Changes in diet resource use by elephants, Loxodonta africana, due to changes in resource availability in the Addo Elephant National Park. by Jana du Toit Submitted in fulfilment of the requirements for the degree of Magister Scientiae in the Faculty of Science at the Nelson Mandela Metropolitan University. 2015 Supervisor: Prof G. I. H. Kerley Co-supervisor: Dr. M. Landman DECLARATION I, Jana du Toit (student number: 214359328), hereby declare that the dissertation for the qualification of Magister Scientiae (Zoology), is my own work and that it has not previously been submitted for assessment or completion of any postgraduate qualification to another University or for another qualification. Faecal samples and forage availability estimates were collected by Dr. M. Landman and her team. Diet quality analysis was done by CEDARA Feed Laboratory, and DNA metabarcoding was done by Dr. P. Taberlet and his team at the Labortoire d’Ecologie Alpine. J. du Toit i ACKNOWLEDGEMENTS I would like to express my deepest gratitude and appreciation to the following people, without whom the completion of this dissertation would not have been possible: This study was funded by a bursary through Prof. Graham Kerley, for which I am deeply thankful. I’d also like to thank SANParks for the opportunity to work in the Addo Elephant National Park, as well as the Mazda Wildlife Fund for providing transport. To my supervisors, Prof. Graham Kerley and Dr. Marietjie Landman, thank you for the opportunity to work on this project, your assistance, support and sharing your knowledge with me. Your strive for excellence motivated me throughout this study. My sincerest thanks to Dr. Marietjie Landman, for allowing me to work on the collected faecal samples and forage availability estimates, the CEDARA Feed Laboratory for the diet quality analysis, and Dr. Pierre Taberlet and his team at the Labortoire d’Ecologie Alpine, for analysing the diet using DNA metabarcoding. To my friends, especially Tiffany Bell, who supported and assisted me throughout this study – you truly made the tough times better. To my parents, Deon and Marica, thank you for all the sacrifices, love and support, and for allowing me to pursue my passion, albeit far from home. To my sisters, Jandi and Babet, thank you for your unwavering emotional support, and constant encouragement. Without my family this would have been a futile attempt, I truly thank each one of you. “If you seek knowledge of the creatures of the earth, come close to Him who created all things, and He will give you enlightenment” anon. ii CONTENTS Declaration i Acknowledgements ii Contents iii Abstract v Chapter 1 1 General introduction 1.1 Introduction 1 1.2 How to choose what to consume? 1 1.3 Theory that predicts diet choice 2 1.4 How can diets shift? 3 1.5 How do we measure diet shifts? 4 1.6 Foraging strategies of herbivores 6 1.7 Elephants as model herbivore 7 1.8 Problem statement, aims and objectives 8 Chapter 2 11 General description of study sites 2.1 The Main Camp and Colchester sections 12 2.1.1 Site description, topography and geology 12 2.1.2 Climate 13 2.1.3 Vegetation 13 2.1.4 Elephant population history and elephants impact case study 15 Chapter 3 17 How does the diet breadth and preference of elephants change with an increase in resource availability? 3.1 Introduction 17 3.1.1 Elephants diet flexibility 17 3.1.2 Elephants impacts on vegetation 19 3.1.3 Hypotheses and aims 19 3.2 Methods 22 3.2.1 Sampling approach 22 3.2.2 Sample collection 23 3.2.3 Sample digestion 23 3.2.4 Microhistological analysis of diet 23 3.2.5 Forage availability estimates 24 3.2.6 Statistical analysis 24 3.3 Results 27 3.3.1 Sampling efficiency 27 3.3.2 Relative forage availability 27 3.3.3 Diet composition 28 3.3.4 Diet preference 31 3.3.5 Plant species vulnerable to elephants herbivory 37 3.4 Discussion 38 3.4.1 Does the diet breadth and preference of elephants change with 38 an increase in resource availability? 3.4.2 Elephants learning foraging behaviour 39 3.4.3 Implications of elephants herbivory 39 3.4.4 Contextualising the study 42 3.4.5 The way forward 44 iii Chapter 4 45 How does the quality of diet change with an increase in resource availability? 4.1 Introduction 45 4.1.1 Determinants of diet quality 45 4.1.2 Hypotheses and aims 47 4.2 Methods 48 4.2.1 Techniques in determining diet quality 48 4.2.2 Diet quality composition 49 4.2.3 Sampling approach and procedure 50 4.2.4 Statistical analysis 51 4.3 Results 51 4.4 Discussion 53 4.4.1 Diet quality requirements of elephants 53 4.4.2 Maintaining diet quality in the Main Camp section 55 4.4.3 Drivers of change in the diet of elephants 55 4.4.4 Consequences and implications of elephants being able to 57 maintain diet quality 4.4.5 Contextualising the study 57 Chapter 5 58 Comparing microhistological analysis to DNA metabarcoding of faeces to describe the diet of elephants. 