Jaguar Survey and Monitoring Techniques and Methodologies: A Review A Submission to the U.S. Fish and Wildlife Service in Partial Fulfillment of Contract F13PX01563 © Daniel Alarcon John Polisar, Tim G. O’Brien, Sean M. Matthews, Jon P. Beckmann, Eric W. Sanderson, Octavio Cesar Rosas-Rosas, and Carlos A. López-González 27 March 2014 Table of Contents Executive Summary ...................................................................................................................... 1 Background ................................................................................................................................... 2 Survey Designs and Statistical Analyses Applied to Data Collected During Jaguar Surveys, Monitoring, and Research .................................................................................................... 5 Abundance and Occurrence ........................................................................................................ 6 Species Distribution Mapping: Modeling presence-only data .................................................... 7 Logistic Regression: Modeling presence-absence data ............................................................. 10 Occupancy: Modeling detection-non-detection data................................................................. 11 Kinds of Occupancy Models ................................................................................................. 14 Capture-Recapture Models for Density Estimation Using Replicated Count Data .................. 17 Poisson Encounter Model ...................................................................................................... 19 Binomial Encounter Model ................................................................................................... 20 Density Estimation Using DNA ............................................................................................ 23 Estimation of Density When Animals Are Not Individually Recognizable ............................. 24 A Bayesian Approach ............................................................................................................ 24 Random Encounter Models ................................................................................................... 26 Estimation of Density and Trends Using Unreplicated Count Data ......................................... 28 Relative Abundance Indices .................................................................................................. 30 Power Analysis Fundamentals .................................................................................................. 32 Field Techniques Applied to Surveying and Monitoring Jaguars ......................................... 33 Sign............................................................................................................................................ 33 Tracks .................................................................................................................................... 34 Kills ....................................................................................................................................... 38 Scats ....................................................................................................................................... 39 Interviews .................................................................................................................................. 42 Remote Cameras ....................................................................................................................... 45 Designing Surveys ................................................................................................................. 48 Refining the Design ............................................................................................................... 52 Setting Camera Traps ............................................................................................................ 54 Using Data for Indices of Species Not Identifiable to Individual Level ............................... 55 Occupancy Surveys ............................................................................................................... 58 Additional Details on Survey Design and Analyses .............................................................. 59 i Density Estimation ................................................................................................................ 60 Hair Collection .......................................................................................................................... 62 Utility, Considerations, and Limitations of Hair Snare Techniques for Jaguars ................... 63 Fecal DNA and Scat Detection Dogs ........................................................................................ 64 Sampling with Dogs .............................................................................................................. 65 DNA analyses ........................................................................................................................ 65 Utility, considerations, and limitations of detection dogs ..................................................... 66 Telemetry .................................................................................................................................. 67 Ecological Monitoring ........................................................................................................... 67 Population Monitoring ........................................................................................................... 68 Population Genetics .................................................................................................................... 70 Recommendations for Surveying in the Northwestern Recovery Unit .................................. 72 Summary and Closing Remarks ................................................................................................ 73 Literature Cited .......................................................................................................................... 74 Appendix 1: Jaguar Capturing and Handling ....................................................................... 111 Background ............................................................................................................................. 111 Capture Methods ..................................................................................................................... 111 Hounds ................................................................................................................................. 112 Snares................................................................................................................................... 113 Box Traps ............................................................................................................................ 114 Immobilization and Handling.................................................................................................. 114 Literature Cited ....................................................................................................................... 116 Appendix 2: Ecological Factors in Human-Jaguar Conflicts and Coexistence .................. 121 Foundations ............................................................................................................................. 121 Prey Selection ...................................................................................................................... 121 Learned behaviors................................................................................................................ 122 Habitat selection .................................................................................................................. 123 Foraging theory and management recommendations .......................................................... 124 Conservation Concepts ............................................................................................................ 125 Interventions to reduce the impact of jaguar attacks on livestock .......................................... 127 Interventions to reduce jaguar predation on livestock ............................................................ 127 Literature Cited ....................................................................................................................... 129 Appendix 3: Glossary ............................................................................................................... 132 Literature Cited ....................................................................................................................... 135 ii Suggested citation: Polisar, J., T. G. O’Brien, S. M. Matthews, J. P. Beckmann, E. Sanderson, O. C. Rosas-Rosas, and C. A. López-González. 2014. Review of Jaguar Survey and Monitoring Techniques and Methodologies. Wildlife Conservation Society final report to the U.S. Fish and Wildlife Service in response to Solicitation F13PX01563, submitted March 27, 2014. 110 pp. plus appendices. iii Executive Summary Jaguars (Panthera onca L.) have lived in the America’s for more than 2 million years, but thousands of years of range expansion were reversed in the last few hundred years, particularly on the northern margin of their range. In the United States, twentieth century records with photographic evidence, skins, and skulls are available from New Mexico,