Clapper Rail Surveys for the

Transcription

1 Clapper Rail Surveys for the 2008 San Francisco Estuary Invasive Spartina Project

2

3 California Clapper Rail Surveys for the San Francisco Estuary Invasive Spartina Project 2008 Prepared by: J. McBroom Olofson Environmental Inc th Street, Suite 216 Berkeley, CA For the State Coastal Conservancy San Francisco Estuary Invasive Spartina Project 1330 Broadway, 13 th Floor Oakland, CA June 30, 2008

4 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 CALFED Bay-Delta Program, Ecosystem Restoration Program (California Department of Fish and Game Interagency Agreement #PO California Wildlife Conservation Board (MOU # and subsequent)

5 Acknowledgements ACKNOWLEDGEMENTS This report would not be possible without the hard work of the OEI field biologists: Ode Bernstein, Jeffery Lewis, Len Liu, Allison Nelson, and Jude Stalker. Additionally, thanks to: Jeanne Hammond, for formatting data tables; Jude Stalker, for organizing site photos; and Jeffery Lewis and Allison Nelson, for creating maps. Also many thanks to Stephanie Ericson, Ingrid Hogle, Peggy Olofson for assistance in the preparation of this report. San Francisco Estuary Invasive Spartina Project i. Clapper Rail Surveys 2008 Report

6

7 Contents CONTENTS 1. Introduction Study Area Methods...5 Field Methods...5 Protocol A: Clapper rail breeding season passive call count survey...5 Protocol C: Clapper rail breeding season active playback surveys...5 Protocol F: Clapper rail habitat assessment surveys...6 Data Collection and Management...6 Data Interpretation and Analysis Results...7 West Central Bay clapper rail region...10 Blackie s Creek (03a) and Mouth (03b)...12 Corte Madera Ecological Reserve (04a)...15 College of Marin (04b)...18 Larkspur Ferry Landing (04e)...20 Riviera Circle (04f)...22 Creekside Park (04g)...23 Upper Corte Madera Creek (04h)...25 Lower Corte Madera Creek (04i)...27 Corte Madera Creek Mouth (04j)...29 Pickleweed Park (09a)...31 Muzzi Marsh (23e)...33 Strawberry Point (23h)...35 Strawberry Cove (23i)...39 San Francisco Peninsula clapper rail region...41 Colma Creek (18a)...43 Navigable Slough...45 Old Marina (18c)...47 Inner Harbor (18d)...49 Confluence Marsh (18f)...51 San Bruno Marsh (18g)...53 San Bruno Creek (18h)...55 Brisbane Lagoon (19a)...57 Sierra Point (19b)...59 Oyster Cove (19c)...61 Oyster Point Marina (19d)...64 Oyster Point Park (19e)...66 San Bruno Point (19f)...68 San Francisco Airport (19h)...70 Mills Creek Mouth (19i)...72 Easton Creek (19j)...74 Sanchez Marsh (19k)...75 San Francisco Estuary Invasive Spartina Project Clapper Rail Surveys 2008 Report iii.

8 Contents Coyote Point Marina (19n)...78 San Mateo Creek (19o)...79 Seal Slough (19p)...80 West Bay Clapper Rail Region...82 Belmont Slough (02a)...84 Outer Bair Island B2 South Quadrant (02d)...87 West Point Slough Northwest (02e)...89 Greco Island North (02f)...90 West Point Slough Southwest and East (02g)...92 Western South Bay Clapper Rail Region...95 Ravenswood Open Space Preserve (02j)...97 Cooley Landing Salt Pond (16)...99 Don Edwards Refuge Clapper Rail Region Dumbarton and Audubon Marsh (05b) Newark Slough (05c) Hayward Clapper Rail Region Oro Loma East (07a) Oro Loma West (07b) Oyster Bay Regional Shoreline (20a) Dog Bone Marsh (20c) Citation Marsh (20d) East Marsh (20e) North Marsh (20f) Bunker Marsh (20g) San Lorenzo Creek (20h) Bockmann Channel (20i) Sulfer Creek (20j) Hayward Landing (20k) Johnson s Landing (20l) Cogswell Marsh Section A (20m) Cogswell Marsh Section B (20n) Cogswell Marsh Section C (20o) HARD Marsh (20s) San Leandro Bay Elsie Roemer (17a) Bay Farm Island (17b) MLK Regional Shoreline (17d) San Leandro Creek (17e) MLK Restoration Marsh (17h) Coliseum Channels (17i) Fan Marsh (17j) Airport Channel (17k) Doolittle Pond (17l) Alameda Island East (17m) East Central Bay Emeryville Crescent West (06b) Rheem Creek (22c) iv. Olofson Environmental, Inc. Berkeley, CA.

