U.S. Fish and Wildlife Service U.S. Department of the Interior National Wildlife Refuge System Whooping Crane Winter Abundance Survey Protocol Aransas National Wildlife Refuge Survey Identification Number: FF02RTAR00-002 Protocol Signature Page Survey Identification Number #: FF02RTAR00-002 Version #: 1.0 Digital Object Identifier: 10.7944/W3159J Protocol Title: Whooping Crane Winter Abundance Survey Protocol Refuge Name: Author, Title, and Affiliation: Aransas National Wildlife Refuge Matthew J. Butler1, Biometrician, U.S. Fish and Wildlife Service Bradley N. Strobel, Wildlife Biologist, U.S. Fish and Wildlife Service Cinthia Eichhorn, Regional Data Manager, U.S. Fish and Wildlife Service Approvals Action Signature/Name Date Submitted By: Matthew J. Butler Biometrician Editor2: Grant Harris Chief Biological Sciences, Region 2 Aransas NWR Sonny Perez Approval: Refuge Manager/Project Leader Refuge Kelly McDowell Supervisor Approval: Texas and Oklahoma Refuge Supervisor Regional I&M Kristine L. Metzger Approval: Inventory & Monitoring Coordinator, Region 2 Version Date Author Change Made Reason for Change 1 Corresponding author, [email protected]. 2 Coordinated internal and external peer-review. Please cite this document as: Butler, M. J., B. N. Strobel, and C. Eichhorn. 2014. Whooping crane winter abundance survey protocol: Aransas National Wildlife Refuge. Survey Identification Number: FF02RTAR00-002. U.S. Fish and Wildlife Service, Austwell, Texas, USA. http://dx.doi.org/10.7944/W3159J. i Revision History Version numbers will be incremented by a whole number (e.g., Version 1.3 to 2.0) when a change is made that significantly affects requirements or procedures. Version numbers will be incremented by decimals (e.g., Version 1.6 to Version 1.7) when there are minor modifications that do not affect requirements or procedures included in the protocol. Rows will be added in the revision history log for each change or set of changes tied to an updated version number. There is no required timeline for revision of the protocol. However, changes to the objectives, sampling design, field methods, or analysis techniques should prompt protocol revision (U.S. Fish and Wildlife Service 2013). Revision History Log Version # Date Revised by Changes Example Date of Revision Name(s)  List items that were changed or revised and specify if changes were minor or major. 1.0 26 March 2014 Matthew Butler  Protocol created. Bradley Strobel Cinthia Eichhorn ii Contents Protocol Signature Page ................................................................................................................... i Revision History ............................................................................................................................. ii Figures............................................................................................................................................. v Tables ............................................................................................................................................ vii Appendices ..................................................................................................................................... ix Acknowledgements ........................................................................................................................ xi Executive Summary ...................................................................................................................... xii Survey Protocol Narrative ............................................................................................................... 1 Element 1: Background and Objectives .................................................................................. 1 Element 2: Pilot Studies........................................................................................................... 9 Element 3: Sampling Design ................................................................................................. 12 Element 4: Field Methods ...................................................................................................... 25 Element 5: Data Management ............................................................................................... 31 Element 6: Data Analysis ...................................................................................................... 34 Element 7: Reporting ............................................................................................................ 35 Element 8: Personnel Requirements and Training ................................................................ 39 Element 9: Operational Requirements ................................................................................... 40 Element 10: References ......................................................................................................... 42 Overview of the Whooping Crane Abundance Protocol .............................................................. 51 Standard Operating Procedures..................................................................................................... 54 Standard Operating Procedure 1: Conducting Surveys ......................................................... 54 Standard Operating Procedure 2: Data Download and Transcription ................................... 61 Standard Operating Procedure 3: Post-flight Data Processing and Formatting .................... 64 Standard Operating Procedure 4: Creating Text Files for Analyses ...................................... 76 iii Standard Operating Procedure 5: Data Preparation for Hierarchical Distance Sampling Analyses using Unmarked ....................................................................................... 81 Standard Operating Procedure 6: Data Archiving ................................................................. 87 iv Figures Figure 1. Aransas National Wildlife Refuge and surrounding areas typically inhabited by wintering whooping cranes; area includes portions of Aransas, Calhoun, and Refugio counties, Texas, USA. ................................................................................................ 2 Figure 2. Comparison of the reported population size from the traditional “census” effort and the maximum count of whooping cranes observed during the traditional “census” effort during a survey year. Surveys were conducted during winter 1980– 2010 on and around Aransas National Wildlife Refuge, Texas, USA. ........................................... 4 Figure 3. Histogram of distances from transect to whooping crane groups observed during aerial surveys along the Texas gulf coast, USA, during the traditional census flights, winter 2010–2011. ............................................................................................................ 10 Figure 4. Sandhill crane decoys (Carry-Lite Decoys, Alabaster, Alabama, USA) were painted to resemble whooping cranes. Some decoys were painted white to resemble adults and some were painted tawny to represent hatch-year birds. Though sandhill cranes are smaller than whooping cranes, their body form is similar resulting in good surrogates for examining factors that influence the detection process. ........................... 11 Figure 5. Locations where whooping cranes have been observed during the traditional surveys on and around Aransas National Wildlife Refuge, Texas, USA, winter 1990–2010. ........................................................................................................................ 13 Figure 6. The sampling frame for monitoring whooping crane on their wintering grounds along the Texas gulf coast, USA. These were not formally defined during the traditional “census” effort. ...................................................................................................... 