted for a degree at this University or any other University. This thesis has been submitted to the Turnitin module (or equivalent similarity and originality checking software) and I confirm that my supervisor has seen my report and any concerns revealed by such have been resolved with my supervisor. I am now presenting the thesis for examination for the Degree of Doctor of Philosophy. NAME: Greg Duckworth STUDENT NUMBER: DCKGRE002 SIGNATURE: DATE: 7 July 2018 TABLE OF CONTENTS Abstract ii Acknowledgements iii Thesis layout vii Chapter 1: General Introduction and background information 1 Chapter 2: Effectiveness of protected areas for bird conservations depends on guild 27 Chapter 3: Why a landscape view is important: nearby urban and agricultural land affects bird abundances in protected areas 54 Chapter 4: The dynamic benefits of protected areas: occupancy and colonization probabilities of common bird species increase in areas with higher proportions of protected areas 96 Chapter 5: Dynamic occupancy model reveals that Cape Rock-jumper (Chaetops frenatus) is disappearing from the hottest part of its range 132 Chapter 6: Synthesis and consolidation 166 Reference list: 178 i ABSTRACT Protected areas are tracts of land set aside primarily for the conservation of biodiversity and natural habitats. They are intended to mitigate biodiversity loss caused by land-use change worldwide. Climate change has been shown to disrupt species' natural distributions and patterns, and poses a significant threat to global biodiversity. The goals of this thesis are to address these important issues, and understand how protected areas and climate change affect the range dynamics of common, resident bird species in South Africa. Common species were used because they have been shown to drive important ecosystem patterns, and a decline in abundance and diversity of common species can indicate drastic declines in ecosystem integrity. This thesis comprises four data chapters; in the first three I model the occupancy dynamics of 200 common, resident bird species in South Africa to gain an understanding of how the proportion of protected areas within a landscape affects common species. For the last data chapter, I examined the effects of protected areas and a changing climate on the range dynamics of Cape Rock-jumper (Chaetops frenatus), a species endemic to the southwestern part of South Africa and whose population is declining rapidly in response to climate change. I modelled its occupancy dynamics in relation to climate, vegetation, and protected area. Overall, my key findings show bird abundances vary widely as a function of protected areas, but on average, bird abundances are higher in regions with a higher proportion of protected areas, compared to regions with a lower proportion. I found that the conservation ability of protected areas was influenced by the type of land-use found in the surrounding landscape. For example, the extent of agricultural land in proximity to a protected area significantly increased the mean abundance of birds in that protected area, whilst the average abundance of most species was not affected by the extent of urban area near protected area. On average, species preferentially colonized and persisted within landscapes with a higher proportion of protected area, compared to landscapes with a lower proportion of protected area. However, protected areas were not able to slow the extinction rate for all species, and the average extinction rate for some groups of species actually increased as the extend of protected areas within a landscape increased. Furthermore, Cape Rock-jumper also preferentially occupied regions with higher proportions of protected area. Despite this, Cape Rock-jumper’s range is predicted to shrink considerably in response to a hotter and mildly drier climate forecast for the region. As a result, Cape Rock-jumper will likely be of conservation concern as the climate over its range continues to change. I conclude that, in general, protected areas are effective at conserving common bird species over a heterogeneous landscape in South Africa, and should be prioritised as key conservation strategies in the future. I further conclude that climate change will be a concern to an endemic species, and to biodiversity in general. This will likely place extra stress on the importance of protected areas to mitigate responses of species to climate change. ii ACKNOWLEDGEMENTS This thesis has occupied five and a half years of my life. Little did I realise, when I first began this thesis, the enormity of the task on which I would embark. I have gained experience and skills in ways I had not even imagined when I originally took up the project, but am all the more grateful for these learning opportunities. Many people have influenced, guided, and helped me along this long path, each of whom have in one way or another shaped this thesis into its final product. It would be remiss to forget anyone’s contribution. If I have overlooked anyone and your name doesn’t appear below, then I’ll firstly accuse the University’s uploading system. If that doesn’t work, then I’ll have to reprint this with your names added. It should go without saying, but I’m going to say it anyway; this thesis would not exist if it were not for my supervisor Res Altwegg. I am deeply indebted him for his professional guidance, support, and encouragement throughout the duration of this study. His continued professional excellence inspired and pushed me throughout my thesis, and encouraged me to make the most of each chapter, particularly towards the last stages. I must mention especially his patience during many discussions in his office about interpretations of the complex analyses and datasets, and for returning chapter drafts so timeously when I was under pressure. I must also express my gratitude to him for giving me the opportunity to present this research at international conferences, and for allowing me to share this research during international research visits. Res’ enthusiasm for statistics, ecology, and science in general is inspiring, and ultimately motivated me to be a better scientist, something which I hope is evident throughout this thesis. Further thanks must go to Res for his patience, understanding, and support during the last two and a half years of my thesis when I was working on my PhD alongside a full-time job. iii This thesis exclusively analysed bird atlas data taken from the South African Bird Atlas Project (SABAP). Grateful thanks therefore go to Professor Les Underhill for running and maintaining this project and for allowing me access to the great volumes of collected data. Thank you to René Navarro and Michael Brooks for maintaining and updating the databases. I am grateful to Michael for helping me with SQL code to obtain the data, and for other such IT-related queries throughout most of the thesis. Furthermore, I am deeply indebted to the atlassers for spending long hours in the field collecting valuable bird distribution data over such large areas. I hope this thesis serves as justification for your continued effort in monitoring biodiversity. Thanks to Richard Flack for permitting me to use his photo of the Cape Rock-jumper in Chapter 5. The SEEC lab was home to me for most of my thesis. Thanks to all the students and researchers that came and went throughout my time there, and with whom I was able to chat and discuss a wide range of topics. Although our busy schedules may not have allowed me to have had detailed conversations with all who came through the SEEC doors, I am grateful for even the smallest of chats and messages of support or encouragement. To the regulars with whom I developed a rapport, thank you for your willingness to listen to me, offer advice, and for creating the amiable attitude that is the SEEC lab. I’d especially like to mention Sunet Hugo. Thanks for being a friend throughout my thesis and for understanding the long road of the PhD. Thanks too for sharing your knowledge so willingly, and I am indebted to you for looking over some analyses and for giving me data visualisation advice. I hope your new adventure in Grahamstown is off to a great start! Thanks to Theoni Photopoulou, Ryan Daniels, and Birgit Erni for reading over previous drafts of sections of my thesis. A little bit further from Cape Town, a special mention must be made of Rheinhardt Scholtz. Thanks for your continued support and encouragement throughout this thesis, for your insights, and for reading over many earlier drafts of each chapter.