9 Contents 5. Permits References Personal Communications Tables Table 1. Summary table of site information, including: type of protocol used, number of survey stations, survey station placement, site area (in acres), area surveyed (in acres), and the proportion of marsh surveyed....3 Table 2. Types of Detection...7 Table 3. Summary results from clapper rail surveys in the West Central Bay Clapper Rail Region Table 4. Summary results from clapper rail surveys in San Francisco Peninsula Clapper Rail Region Table 5. Summary results from clapper rail surveys in the West Bay Clapper Rail Region Table 6. Summary results from clapper rail surveys in the Western South Bay Clapper Rail Region Table 7. Summary results from clapper rail surveys in Don Edwards Refuge Clapper Rail Region Table 8. Summary results from clapper rail surveys in the Hayward Clapper Rail Region Table 9. Summary results from clapper rail surveys in San Leandro Bay Table 10. Summary results from clapper rail surveys in the East Central Bay Clapper Rail Region Figures Figure 1. Clapper Rail Regions...2 Figure 2. Map of clapper rail survey region and site boundaries in the West Central Bay Clapper Rail Region...11 Figure 3. Blackie's Creek...12 Figure 4. Mouth of Blackie's Creek...13 Figure 5: Map of clapper rail survey results (stations only?) at Blackie s Pasture (03a & b)...14 Figure 6. Corte Madera Ecological Reserve...15 Figure 7. Corte Madera Creek, view from boardwalk...16 Figure 8. Map of clapper rail survey results at Corte Madera marsh Reserve (04a)...17 Figure 9. College of Marin...18 Figure 10. Map of clapper rail survey results at College of Marin Figure 11. Larkspur Ferry Landing...20 Figure 12. Map of clapper rail survey results at Larkspur Ferry Cover (04e)...21 Figure 13. Riviera Circle...22 Figure 14. Creekside Park...23 Figure 15. Map of clapper rail survey results at Creekside Park (04g)...24 Figure 16. Upper Corte Madera Creek...25 Figure 17. Map of clapper rail survey results at Upper Corte Madera Creek (04h)...26 Figure 18. Lower Corte Madera Creek (04i)...27 San Francisco Estuary Invasive Spartina Project v. Clapper Rail Surveys 2008 Report

10 Contents Figure 19. Map of clapper rail survey results at Lower Corte Madera Creek (04i) Figure 20. Corte Madera Creek Mouth...29 Figure 21. Map of clapper rail survey results at Corte Madera Creek Mouth (04j)...30 Figure 22. Pickleweed Park...31 Figure 23. Map of clapper rail survey results at Pickleweed Park Figure 24. Muzzi Marsh...33 Figure 25. Map of clapper rail survey results at Muzzi Marsh (23e) Figure 26. Strawberry Point...36 Figure 27. Strawberry Point...36 Figure 28. Strawberry Point...37 Figure 29. Map of clapper rail survey results at Strawberry Point (23h) Figure 30. Strawberry Cove...39 Figure 31. Map of clapper rail survey results at Strawberry Cove (23i) Figure 32. Map of clapper rail survey region and site boundaries in the San Francisco Peninsula Clapper Rail Region...42 Figure 33. Colma Creek...43 Figure 34. Map of clapper rail survey results at Colma Creek (18a) Figure 35. Navigable Channel...45 Figure 36. Map of clapper rail survey results at Navigable Channel (18b)...46 Figure 37. Map of clapper rail survey results at Old Marina (18c) Figure 38. Inner Harbor...49 Figure 39. Map of clapper rail survey results at Inner Harbor (18d)...50 Figure 40. Map of clapper rail survey results at Confluence marsh (18f)...52 Figure 41. San Bruno Marsh...53 Figure 42. Map of clapper rail survey results at San Bruno Marsh (18g) Figure 43. San Bruno Creek...55 Figure 44. Map of clapper rail survey results at San Bruno Creek (18h)...56 Figure 45. Brisbane Lagoon...57 Figure 46. Map of clapper rail survey results at Brisbane Lagoon & Channel (19a)...58 Figure 47. Sierra Point...59 Figure 48. Map of clapper rail survey results at Sierra Point (19b) Figure 49. Oyster Cove...61 Figure 50. Oyster Cove...62 Figure 51. Map of clapper rail survey results at Oyster Cove (19c)...63 Figure 52. Oyster Point Marina...64 Figure 53. Map of clapper rail survey results at Oyster Point Marina (19d)...65 Figure 54. Oyster Point Park...66 Figure 55. Map of clapper rail survey results at Oyster Point Park (19e)...67 Figure 56. Map of clapper rail survey results at San Bruno Point (19f)...69 Figure 57. San Francisco Airport...70 vi. Olofson Environmental, Inc. Berkeley, CA.