14 Figure 7. The sampling design for whooping crane surveys on their wintering grounds has nested sampling units. ............................................................................................... 17 Figure 8. The sampling frame and survey transects for monitoring whooping cranes on their wintering grounds along the Texas gulf coast, USA. Transects are spaced at 1-km intervals. .............................................................................................................................. 18 Figure 9. Box plots describing chronology of whooping crane arrival and departure on the Texas gulf coast, USA. Data from periodic aerial surveys, centered on Aransas National Wildlife Refuge, conducted during the winters of 1950–2011. Solid black lines represent the median proportion of the annual maximum count by date. Boxes contain the 0.25 and 0.75 quantiles of data, while the lines span the entire dataset except outliers (black circles). The red box represents the time of year during which effort will be exerted to estimate the whooping crane abundance, age-ratios, and number of recruitive pairs in the primary sampling frame (Sampling Objectives 1–3). Blue boxes represent times in which additional survey effort could be exerted for other monitoring objectives. .................................................................................................... 19 v Figure 10. Ratio and 95% confidence intervals of hatch-year (HY) to after-hatch- year (AHY) whooping cranes observed during the traditional “census” effort from 1980–2010 on and around Aransas National Wildlife Refuge, Texas, USA. We only used data from surveys conducted between 28 November–26 December. The estimates were based on multiple samples with replacement ratio estimator where each survey represented a sample (Skalski et al. 2005). During winter 2008–2009, only one survey was conducted between 28 November–26 December, so we used an estimator based on a single sample survey (Skalski et al. 2005). ................................................. 21 Figure 11. Multiple whooping cranes observed with species of other white birds during traditional winter surveys along the Texas gulf coast, USA. Photograph taken by T. Stehn. ................................................................................................................................... 24 Figure 12. Predicted probability of detection for whooping crane decoy groups on Aransas National Wildlife Refuge, Texas, USA. Predictions based on logistic regression of detection with covariates of group size, distance from transect (quadratic effect), and sun position. Solid line is sun at observer’s back, dashed line is sun overhead, and dotted line is sun in observer’s face. The decoy experiment was conducted from a fixed-wing aircraft with pontoons resulting in reduced detection probability near the line. Such aircraft will not be used in future surveys. ................................. 27 Figure 13. Allocation of observer search effort for distance sampling-based survey methods for wintering whooping cranes along the Texas gulf coast, USA. The gray area represents search effort by the front seat observer and the blue area represent search effort by the back seat observer. ........................................................................................ 28 Figure 14. Overview of data management and data archiving for winter aerial surveys of whooping cranes on the Texas gulf coast, USA. ......................................................... 33 Figure 15. Reporting schedule for whooping crane monitoring activities on and around Aransas National Wildlife Refuge, Texas, USA. ............................................................. 38 Figure A1. Power curves for determining the coefficient of variation of abundance estimates required to detect a given decline in abundance; based on 1-tailed z-test ( . The solid line represents a 20% decline, the dashed line is a 15% decline, the dot-dashed line is a 10% decline, and the dotted line is a 5% decline. ..................... 92 Figure A2. Power curves for determining the coefficient of variation of abundance estimates required to detect a given decline in abundance; based on 1-tailed z-test ( . The solid line represents a 20% decline, the dashed line is a 15% decline, the dot-dashed line is a 10% decline, and the dotted line is a 5% decline. ................................... 93 Figure A3. Power curves for determining the coefficient of variation of abundance estimates required to detect a given decline in abundance; based on 1-tailed z-test ( . The solid line represents a 20% decline, the dashed line is a 15% decline, the dot-dashed line is a 10% decline, and the dotted line is a 5% decline. ..................... 93 vi Tables Table 1. The number of transects and survey effort (i.e., total transect length) for the regions within the Primary and Secondary Sampling Frames. ..................................................... 15 Table 2. The minimum number of whooping cranes groups that must be detected in a secondary region before that secondary region will be included in the primary sampling frame for future surveys. ............................................................................................... 16 Table 3. Hardware needed to conduct aerial surveys for whooping cranes on their wintering grounds along the Texas gulf coast, USA. ................................................................... 26 Table 4. Estimated budget for monitoring whooping cranes on their wintering grounds along the Texas gulf coast, USA. .................................................................................... 41 Table 5. Estimated staff time to complete annual monitoring of whooping cranes on their wintering grounds along the Texas gulf coast, USA. Estimates based on number of times and duration of each activity during winter 2011–2012. ................................................ 41 Table A1. The number of surveys that need to be conducted in the Primary Sampling Frame to obtain a target coefficient of variation for the abundance estimate. Based on data collected during winter 2011–2012. ...................................................................................... 91 Table A2. Estimated precision of abundance estimates required to detect a population trend from distance sampling-based aerial surveys for whooping cranes along the Texas gulf coast, USA................................................................................................... 94 Table E1. Generalization of the Texas Ecological Systems Classification scheme into 6 general vegetation classes for use in hierarchical distance sampling models. ......................... 122 Table G1. The survey_mmddyy feature class has the following attributes. .............................. 127 Table G2. The transects_ideal_primary and transects_ideal_secondary feature classes have the following attributes........................................................................................... 128 Table G3. The cranes_mmddyy feature class has the following attributes. .............................. 128 Table G4. The CDS_mmddyy file has the following attributes................................................. 129 Table G5. The HDS_mmddyy has the following attributes. ...................................................... 129 Table G6. The gen_near_tbl_mmddyy has the following attributes. ........................................ 129 Table G7. The transects_mmddyy has the following attributes. ............................................... 130 Table G8. The flight_mmddyy file has the following attributes. ............................................... 130 vii