PHYSIOLOGICAL AND ECOLOGICAL EFFECTS OF FENCING ELEPHANTS IN MONTANE FORESTS, KENYA J MORRISON PHD 2019 PHYSIOLOGICAL AND ECOLOGICAL EFFECTS OF FENCING ELEPHANTS IN MONTANE FORESTS, KENYA JACQUELINE ANNE MORRISON A Thesis Submitted In Partial Fulfilment Of The Requirements Of The Manchester Metropolitan University For The Degree Of Doctor Of Philosophy FACULTY OF SCIENCE AND ENGINEERING AT THE MANCHESTER METROPOLITAN UNIVERSITY IN COLLABORATION WITH CHESTER ZOO JULY 2019 The copyright of this thesis belongs to the author under the terms of the Copyright Act 1987 as qualified by Regulation 4(1) of the Manchester Metropolitan University Intellectual Property Regulations. Due acknowledgement shall always be made of the use of any material contained in, or derived, from this thesis. © Jacqueline Morrison, 2019. All rights reserved ii DECLARATION I hereby declare that the work has been completed by myself and no portion of the work contained within this Thesis has been submitted in support of any application for any other degree or qualification on this, or any other university or institution of learning. Jacqueline Anne Morrison, 2019 iii Acknowledgements Completion of this thesis could not have been possible without the support from a number of people and organisations. First and foremost, I want to thank my director of studies, Dr Bradley Cain. It has been an honour to be his first PhD student. Not only has he offered continuous support and encouragement, he has taught me the necessary skills to undertake this work and has also helped me to develop a number of working relationships with a variety of conservation organisations. Without his help and patience, this thesis would not have been possible, and I could not have imagined having a better mentor for my PhD studies. I would also like to thank the rest of my supervisory team; Dr Martin Jones, Dr Elias Symeonakis, and Dr Susan Walker for their expertise within their fields and for their insightful comments on each chapter which enabled me to address the research questions from various perspectives. The laboratory work was undertaken at the endocrine laboratory at Chester Zoo, I would like to thank all of the laboratory staff, but particularly Rebecca Mogey for her extensive guidance and encouragement particularly during the final month of analysis. I sincerely thank the Kenya Wildlife Service (KWS) for allowing me to undertake this project, particularly the support from all within the elephant program. Furthermore, I am grateful to all of the staff from the Mountain Conservation Area (MCA) where this research was predominantly based. I would like to thank the current senior scientist of the MCA, Dr Fred Omengo who provided me with his extensive knowledge of the study area, valuable comments on chapters submitted for publication, and support during the process of exporting my samples to the UK. I would also like to thank the research and monitoring staff from the private conservancies for their permission to conduct research on their reserves enabling valuable control populations, namely, Dr David Kimiti, Geoffrey Chege, and Samual Mutisya. I would like to express my gratitude to all of the people that have assisted me during my time in the field and made me feel welcome and surrounded with support. Particular thanks to all of the rangers from KWS, Ol Pejeta Conservancy, Samburu National Reserve, and Lewa Wildlife Conservancy. They not only assisted me with locating elephants and the collection of dung samples which proved challenging especially in the dense forest of the Aberdare National Park, but also for keeping me safe in challenging situations, and provided iv me with friendship during long durations in remote environments. Thanks also to the KWS scientists, Peris Lare, Redempta Njeri, Caroline Kawira, Luke Lukaria, George Anyona, and the elephant co-ordinator Francis Kobia at Lewa Wildlife Conservancy for their assistance not only in the field, but during the lengthy process in the laboratory preparing my samples for export. And finally, to Antony Wandera for his continued support throughout my time in Kenya, not only for his extensive knowledge, but also for making me to feel a part of his family. In addition, thank you to my fellow PhD students and friends who have offered me support during challenging times and helped to keep me sane either in the field or during analysis and write up. There are too many to name all of you, but in particular Giada Porcedda, Marianne Delauney, Grace Ellison, Tommy Sandri, and Sarah Scott. I gratefully acknowledge the funding received towards my PhD which was provided by Manchester Metropolitan University, and the North of England Zoological Society, Chester Zoo. Thanks particularly to Sue Walker and Simon Dowell, for