11 Contents Figure 58. Map of clapper rail survey results at San Francisco Airport (19h)...71 Figure 59. Mills Creek Mouth...72 Figure 60. Map of clapper rail survey results at Mills Creek Mouth (19i) Figure 61. Easton Creek...74 Figure 62. Sanchez Marsh...75 Figure 63. Sanchez Marsh...76 Figure 64. Map of clapper rail survey results at Sanchez Marsh (19k)...77 Figure 65. Coyote Point Marina...78 Figure 66. San Mateo Creek...79 Figure 67. Seal Slough...81 Figure 68. Racoon tracks at Seal Slough...81 Figure 69. Map of clapper rail survey region and site boundaries in the West Bay Clapper Rail Region Figure 70. Belmont Slough...85 Figure 71. Map of clapper rail survey results at Belmont Slough (02a) Figure 72. Bair Island...87 Figure 73. Map of clapper rail survey results at Bair Island South Quadrant (02d)...88 Figure 74. Greco Island North...90 Figure 75. Map of clapper rail survey results at Greco island North (02f) Figure 76. West Point Slough Southwest and East...92 Figure 77. West Point Slough Southwest and East...93 Figure 78. Map of clapper rail survey results at West Point Slough (02g)...94 Figure 79. Map of clapper rail survey region and site boundaries in the Western South Bay Clapper Rail Region...96 Figure 80. Ravenswood Open Space Preserve...97 Figure 81. Map of clapper rail survey results at Ravenswood Open Space (02j) Figure 82. Cooley Landing Salt Pond Figure 83. Map of clapper rail survey results at Cooley Landing (16a) Figure 84. Map of clapper rail survey region and site boundaries in the Don Edwards Refuge Clapper Rail Region Figure 85. Dumbarton and Audubon Marsh Figure 86. Map of clapper rail survey results at Dumbarton Marsh (05b) Figure 87. Newark Slough Figure 88. Map of clapper rail survey results at Newark Slough (05c) Figure 89. Map of clapper rail survey region and site boundaries in the Hayward Clapper Rail Region Figure 90. Oro Loma East Figure 91. Oro Loma East Figure 92. Map of clapper rail survey results at Oro Loma East (07a) Figure 93. Oro Loma West Figure 94. Map of clapper rail survey results at Oro Loma West (07b) San Francisco Estuary Invasive Spartina Project Clapper Rail Surveys 2008 Report vii.

