(Title of the Thesis)*

The Application of Occupancy Modeling to Evaluate the Determinants of Distribution of Jaguars Panthera onca, Pumas Puma concolor, and Valued Prey Species in a Protected Area by Holly Booker A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Master of Environmental Studies in Environment and Resource Studies Waterloo, Ontario, Canada, 2016 © Holly Booker 2016 AUTHOR'S DECLARATION I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii Abstract In the past four decades, both biodiversity and individual populations of numerous species in the tropics have consistently declined. Tropical forests constitute only 6% to 7% of the Earth’s surface, yet they contain more than half of all species richness, making them a significant reservoir for global biodiversity. Maintaining healthy populations of both predators and prey in the tropics is therefore crucial for supporting dynamic ecosystems and for preserving biodiversity. As apex predators, jaguars Panthera onca and pumas Puma concolor play a critical role in helping to support dynamic tropical ecosystems. Correspondingly, prey species of value to these felids are equally important. Ecological models have become valuable tools for facilitating an understanding of how species distribution is influenced by natural landscape variables and anthropogenic factors. The objectives of this study were to utilize hierarchical occupancy modeling to assess if jaguars, pumas, and valued prey species (brocket deer Mazama sp., white-tailed deer Odocoileus virginianus, collared peccary Pecari tajacu, white-lipped peccary Tayassu pecari, lowland paca Cuniculus paca, Central American agouti Dasyprocta punctate, and white-nosed coati Nasua narica) are non-randomly distributed across the Calakmul Biosphere Reserve in Campeche, Mexico, and how natural and anthropogenic features are influential in shaping this distribution. Because felid distribution is thought to largely depend on prey availability, latent occupancy estimates for focal prey were also incorporated into occupancy models for jaguars and pumas. Spoor sampling was conducted using line transects in four survey areas throughout the core and buffer zone of the reserve from June 25th to August 8th, 2013. Detection histories for focal species were utilized for occupancy modeling that was completed in the ‘unmarked’ package in R. It was determined that distribution was random for brocket and white-tailed deer species, was largely random for collared peccary, and non-random for white-lipped peccary, large prey as a group, and medium prey species collectively. Model averaged occupancy of collared peccary was 30% higher than it was for white-lipped peccary and occupancy was weakly associated with increasing tree species richness. White-lipped peccary occupancy was lower in areas with decreased tree species richness and diminished total basal area, likely corresponding to disturbed habitat. Occupancy of large prey as a collective group had a weak negative association with proximity to water (aguadas specifically). A weak association of site (survey area) was found for occupancy of medium prey collectively, as models exhibited higher occupancy estimates for the survey areas located in the core zone of the CBR, which is an area intended to be free of disturbance. Distribution of jaguars and pumas was found to be primarily influenced by occupancy of brocket deer and medium prey species. There was also a weak negative association with proximity to an aguada. Results from this study reinforce the need for evaluating tropical species occupancy, as understanding the factors that are influential in determining distribution is quite complex. Due to the troubling status of jaguars and pumas, understanding how landscape variables, as well as prey occupancy, influences their distribution is of utmost importance to ensure that critical habitat is protected and/or restored and that human-wildlife conflicts are minimized. This study is the first to explicitly integrate both landscape variables and latent occupancy of prey species as covariates in occupancy models for jaguars and pumas and it adjoins only a handful of studies that model occupancy of the focal species in Mexico. iii Acknowledgements I would like to thank the numerous people who helped to make this research, and ultimately my thesis, possible. I was lucky enough to have three incredible academics by my side that assisted me immensely throughout this process. My co-advisor, Dr. Stephen Murphy, who was always encouraging, supportive, uplifting, and always able to offer incredibly insightful and thought provoking advice. My other co-advisor, Dr. Bradley Fedy, whose impressive experience as an ecologist, extensive knowledge base, and encouragement brought invaluable guidance to my thesis and my life. I am pretty sure there is nothing that he does not know how to do. Finally, Dr. Jeffrey Row; without his extensive knowledge of R, this thesis would not have been possible. Thank you for your incredible patience, your coding wisdom and wizardry, and continuous support right from the beginning. I would like to thank Operation Wallacea and Dr. Kathy Slater. This organization and Dr. Slater’s work are pivotal to the conservation of Calakmul Biosphere Reserve and I was so lucky to have the opportunity to work with them. I would also like to acknowledge the local people of the CBR that were instrumental in the logistics of the field season and for their incredible wealth of indigenous knowledge and desire to conserve this special place. Thank you to Drs. Leslie King and Alison Moran who encouraged me to pursue my degree and helped me to believe it was possible. I will always be grateful to my mom, Kathy, for her endless support, love, and faith that I can do anything, no matter how wild it seems. I am also forever indebted to my incredible sister-in-law, Jody; if not for her help with my daughter, this thesis would never have been finished. Isla and I are so lucky to have you in our lives. Finally, thank you to my amazing husband, Danny, who has whole-heartedly supported me in every way, even when my ideas are completely crazy. His ceaseless optimism and easygoing demeanor have been my saving grace countless times. From moving to Vancouver Island for a year, to hiking through the rainforests of Indonesia, and even living in a tent in the jungles of Mexico for fieldwork, I am unbelievably fortunate to have had him by my side in all of our adventures. You are my number one fan and without your love and support none of this would have been possible. iv Dedication This thesis is dedicated to my incredible, wonderful, enchanting, and inquisitive, daughter, Isla. Never believe that you can’t because you are capable of anything. To quote William Shakespeare, “And though she be but little, she is fierce.” This could not be truer for my little girl and I could not be more proud. I love you with all my heart. v Table of Contents AUTHOR'S DECLARATION .......................................................................................................... ii Abstract ........................................................................................................................................... iii Acknowledgements .......................................................................................................................... iv Dedication......................................................................................................................................... v Table of Contents ............................................................................................................................. vi List of Figures .................................................................................................................................. ix List of Tables .................................................................................................................................... x Chapter 1 Introduction and Literature Review ................................................................................... 1 1.1 Global Biodiversity and Wildlife Population Declines.............................................................. 1 1.2 Predator and Prey Dynamics .................................................................................................... 2 1.3 Focal Species ........................................................................................................................... 3 1.3.1 Predators ........................................................................................................................... 3 1.3.2 Prey .................................................................................................................................. 6 1.4 Monitoring the Status of Felids and Their Prey ...................................................................... 10 1.5 Modeling Approach ............................................................................................................... 11 1.6 Modeling Covariates .............................................................................................................. 13 1.7 Model Fitting and Selection ................................................................................................... 15 1.7.1 Model Fitting

Load more