their continued support, particularly via the ‘Conservation Scholars and Fellows Programme. Finally, above all else I would like to thank my parents who have offered me nothing but love and support throughout not only the PhD process, but my entire academic journey. v This thesis is dedicated to my parents for their continued support vi Abstract Worldwide, wildlife populations are declining at an unprecedented rate, anthropogenic influences including habitat-loss, poaching, and over-exploitation are driving many species to extinction. A rapidly increasing human population and subsequent conversion of land use, has intensified a competition of resources between humans and wildlife. Human elephant conflict (HEC) is a prominent concern and whilst many attempts have been made to mitigate conflict, many are unsuccessful, as such, Kenya embarked on the necessary strategy of fencing its montane forests to separate elephants from people. Whilst fencing successfully reduced conflict, the physiological and ecological effects of confining elephants in forests is unknown. This thesis is the first study examining the impact of fencing elephants in montane forests, on both the ecological impact on the integrity of the forest habitat, and the impact of isolation on the demographic structure, and physiology of the elephant population. The outcomes of this study will be used to inform the future management of elephant populations in forest habitats throughout their range. Chapters of this thesis address the following outcomes; (1) the impact of confining African elephants (Loxodanta africana) on the extent and quality of a forest habitat and (2) to provide a density estimate of elephants in a montane forest by employing the Random Encounter Model (REM) with camera traps. Additionally (3), it also assesses the impact of restricting dispersal on the demographic structure of elephant populations compared to free-roaming populations, and (4) examines the physiological effect of confinement on elephants. To provide an assessment of the impact of confinement on the forest habitat, changes in the forest canopy were mapped by applying the Breaks For Additive Season and Trend (BFAST) model using a time-series of MODIS satellite data on the 2 fenced forest habitats of varying sizes. Change maps produced from the BFAST model on MODIS time- series data revealed that 13% of the Aberdare National Park had undergone a change in vegetation, with 0.9% loss to the forest. Similarly, the Shimba Hills National Reserve underwent significant change over the 12-year period, averaging a 9% change in the area per year with both positive ‘greening’ events and forest degradation. Density estimates calculated from the REM yielded results averaging 0.49 elephants/ km2 which falls in line with expected estimates in protected areas. Demographic results determined that the age vii class frequencies for the Aberdare Conservation Area (ACA) were significantly different to parity (x2 = 147.24, df = 2, p-value < 0.001), showing a skewed age distribution towards adults and sub-adults and a lower proportion of juveniles. Comparison of the age class frequencies in the ACA to 3 populations from published data of known status (stable, and rapidly increasing) revealed that the ACA population were significantly different to both stable populations (x2 = 495.05, p-value < 0.001; x2 = 215.98, p-value < 0.001), and the rapidly increasing population (x2 = 329.1, p-value < 0.001). The number of dependents to adult females was significantly lower compared to the control populations (x2 = 9.0872, df = 3, p-value = 0.02815). Endocrine analysis of adrenal activity found significant differences in FGM concentrations between the confined ACA population, a free-roaming savannah population, and a population from a montane forest that utilises a wildlife corridor to the lowland savannah (R2 =0.2331, F = 35.1, df= (2), 231, p-value < 0.001). At 3.73 ng/g (95%CI, 3.35-4.16), the confined ACA population is 91% higher than the Lewa Wildlife Conservancy (LWC) population with a wildlife corridor (1.95 ng/g, 95% CI, 1.72-2.21) and 68% higher than the Samburu National Reserve (SNR) population (2.22 ng/g, 95% CI, 1.98-2.59). No significant differences in FGMs were observed between the two free-roaming (LWC and SNR) populations. The greatest difference in FGM concentrations were observed in the sub- adult age class, with the ACA averaging 4.13 ng/gm (95% CI, 3.58-4.76) compared to 1.87 ng/g (95% CI, 1.59-2.1) in the LWC, and 2.74 ng/g, (95% CI, 2.28-3.30) in the SNR. Whilst the ACA exhibited only small-scale degradation, and the current density of elephants falls within the expected densities for protected areas. Significant differences were observed in the demographic structure and physiological