12 Contents Figure 95. Oyster Bay Regional Shoreline Figure 96. Map of clapper rail survey results at Oyster Bay Regional Shoreline (20a) Figure 97. Dog Bone Marsh Figure 98. Dog Bone Marsh Figure 99. Map of clapper rail survey results at Dog Bone Marsh (05b) Figure 100. Citation Marsh Figure 101. Map of clapper rail survey results at Citation Marsh (20d) Figure 102. East Marsh Figure 103. North Marsh Figure 104. Map of clapper rail survey results at North Marsh (20f) Figure 105. Bunker Marsh Figure 106. Map of clapper rail survey results at Bunker Marsh (20g) Figure 107. San Lorenzo Creek Figure 108. Map of clapper rail survey results at San Loernzo Creek (20h) Figure 109. Bockmann Channel Figure 110. Map of clapper rail survey results at Bockmann Channel (20i) Figure 111. Sulfer Creek Figure 112. Map of clapper rail survey results at Sulpher Creek (20j) Figure 113. Johnson's Landing Figure 114. Map of clapper rail survey results at Johnson's Landing (20l) Figure 115. Cogswell Marsh, Section A Figure 116. Map of clapper rail survey results at Cogswell Marsh Section A (20m) Figure 117. Cogswell Marsh, Section B Figure 118. Map of clapper rail survey results at Cogswell Section B (20n) Figure 119. Cogswell Marsh, Section C Figure 120. Map of clapper rail survey results at Cogswell Marsh, Section C (20o) Figure 121. Western tip of HARD Marsh, showing most vegetated portion of site Figure 122. Map of clapper rail survey results at HARD Marsh (20s) Figure 123. Map of clapper rail survey region and site boundaries in the San Leandro Bay Clapper Rail Region Figure 124. Elsie Roemer Figure 125. Map of clapper rail survey results at Elsie Roemer (17a) Figure 126. Bay Farm Island Figure 127. Map of clapper rail survey results at Bay Farm Island (17b) Figure 128. MLK Regional Shoreline Figure 129. Map of clapper rail survey results at MLK Regional Shoreline (17d) Figure 130. San Leandro Creek Figure 131. Map of clapper rail survey results at San Leandro Creek (17e) Figure 132. MLK Restoration Marsh Figure 133. MLK Restoration Marsh viii. Olofson Environmental, Inc. Berkeley, CA.

13 Contents Figure 134. Map of clapper rail survey results at MLK Restoration Marsh (17h) Figure 135. Coliseum Channels Figure 136. Map of clapper rail survey results at Coliseum Channels (17i) Figure 137. Fan Marsh Figure 138. Map of clapper rail survey results at Fan marsh (17j) Figure 139. Airport Channel Figure 140. Map of clapper rail survey results at Airport Channel (17k) Figure 141. Doolittle Pond Figure 142. Map of clapper rail survey results at Doolittle Pond (17l) Figure 143. Alameda Island East Figure 144. Map of clapper rail survey results at Alameda Island (17m) Figure 145. Map of clapper rail survey region and site boundaries in the Easter Central Bay Clapper Rail Region Figure 146. Map of clapper rail survey results at Emeryville Crescent (06b) Figure 147. Rheem Creek Figure 148. Map of clapper rail survey results at Rheem Creek (22c) San Francisco Estuary Invasive Spartina Project Clapper Rail Surveys 2008 Report ix.

14

15 1. Introduction 1. INTRODUCTION The Invasive Spartina Project (ISP) is a coordinated regional effort to eliminate introduced species of Spartina (cordgrass) from the San Francisco Bay Estuary. To achieve this goal, the ISP requires information on the population of endangered California clapper rail in the marshes affected by the non-native cordgrass invasion. Annual breeding-season surveys provide a standardized measure of clapper rail presence and distribution in marshes throughout the Estuary. This information guides the ISP in the planning, permitting, and implementation of treatment strategies and helps to minimize the impacts of Spartina control on rail populations. In collaboration with other organizations (including PRBO, USFWS, and EBRPD), Olofson Environmental, Inc (OEI) conducted California clapper rail surveys to inform the ISP about rail populations at sites slated for Spartina treatment in The trained and permitted staff at OEI performed standard-protocol surveys at 73 sites between January 15 and April 15, The data were gathered in a geodatabase for analysis and summarized on a site-by-site basis. This report describes the geographic scope of the study, outlines the methods used to collect and analyze the data, and presents the results of these surveys. San Francisco Estuary Invasive Spartina Project 1. Clapper Rail Surveys 2008 Report

16 2. Study Area 2. STUDY AREA The clapper rail biologists at OEI assessed 73 sites within eight regions of the San Francisco Estuary for the presence of California clapper rail during the 2008 breeding season (Table 1). The study area spanned the counties of Alameda, Contra Costa, Marin, San Francisco, and San Mateo and represented a subset of sites slated for non-native Spartina treatment in To analyze broader-scale trends in California clapper rail abundance, sites were grouped into larger regional boundaries, based on areas designated by USFWS (Figure 1). Each region is composed of a varying number of Spartina treatment sites and area of tidal marsh habitat. Of the ten defined regions, only eight are presented in this report: West Central Bay; San Francisco Peninsula; West Bay; Western South Bay; Don Edwards National Wildlife Refuge (D.E.N.W.R.); Hayward; San Leandro Bay; and East Central Bay. Figure 1. Clapper Rail Regions 2. Olofson Environmental, Inc. Berkeley, CA.