5.1 Introduction 58 5.1.1 Techniques to determine diets of herbivores 58 5.1.2 Hypotheses and aims 60 5.2 Methods 60 5.2.1 Sampling approach 60 5.2.2. Microhistological analysis 60 5.2.3 DNA metabarcoding 60 5.2.4 Statistical analysis 61 5.3 Results 62 5.4 Discussion 64 5.4.1 Comparison of the two techniques 64 5.4.2 The way forward 66 Chapter 6 68 Summary and concluding remarks 6.1 Synthesis of results 68 6.1.1 How the diet, preference and diet quality of elephants changes, 68 with an increase in resource availability. 6.1.2 Comparing the diet of elephants using microhistological analysis 71 to DNA metabarcoding of faeces 6.2 Contextualizing the study 72 6.3 The way forward 73 6.4 Conclusion 74 References 76 Appendix 1 The proportion (± SD) of elephants diet for the Principal Diet Items 96 indicating significant preference or avoidance for the Main Camp and the Colchester sections. Appendix 2 Rainfall (mm) recorded in the Addo Elephant National Park during 100 January 2007 to April 2008 for the study period (June 2007 to April 2008) of de Klerk (2009). Appendix 3 The method used to in DNA metabarcoding for identification of the 101 diet of elephants in the Addo Elephant National Park during February 2014. Appendix 4 The proportion (± SD) of plant families identified in the diet of 102 elephants using Microhistological analysis and DNA metabarcoding. iv ABSTRACT Animals are restricted in their diets by several factors, most notably the availability and quality of resources. Variation in resource availability causes herbivores to shift their diets seasonally and spatially. Elephants (Loxodonta africana), are known to have extensive impacts on plant communities, altering ecosystem functioning and causing a decline in biodiversity. In enclosed areas, these impacts are increased leading to a decline in resource availability and presumably resource quality. In the Addo Elephant National Park, the Main Camp section has a history of high elephant impacts and therefore reduced resource availability. Whereas, the recently added Colchester section has greater resource availability, due to the absence of elephants in this section since the fencing of the Park. This study investigated the changes in diet (diet breadth, preference and diet quality) of elephants due to an increase in resource availability. Three alternative hypotheses were contrasted: 1) elephants as generalist foragers, 2) elephants as optimal foragers, or 3) elephants learning foraging behaviour. Using microhistological analysis, the diets of elephants were described over five sampling periods (August 2010 – February 2014) in both sections. Forage availability was estimated using a modified line-intercept method, and was used to determine changes in preference by relating forage availability to use. In the Colchester section the diet breadth of elephants increased, and was coupled with a high initial variation between the diets of elephants, which decreased in subsequent sampling periods. This supported the elephants learning foraging behaviour hypothesis. However, there was no increase in diet preference by elephants in the Colchester section, which supported the elephants as generalist foragers hypothesis. There was also no difference in the diet quality of elephants in the Main Camp and Colchester sections, which did not support any of the three hypotheses. The elephants learning foraging behaviour hypothesis is proposed to be the link between the alternate two hypotheses, and given enough time, either of the two could be supported. The lack of difference in preference and diet quality between elephants in the Main Camp and Colchester sections is hypothesised to be due to the population level (not measured for individuals) at which these were measured. Microhistological analysis of faeces was used to describe the diet of elephants, which was compared to the diet described by DNA metabarcoding. Microhistological analysis is a traditional, favoured technique used in describing the diet of wild herbivores, whereas DNA metabarcoding is a relatively new and untested technique. These two techniques have not yet been compared in the diet of megaherbivores. Results indicated that microhistological analysis identified significantly more grass in the diet of elephants, than DNA metabarcoding did, which was expected as previous studies also found overestimation of grasses. Microhistological analysis identified more plant families in the diet of elephants, than DNA metabarcoding. Most of the differences between the two techniques can be attributed to the difference in taxonomic resolution, which was due to the lack of a complete reference collection for DNA metabarcoding.