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California Clapper Rail ( Rallus Longirostris Obsoletus ) Population Monitoring: 2005-2011 Final Technical Report

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California Clapper Rail ( Rallus longirostris obsoletus ) Population monitoring: 2005-2011 Final Technical Report Leonard Liu, Julian Wood, Nadav Nur, Leo Salas, and Dennis Jongsomjit PRBO Conservation Science 3820 Cypress Drive #11, Petaluma, CA 94954 California Clapper Rail Population Monitoring 2005-2011 Final Report Table of Contents ACKNOWLEDGMENTS.......................................................................................3 EXECUTIVE SUMMARY.......................................................................................4 INTRODUCTION ..................................................................................................6 METHODS ..............................................................................................................9 FIELD SURVEYS .................................................................................................................... 9 ANALYSES ......................................................................................................................... 10 MODEL APPROACH ............................................................................................................. 11 ECOLOGICAL MODEL ........................................................................................................... 11 Detection Sub-model. ............................................................................................................................. 11 Abundance Sub-model. .......................................................................................................................... 12 SITE MODEL ...................................................................................................................... 13 YEAR MODEL .................................................................................................................... 13 LANDSCAPE MODEL ............................................................................................................ 14 POPULATION ESTIMATES ...................................................................................................... 14 RESULTS...............................................................................................................15 ECOLOGICAL MODEL ........................................................................................................... 15 Detection sub-model. ............................................................................................................................. 15 Abundance Sub-model. .......................................................................................................................... 16 SITE MODEL ..................................................................................................................... 17 ANNUAL VARIATION IN DENSITY ........................................................................................... 18 LANDSCAPE MODEL ............................................................................................................ 18 POPULATION ESTIMATES ...................................................................................................... 19 DISCUSSION........................................................................................................19 DETECTION PROBABILITY ...................................................................................................... 19 HABITAT SUITABILITY .......................................................................................................... 20 POPULATION SIZE OF CALIFORNIA CLAPPER RAIL AND ITS IMPLICATIONS ......................................... 21 CHANGE IN POPULATION SIZE , RECENT TRENDS , AND SHIFTS IN DISTRIBUTION ............................... 21 HISTORICAL ABUNDANCE AND DISTRIBUTION , COMPARISON WITH THE PRESENT ............................ 22 EVALUATION OF THE LANDSCAPE MODEL ................................................................................ 23 RECOMMENDATIONS.......................................................................................24 CONSERVATION AND MANAGEMENT RECOMMENDATIONS ........................................................ 24 MONITORING RECOMMENDATIONS ....................................................................................... 26 NEXT STEPS AND RECOMMENDATIONS FOR FUTURE STUDIES ..................................................... 27 Pilot protocol ......................................................................................................................................... 27 Clapper Rail life history and demography ................................................................................................ 28 LITERATURE CITED...........................................................................................29 TABLES………………………………………………………………………………..34 FIGURES……………………………………………..………………………………..54 APPENDIX……………………………………………………………………...…….79 2 California Clapper Rail Population Monitoring 2005-2011 Final Report Suggested citation Liu, L., J. Wood, N. Nur, L. Salas, and D. Jongsomjit. 2012. California Clapper Rail ( Rallus longirostris obsoletus ) Population monitoring: 2005-2011. PRBO Technical Report to the California Department of Fish and Game. Acknowledgments PRBO data collected under TE-807078-10 and -12 from USFWS and a Memorandum of Understanding between California Dept. of Fish and Game and PRBO (3/14/2003-3/14/2005; 4/23/2010). This project was made possible with additional funding from the Grand Foundation and the California State Coastal Conservancy’s Invasive Spartina Project. In addition to our collaborators (Avocet Research Associates, California Department of Fish and Game, California Coastal Conservancy’s Invasive Spartina Project, U.S. Fish and Wildlife Service, East Bay Regional Park District, and H.T. Harvey and Associates), PRBO benefited greatly from the assistance of a number of other individuals, organizations and agencies who helped with site access: California Department of Transportation, City of Palo Alto, City of Petaluma, City of Redwood City, Marin Audubon Society, Pacific Gas and Electric Company, Ryan Phelan, Port of Sonoma, San Mateo Department of Transportation, Shell Oil Company, and Vallejo Sanitation and Flood Control District. We would also like to thank Elizabeth Brusati, Craig Cummings, Loring Dales, Anna Doty, Natasha Dvorak, Joe Eaton, Megan Elrod, Sarah Estrella, Dea Freid, Jeanne Hammond, Terra Hendrich, Mark Herzog, Ingrid Hogle, Beth Huning, Rick Johnson, Robin Leong, Molly McNamara, Eric Pilotte, Orien Richmond, John Robeson, Christina Sloop, Bill Stagnaro, Ron Sullivan, Karen Taylor, Laura Valoppi, Erika Walther, Amber Wingert, and Jason Yakich who contributed their time to assist with this effort. This is PRBO contribution number 12220. 3 California Clapper Rail Population Monitoring 2005-2011 Final Report Executive Summary In 2005, PRBO Conservation Science led a multi-partner effort to develop standardized survey protocols and determine population size and trends for the endangered California Clapper Rail in the San Francisco Bay Estuary. Partners contributing to the standardized protocol dataset included the U. S. Fish and Wildlife Service, California Department of Fish and Game, California Coastal Conservancy’s San Francisco Estuary Invasive Spartina Project, Avocet Research Associates, and East Bay Regional Park District. Data were collected from 212 marsh sites throughout the San Francisco Bay Estuary from 2005 through 2011 using standardized point count protocols to assess abundance and distribution and the relationship to habitat and landscape features. Data were analyzed using imperfect detection models or “zero-inflated models” that assume that some visits with no detections are in fact false zeroes meaning an individual was present but not detected. Failure to account for excess zeroes in the dataset can result in underestimates of true abundance. By correcting for imperfect detection, the statistical models can overcome an important bias affecting estimates of rail abundance. The California Clapper Rail population was relatively stable in 2005-2007, declined significantly in 2008 (51%), which was followed by low but relatively stable densities in 2009-2011. The decline in the South Bay (south of the San Francisco-Oakland Bay Bridge) was steeper and densities lower than in the North Bay during the period 2008- 2011. The California Clapper Rail range-wide population size was estimated at 1,167 individuals (range 954 to 1426) during 2009–2011. This estimate was developed by combining the site-specific densities from surveyed sites with predicted densities from unsurveyed areas using a statistical model that incorporated 15 key physical predictor variables that characterized marsh habitat and landscape condition in relation to Clapper Rail density. By accounting for fine-scale variation in habitat conditions relevant to Clapper Rails, this method represents a significant improvement over previous population estimates that simply applied average densities to total marsh area. Marsh complexes with the highest densities identified by our models were found along the western shores of San Pablo Bay from China Camp to Petaluma River and Corte Madera area. Marsh complexes in the South Bay with relatively high densities included East Palo Alto-Guadalupe Slough and Bair-Greco-Ravenswood. Time of season and time of day were the most important factors affecting Clapper Rail probability of detection. The effect of Julian day on probability of detection
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