17 2. Study Area Table 1. Summary table of site information, including: type of protocol used, number of survey stations, survey station placement, site area (in acres), area surveyed (in acres), and the proportion of marsh surveyed. Site Name and ID Survey Type No. Survey Stations Station Placement Site Area (Acre) Survey Area (Acre) Proportion of Site Surveyed West Central Bay Blackies Pasture (03a&b) F>C 3 Footpath % Corte Madera Marsh Reserve (04a) A 0 Footpath & boardwalk % College of Marin (04b) C 2 Footpath % Larkspur Ferry Cove (04e) C 1 Footpath % Riviera Circle (04f) F 0 Road ¹ 100% Creekside Park (04g) A 3 Footpath % Upper Corte Madera Creek (04h) A 5 Footpath % Lower Corte Madera Creek (04i) C 4 Footpath % Corte Madera Creek Mouth (04j) A 6 Footpath & % boardwalk Pickleweed Park (09a) A 3 Footpath % Muzzi Marsh (23e) A 6 Levee % Strawberry Point (23h) F>C 0 Footpath % Strawberry Cove (23i) F>C 0 Footpath % San Francisco Peninsula Colma Creek (18a) A 6 Footpath % Navigable Channel (18b) A 2 Footpath % Old Marina (18c) A 1 Footpath % Inner Harbor (18d) A 3 Footpath % Sam Trans Peninsula (18e) A 3 Footpath % Confluence Marsh (18f) A 0 Footpath % San Bruno Marsh (18g) A 6 Footpath % San Bruno Creek (18h) C 3 Road % Brisbane Lagoon (19a) C 8 Footpath % Sierra Point (19b) A 2 Footpath % Oyster Cove (19c) A 2 Footpath % Oyster Point Marina (19d) F>C 1 Road % Oyster Point Park (19e) C 2 Footpath % San Bruno Point (19f) A 2 Footpath % San Francisco Airport (19h) A 7 Road % Mills Creek Mouth (19i) A 1 Footpath % Easton Creek Mouth (19j) F 1 Road ¹ 100% Sanchez Marsh (19k) F>C 3 Footpath & boardwalk % Coyote Point Marina (19n) F 0 Footpath ¹ 100% San Mateo Creek (19o) F 0 Footpath ¹ 100% Seal Slough (19p) A 6 Footpath % West Bay Belmont Slough (02a) A 8 Levee % B2 South Quadrant (02d) A 8 Levee % West Point Slough Northwest (02e) F 1 Footpath ¹ 100% San Francisco Estuary Invasive Spartina Project 3. Clapper Rail Surveys 2008 Report

18 2. Study Area No. Survey Stations Site Area (Acre) Survey Area (Acre) Proportion of Site Surveyed Site Name and ID Survey Type Station Placement Greco Island North (02f) A 8 Boardwalk % West Point Slough SW/SE (02g) C 4 Footpath % Western South Bay Ravenswood Open Space (02j) A 3 Levee % Cooley Landing Salt Pond (16a) A 8 Footpath % Don Edwards NWR Dumbarton / Audubon (05b) A 7 Levee & % Boardwalk Newark Slough (05c) A 7 Levee % Hayward Oro Loma East (07a) A 5 Levee % Oro Loma West (07b) A 16 Levee % Oyster Bay (20a) A 6 Footpath % Dogbone Marsh (20c) A 3 Footpath % Citation Marsh (20d) A 7 Levee % East Marsh (20e) A 0 Levee % North Marsh (20f) A 6 Footpath % Bunker Marsh (20g) A 8 Levee % San Lorenzo Creek (20h) A 5 Varied % Bockmann Channel (20i) A 2 Levee % Sulphur Creek (20j) A 3 Footpath % Hayward Landing (20k) A 6 Footpath % Johnson's Landing (20l) A 3 Footpath % Cogswell Marsh, A (20m) A 8 Levee % Cogswell Marsh, B (20n) A 8 Levee % Cogswell Marsh, C (20o) A 6 Levee % HARD Marsh (20s) A 5 Levee % San Leandro Bay Elsie Roemer (17a) A 6 Footpath % Bay Farm Island (17b) A 7 Footpath % MLK Regional Shoreline (17d) A 13 Footpath % San Leandro Creek (17e) A 8 Footpath % MLK Restoration Marsh (17h) A 7 Footpath % Coliseum Channels (17i) F>C 2 Footpath % Fan Marsh (17j) A 3 Road & % Levee Airport Channel (17k) A 15 Road % Doolittle Pond (17l) A 2 Road % Alameda Island (17m) A 5 Footpath % East Central Bay Emeryville Crescent (06b) A 6 Road % Rheem Creek (22c) A 4 Footpath % ¹ Area surveyed for clapper rail habitat only (F-survey) 4. Olofson Environmental, Inc. Berkeley, CA.

