Protocol of Jaguar Survey and Monitoring Techniques and Methodologies A Submission to the U.S. Fish and Wildlife Service in Partial Fulfillment of Contract F13PX01563 16 October 2014 © Daniel Alarcon John Polisar, Sean M. Matthews, Rahel Sollman, Marcella J. Kelly, Jon P. Beckmann, Eric W. Sanderson, Kim Fisher, Melanie Culver, Rodrigo Núñez, Octavio C. Rosas Rosas, Carlos A. López González, Bart J. Harmsen, Tim G. O’Brien, Carlos De Angelo, and Fernando C. C. Azevedo TABLE OF CONTENTS Table of Contents ........................................................................................................................... i Table of Tables ............................................................................................................................. iv Table of Figures............................................................................................................................. v Executive Summary ...................................................................................................................... 1 Monitoring and Jaguar Conservation ......................................................................................... 4 Jaguars Across the Northwestern Recovery Unit ...................................................................... 7 Jaguars in the Americas............................................................................................................... 7 Range Retraction on the Limits of Jaguar Range ........................................................................ 7 Jaguar Conservation 1973 to Present .......................................................................................... 8 Jaguars in Mexico........................................................................................................................ 9 Monitoring Jaguars in the NRU and Range Wide..................................................................... 10 Jaguar Status and Habitats in the NRU ..................................................................................... 10 Borderlands Secondary Area ................................................................................................. 11 Sonora Core Area ................................................................................................................. 14 Sinaloa Secondary Area......................................................................................................... 17 Jalisco Core Area ................................................................................................................... 18 Presence-Absence and Occupancy ............................................................................................ 22 Practical Considerations ............................................................................................................ 22 Survey Protocol for Monitoring Jaguar Occupancy .................................................................. 24 Defining and Choosing Sample Units ................................................................................... 25 Spatial Coverage of the Sample Unit .................................................................................... 26 Sampling Duration ................................................................................................................. 26 Setting Cameras ..................................................................................................................... 27 Data Recording ...................................................................................................................... 29 Data Analysis ......................................................................................................................... 31 Equipment and Costs ............................................................................................................. 31 Logistical Challenges ............................................................................................................ 32 Occupancy Modeling ................................................................................................................ 33 Types of Occupancy Models ................................................................................................. 33 Pilot Data ............................................................................................................................... 35 Measuring Trends in Occupancy ........................................................................................... 35 Power Analysis ...................................................................................................................... 36 i Occupancy Modeling for Prey Species ................................................................................. 37 Sign-based Occupancy Sampling for Jaguars ....................................................................... 39 Conclusion ................................................................................................................................. 40 Abundance and Density .............................................................................................................. 42 Practical Considerations ............................................................................................................ 44 Survey Protocol for Monitoring Jaguar Abundance and Density ............................................. 47 Abundance/Density Estimation Field Techniques ................................................................ 47 Choosing Sampling Sites ....................................................................................................... 47 Trap Distance, Camera Numbers, and Spatial Extent ........................................................... 48 Genetic Sampling for Abundance and Density ..................................................................... 49 Sampling Duration ................................................................................................................. 50 Setting and Checking Cameras .............................................................................................. 51 Surveying with Scat-Detection Dogs .................................................................................... 52 Data Recording ...................................................................................................................... 52 Data Analysis ......................................................................................................................... 55 Equipment and Costs ............................................................................................................. 56 Logistical Challenges ............................................................................................................ 58 Capture-Recapture Modeling for Abundance and Density Estimation ..................................... 58 Types of Abundance/Density Models ................................................................................... 58 Pilot Data ............................................................................................................................... 61 Measuring Trends in Abundance/Density ............................................................................. 61 Conclusion ................................................................................................................................. 62 Population Genetics .................................................................................................................... 64 Jaguar Scat Collection ............................................................................................................... 65 Opportunistic Searches .......................................................................................................... 65 Scat Collection ....................................................................................................................... 65 Sampling Using Scat-Detection Dogs ................................................................................... 67 Equipment and Costs ............................................................................................................. 68 Laboratory Genetic Methods ..................................................................................................... 68 DNA Isolation From Scat ...................................................................................................... 68 Species Identification ............................................................................................................ 69 Individual Identification ........................................................................................................ 70 Costs ...................................................................................................................................... 70 Analysis of Jaguar Scat Genetic Data ....................................................................................... 70 ii Species Identification ............................................................................................................ 70 Individual Identification and Population Genetics ................................................................ 70 Demographic Parameters and Spatial Ecology ........................................................................ 71 Dispersal and Long-Distance Movements ...............................................................................