Behavior and Ecology of the Riparian Brush Rabbit at the San Joaquin
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BEHAVIOR AND ECOLOGY OF THE RIPARIAN BRUSH RABBIT AT THE SAN JOAQUIN RIVER NATIONAL WILDLIFE REFUGE AS DETERMINED BY CAMERA TRAPS A Thesis Presented to the Faculty of California State University, Stanislaus In Partial Fulfillment of the Requirements for the Degree of Master of Ecology and Sustainability By Celia M. Tarcha May 2020 CERTIFICATION OF APPROVAL BEHAVIOR AND ECOLOGY OF THE RIPARIAN BRUSH RABBIT AT THE SAN JOAQUIN RIVER NATIONAL WILDLIFE REFUGE AS DETERMINED BY CAMERA TRAPS By Celia M. Tarcha Signed Certification of Approval page is on file with the University Library Dr. Patrick A. Kelly Date Professor of Zoology Dr. Michael P. Fleming Date Associate Professor of Biology Education Dr. Marina M. Gerson Date Professor of Zoology Matthew R. Lloyd Date U.S. Fish and Wildlife Service © 2020 Celia M. Tarcha ALL RIGHTS RESERVED DEDICATION For my family, living and departed, who first introduced me to wildlife and appreciating inconspicuous beauty. iv ACKNOWLEDGEMENTS I wish to express my deepest gratitude to my committee members, Matt Lloyd, Dr. Fleming, Dr. Gerson, and Dr. Kelly, for their time and effort towards perfecting this project. I would also like to thank Eric Hopson, refuge manager of San Joaquin River National Wildlife Refuge for his insight and field support. Thank you as well to refuge biologists Fumika Takahashi and Kathryn Heffernan for their field surveys and reports. Additional thanks to Camera Bits Inc. for their donation of the Photomechanic license. I would like to thank the CSU Stanislaus Department of Biological Sciences for their help and support. Thank you to Bernadette Paul of the Endangered Species Recovery Program for her equipment management and support. A special thanks to Scott Phillips of the Endangered Species Recovery Program for his statistical and GIS assistance. Thank you to student Rachael Devaughn for entering my vegetation data. Additionally, thank you to my uncle, Greg Tarcha, and aunt, Carmen Gonzalez, for data management advice. I would like to pay my special regards to my undergraduate professors at San Jose State University, Professor Trewhitt, Dr. Smith, Dr. Lambrecht, Dr. Myatt, and Dr. Bros, who prepared and inspired me to pursue wildlife biology and higher education. Lastly, I would like to thank my parents Mark and Cora Tarcha, my extended family, and my friends for their love and support that carried me through this project. v TABLE OF CONTENTS PAGE Dedication ............................................................................................................... iv Acknowledgements ................................................................................................. v List of Tables .......................................................................................................... viii List of Figures ......................................................................................................... xi Abstract ................................................................................................................... xiv CHAPTER I. Introduction ........................................................................................... 1 II. Background ........................................................................................... 5 Ecology and Conservation ........................................................ 5 Geographic and Regulatory Setting .......................................... 7 Previous Riparian Brush Rabbit Research and Emerging Technologies ............................................................................. 10 Environmental Threats to Riparian Brush Rabbit Recovery .... 13 III. Methods................................................................................................. 17 Camera Survey .......................................................................... 19 Vegetation Surveys ................................................................... 23 Photo Processing ....................................................................... 24 Data Analysis ............................................................................ 28 IV. Results ................................................................................................... 34 Riparian Brush Rabbit Activity ................................................ 35 Riparian Brush Rabbit Community Ecology ............................ 53 Riparian Brush Rabbit Utilization of Habitat ........................... 57 Riparian Brush Rabbit Behavior Types .................................... 60 Documented Animals................................................................ 70 Extent of Habitat Use ................................................................ 73 Vegetation ................................................................................. 77 vi V. Discussion ............................................................................................. 84 Riparian Brush Riparian Activity ............................................. 84 Riparian Brush Rabbit Interactions ........................................... 86 Riparian Brush Rabbit Habitat Use........................................... 96 Effects of the 2017 Flood on the Riparian Brush Rabbits of San Joaquin River National Wildlife Refuge................................... 101 Future Research ........................................................................ 104 In Conclusion ............................................................................ 107 References ............................................................................................................... 112 Appendices A. Camera Site Summaries .............................................................................. 127 B. Ethogram and Behavior Tags ...................................................................... 146 C. Photograph Tag Assignment and Definitions ............................................. 147 D. Log of Camera Status.................................................................................. 150 E. Discussion of the Behavioral Repertoire of the Riparian Brush Rabbit ..... 151 a. Behavior Tag Summaries ................................................................ 151 b. Behavior Results ............................................................................. 178 F. Effectiveness of Camera Traps to Study Riparian Brush Rabbit Behavior 179 a. Impacts of Site Choice and Design ................................................. 179 b. Camera Model Performance ........................................................... 180 c. Studying Riparian Brush Rabbit Activity ....................................... 181 d. Studying Riparian Brush Rabbit Behavior and Intraspecific Interactions ...................................................................................... 182 e. Studying Riparian Brush Rabbit Interspecific Interactions and Community Ecology ....................................................................... 183 vii LIST OF TABLES TABLE PAGE 1. Camera sessions and dates during the flood of 2017 ........................................ 18 2. Camera sessions and dates after 2017 floodwaters began to recede ................. 18 3. Habitat resources present at each site ............................................................... 22 4. Orientations and alterations to camera sites ...................................................... 22 5. Number of photos collected at each site by month ........................................... 35 6. Number of days cameras were active at each site ............................................. 35 7. Results of single factor analysis of variance (ANOVA) for all time periods separately .......................................................................................................... 42 8. Results of single factor analysis of variance (ANOVA) between time periods with dawn and dusk combined into one group, crepuscular ..................................... 42 9. Results of single factor analysis of variance (ANOVA) between the number of times riparian brush rabbits were at rest and active in the grouped data .......... 45 10. Results of t-Test of riparian brush rabbit rest and activity................................ 45 11. Analysis of variance (ANOVA) between activity with and without the tag vigilant .............................................................................................................. 47 12. Analysis of variance (ANOVA) between times RBR were inactive, resting or vigilant, and active ............................................................................................ 47 13. Number of photos recorded per species and proportion of tagged photos ....... 54 14. Number of photos with different numbers of riparian brush rabbit co-occurring per site ............................................................................................................... 56 15. Count of photos with each vegetation tag ......................................................... 59 viii 16. Number of behavior types and individual riparian brush rabbit recordings across sites with proportion calculated as a percentage ............................................... 60 17. Results of single factor analysis of variance (ANOVA) comparing the numbers of individual, intraspecific, and interspecific behaviors ....................................... 61 18. Results of t-Test comparing the means of individual and intraspecific behaviors of riparian brush rabbits .......................................................................................