19 3. Methods 3. METHODS 3.1 FIELD METHODS California clapper rail surveys were conducted between January 15 and April 15, 2008, using standardized survey protocols approved by the USFWS (Appendix 1). All surveys were conducted by the trained and permitted avian field biologists at Olofson Environmental Inc: Ode Bernstein, Jeffery Lewis, Len Liu, Jen McBroom, Allison Nelson, and Jude Stalker. The three types of survey protocols employed by OEI biologists in 2008 are summarized below. Protocol A: Clapper rail breeding season passive call count survey Protocol A is the standard walking transect survey protocol written by USFWS biologists and used by researchers throughout the San Francisco Estuary to document California clapper rail presence during the breeding season and to calculate rail relative abundance and/or density. Typically, survey stations were placed at 200-meter (m) intervals on peripheral paths around the site. In large marsh parcels, PRBO surveyors placed stations at 400 m intervals, as recommended by Conway in Standardized North American Marsh Bird Monitoring Protocols (2005). The number of survey stations established at each site varied due to site size, configuration, and accessibility. The locations of the survey stations were entered into a GIS and navigated to in the field using a GPS unit. For consistency and repeatability, all efforts were made to use the same survey station locations that were established during the previous survey seasons (see Appendix 2 for a complete list of survey stations used in 2008). Sites were visited three times during the season, with at least 10 days between visits. During the first two rounds, a trained observer stood at each point for 10 minutes, recording all rails detected visually or aurally. For each bird or pair of birds detected, the observer recorded: (1) the number of birds, (2) the call type, and (3) distance and angle on a pre-printed datasheet. Additionally, the approximate locations of each rail/pair were plotted on a field map of the site. Pre-recorded clapper rail vocalizations were used at survey stations on the third visit to elicit response from rails if no rails were detected during the two previous passive surveys (or during the first five minutes of the third survey) within 200 m of the survey station. The pre-recorded vocalizations were provided by U.S. Fish and Wildlife Service and were played for one minute from a compact disc player with portable speakers. If a clapper rail responded during the broadcast call, the speakers and player were immediately turned off. Protocol C: Clapper rail breeding season active playback surveys A modified protocol for clapper rail call count surveys was developed by USFWS and ISP staff to maximize the chances of detecting rails at sites that have a low probability of supporting clapper rails. These sites are typically isolated, small marsh patches which provide marginal or low-quality rail habitat and where clapper rails have not previously been detected. To determine whether Protocol C was appropriate to use, sites were first evaluated by a clapper rail biologist. Protocol C is identical to the standard walking transect survey (Protocol A), except that it allows permitted biologists to play pre-recorded rail vocalizations during the first (and subsequent) visits to a site. If a rail is detected, the recording must be immediately switched off and cannot be played San Francisco Estuary Invasive Spartina Project 5. Clapper Rail Surveys 2008 Report

