2012 CLAPPER RAIL SURVEYS FOR THE SAN FRANCISCO ESTUARY INVASIVE SPARTINA PROJECT California Clapper Rail Surveys for the San Francisco Estuary Invasive Spartina Project 2012 Prepared by: Jen McBroom Olofson Environmental, Inc. 2612‐A 8th Street Berkeley, CA 94710 Contact: [email protected] For the State Coastal Conservancy San Francisco Estuary Invasive Spartina Project 1330 Broadway, 13th Floor Oakland, CA 94612 December 2012 ACKNOWLEDGEMENTS This report was designed and prepared under the direction of Jen McBroom, the Spartina Project Clapper Rail Monitoring Manager, with considerable hard work by Jen and other OEI biologists and staff, including Jeanne Hammond, Jeffrey Lewis, Jude Stalker, Stephanie Chen, Tobias Rohmer, Tripp McCandlish, and Whitney Thornton. Many thanks to Ingrid Hogle, who compiled and analyzed all Spartina data presented here. We are especially grateful for the support of our partners who shared clapper rail survey data that they collected over the past six years: PRBO Conservation Science, USFWS, East Bay Regional Park District, and Avocet Research and Associates. Cover photo ©Allen Hirsch, Oakland, California. http://allenh.zenfolio.com/. A California clapper rail (Rallus longirostris obsoletus) shakes off water after a swim at Arrowhead Marsh, Oakland, California. The ruffled orange breast feathers indicate that this bird carries a “backpack harness transmitter” secured by two straps encircling the bird’s breast. This bird is one of several dozen birds included in a recent study conducted by biologists at U.S. Geological Survey Western Ecological Research Center (http://www.werc.usgs.gov/Project.aspx?ProjectID=152). This report was prepared for the California Coastal Conservancy’s San Francisco Estuary Invasive Spartina Project with support and funding from the following contributors: California Coastal Conservancy California Wildlife Conservation Board (MOU #99‐054‐01 and subsequent) National Oceanic and Atmospheric Administration through the American Reinvestment and Recovery Act (Federal Grant #NA09NMF4630318) United Stated Fish and Wildlife Service, Southwest Region (Contract #F12PX00504) Table of Contents 1. Introduction ................................................................................................................................. 1 2. Study Area ................................................................................................................................... 3 3. Methods .................................................................................................................................... 13 3.1 Field Methods ...................................................................................................................... 13 Protocol A: Passive Call Count Survey ............................................................................... 13 Protocol C: Active Call Count Survey .................................................................................. 14 Protocol B: Stationary Call Count Survey ........................................................................... 14 Protocol F: Habitat Assessment Survey ............................................................................. 14 National Marsh Bird Monitoring Protocol (Pilot Study) ................................................... 14 3.2 Data Management ............................................................................................................... 15 3.3 Data Interpretation.............................................................................................................. 16 4. 2012 Survey Results ................................................................................................................... 17 4.1 Bay Bridge North Region ..................................................................................................... 18 4.2 San Leandro Bay Region ...................................................................................................... 21 4.3 Hayward Region................................................................................................................... 24 4.4 Union City Region ................................................................................................................ 27 4.5 Dumbarton South – Newark, Alviso, & Mountain View Regions ........................................ 30 4.6 San Mateo Region ............................................................................................................... 33 4.7 San Francisco Peninsula Region ........................................................................................... 36 4.8 Marin Region ....................................................................................................................... 39 4.9 San Pablo Bay – Vallejo and Petaluma Regions ................................................................... 42 4.10 Pilot Study on National Marsh Bird Monitoring Protocol ................................................. 44 5. Discussion .................................................................................................................................. 45 6. Permits ....................................................................................................................................... 47 7. References ................................................................................................................................. 49 Appendix 1: Standard Survey Protocols for California Clapper Rails in the San Francisco Estuary ....................................................................................................................................................... 51 Appendix 2: National Marsh Bird Monitoring Protocol (Pilot Project) ......................................... 63 Appendix 3: 2012 Survey Station Coordinates .............................................................................. 81 Appendix 4: Database Design ........................................................................................................ 95 Appendix 5: Clapper Rail Survey Forms ....................................................................................... 101 Appendix 6: 2012 Clapper Rail Survey Results ............................................................................ 107 Invasive Spartina Project i 2012 Clapper Rail Monitoring Report Table of Figures Figure 1. Map of regional boundaries ............................................................................................. 5 Figure 2. Map of clapper rail presence and absence in the Bay Bridge North Region .................. 20 Figure 3. Image of Grindelia stricta plantings at Arrowhead Marsh ............................................. 21 Figure 4. Map of clapper rail presence and absence in the San Leandro Bay Region. .................. 23 Figure 5. Image of the Hayward shoreline looking north from the San Mateo Bridge ................. 24 Figure 6. Map of clapper rail presence and absence in the Hayward Region. .............................. 26 Figure 7. An aerial image of the Eden Landing complex ............................................................... 27 Figure 8. Map of lclapper rai presence and absence in the Union City Region ............................ 29 Figure 9. Image of Calaveras Marsh from above ........................................................................... 30 Figure 10. Map of clapper rail presence and absence in the Dumbarton Bridge South Region ... 32 Figure 11. Map of clapper rail presence and absence in the San Mateo Region .......................... 35 Figure 12. Photo series documenting change in habitat over time at Colma Creek ..................... 36 Figure 13. Map of clapper rail presence and absence in the San Francisco Peninsula Region ..... 38 Figure 14. Map of clapper rail presence and absence in the Marin Region .................................. 41 Figure 15. Photo overlooking the large shoreline of Mare Island’s San Pablo Bay NWR .............. 42 Figure 16. Map showing clapper rail presence and absence in Vallejo and Petaluma Region ..... 43 Figure 17. Comparison of the detection frequency between two survey methods ..................... 44 Table of Tables Table 1. Summary table of site information grouped by region ................................................... 4 Table 2. Clapper rail detection types. ............................................................................................ 16 Table 3. Clapper rail and Spartina summary results from 2008‐2012 at all regions ..................... 17 Table 4. Clapper rail and Spartina results from 2008‐2012 at Bay Bridge North Region. ............. 19 Table 5. Clapper rail and Spartina results from 2008‐2011 in the San Leandro Bay Region. ....... 22 Table 6. Clapper rail and Spartina results from 2008 – 2012 in the Hayward Region. ................. 25 Table 7. Clapper Rail and Spartina results from 2008 – 2011 in the Union City Region. .............. 28 Table 8. Clapper rail and Spartina results from 2008 – 2012 south of the Dumbarton Bridge. ... 31 Table 9. Clapper rail and Spartina results from 2008‐2012 in the San Mateo Region .................. 34 Table 10. Clapper rail and Spartina results from 2008‐2012 in San Francisco Peninsula Region . 37 Table 11. Clapper rail and Spartina results from 2008‐2012 in the Marin Region........................ 40 Table 12. Clapper rail and Spartina results at two sites in San Pablo Bay. ................................... 42