20 3. Methods again within 200 m of the detection. To determine with sufficient certainty that rails do not occur at a site, three visits with no rail detections are required. Sites where rails are determined to be absent can be treated during the rail-breeding season, maximizing the potential window of time available for treatment. Protocol F: Clapper rail habitat assessment surveys This protocol was developed by ISP staff, in association with Jules Evens (ARA) and Joy Albertson (USFWS), to determine whether apparently marginal habitat meets a suggested minimum set of criteria for likely clapper rail use. These criteria include restoration status, salinity, tidal regime, marsh size and configuration, levee configuration, marsh elevation, presence of upper marsh vegetation, degree of non-native Spartina invasion, distance from the nearest marsh with known clapper rails, degree of channelization, and amount of open water (ponding). If at least four criteria related to probable clapper rail presence were met, there was sufficient probability that clapper rails were present, and a recommendation was made for further call count surveys, usually Protocol C. If these criteria were not met, the site was assumed to not support clapper rails, and no further clapper rail surveys were recommended. 3.2 DATA COLLECTION AND MANAGEMENT We used ArcEditor 9.2 (Environmental Systems Research Institute Inc., Redlands, CA) to create a personal geodatabase to store and manage clapper rail survey data in The design of the geodatabase was based on a preexisting Access database developed by PRBO Conservation Science in All table and query elements of the Access database were preserved in the geodatabase, along with the spatial components of the data. For instance, weather data (temperature, cloud cover, wind speed, and precipitation) were recorded for each round within the polygon delineating the boundary of the site surveyed (see Appendix 3 for complete geodatabase design). Data were recorded in the field on paper datasheets (Appendix 4), on paper field maps, and in our handheld Trimble GeoXT (Trimble, Sunnyvale, CA) GPS units with ArcPad 7.1 mapping software (Environmental Systems Research Institute, Redlands, CA). The GPS units were used both to navigate to our survey stations and to digitally record data in the field. During a survey, stations and site boundaries were updated in ArcPad with current visit and weather information. Each rail observation was recorded on a paper datasheet with time detected, call type, number of rails, distance, and direction to the observed rail. Additionally, each rail was assigned a map reference identification letter or number and the approximate location of each rail detected was recorded on a paper field map. On the backside of the datasheet, site information and habitat descriptions were noted, along with any other birds observed at the site. In the office, data were uploaded from the GPS units and checked-in to the appropriate geodatabase at the office. Each observer maintained his/her own personal geodatabase during the field season. Data entered into ArcPad in the field were added to the observer s geodatabase and reviewed for quality and accuracy. Additionally, rail observation data that were recorded on a datasheet in the field were entered into the geodatabase. We used the Direction/Length tool in ArcEditor 9.2 to enter the direction (in degrees) and distance (in meters) in order to create a line feature, which we called offsets (Appendix 1). A point feature, called location, was created at the end of each offset line to represent the location of each unique rail/pair. When a rail was detected from more than one station, the location point feature was moved toward the intersection of the offset lines, to triangulate an more precise position of the observed rail. 6. Olofson Environmental, Inc. Berkeley, CA.

21 3. Methods At the end of the field season, all data were proofed against original datasheets for accuracy. Once data were reviewed for quality and accuracy, all data were combined into a single geodatabase for analysis. 3.3 DATA INTERPRETATION AND ANALYSIS Each type of detection represented a standardized range of individual clapper rails (Table 2). For instance, a clatter, which may represent a single unmated bird or a pair, was recorded as a range of one to two birds. These ranges were summed at the end of each round to estimate the total number of rails detected (represented as a range of the minimum possible rails detected to the maximum possible rails detected). Birds that were detected from more than one station or by more than one observer during a single round were counted only once toward the total range of rails detected. Once all data were summed for each round at each site, we used the highest count to determine the final range of rails detected for each site. These data were then used to calculate the minimum and maximum density (number of birds per unit area) at each site. To arrive at a density estimate, we needed to estimate the number of rails per acre. First, we used existing ISP site boundaries to calculate total site area in acres using ArcEditor 9.2. Next, we created 200 meter buffers around each survey stations to approximate the maximum distance for most clapper rail detections under moderate survey conditions. The area of overlap between the survey station buffers and the site boundaries was calculated (in acres) and called the survey area. Finally, we divided the number (maximum and minimum) of clapper rails detected within the survey area by the survey area (acres) to estimate the density (high and low) of clapper rails per acre. At the 27 sites where the survey area was less than 85% of the site area, we used the calculated densities to estimate the clapper rail population at the entire site. This was simply done by multiplying the density estimates by the site area (acres), assuming that the habitat quality was similar across the entire site and that the density of clapper rails was similar across the entire site. These assumptions were not true at Cooley Landing and San Leandro Creek, where the habitat is heterogeneous. At these sites, we used the highest count data as our final population estimate. Table 2. Types of Detection Detection Number of Rails type Description Min Max C "Clatter" 1 2 D Duet - two (or more) simultaneous "clatters" 2 2 (or more) K "Kek" 1 2 AK Aggitated "kek" 1 2 kkb "Kik-kik-burr" 1 2 SK "Squawk" 1 2 SC "Screech" 1 2 CH "Churr" 1 2 P "Purr" 1 2 V Visual 1 2 San Francisco Estuary Invasive Spartina Project 7. Clapper Rail Surveys 2008 Report

22