2011 Annual Report to U.S. Fish and Wildlife Service: California Clapper Rail (Rallus longirostris obsoletus) TE

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1 2011 Annual Report to U.S. Fish and Wildlife Service: California Clapper Rail (Rallus longirostris obsoletus) TE Submitted to U.S. Fish and Wildlife Service, Sacramento January 31, 2012 Submitted by PRBO Conservation Science Leonard Liu, Julian Wood, Leo Salas, and Nadav Nur PRBO Conservation Science, 3820 Cypress Drive #11, Petaluma, CA Contact: INTRODUCTION The California Clapper Rail (Rallus longirostris obsoletus) is one of the most endangered species in California. The species is dependent on tidal wetlands, which have decreased over 75% from the historical extent in San Francisco Bay. A complete survey of its population and distribution within the San Francisco Bay Estuary was begun in In 2011, PRBO Conservation Science (PRBO) completed the seventh year of field work designed to provide an Estuary-wide abundance estimate and examine the temporal and spatial patterns in California Clapper Rail populations. Field work was performed in collaboration with partners conducting call-count surveys at complementary wetlands (Avocet Research Associates [ARA], California Department of Fish and Game [CDFG], California Coastal Conservancy s Invasive Spartina Project [ISP], and U.S. Fish and Wildlife Service [USFWS]). This report details PRBO s California Clapper Rail surveys in 2011 under U.S. Fish and Wildlife service permit TE We also present the results of a preliminary analysis of California Clapper population trends , and results of an analysis performed for a poster presentation at the State of the Estuary conference into detectability of Clapper Rails during the surveys (Appendix 1). A final report for the Section 6-funded project, Temporal and spatial patterns in population trends of the California clapper rail (Rallus longirostris obsoletus) in the San Francisco Estuary: population models and development of methodology and protocol for long-term monitoring, will be presented to CDFG July 1, The final report will contain: an estimate of population levels for the entire San Francisco Estuary using 2005 through 2011 survey data; an examination and description of the annual and spatial variability in abundance estimates; analyses of habitat and landscape predictors of rail presence and abundance; and recommendations for implementation of California Clapper Rail long-term monitoring, including level of effort (and therefore costs). METHODS Call-count surveys were initiated January 15 and continued until April 15. PRBO surveyed 50 marshes in the Estuary; 33 s were in San Pablo Bay, 6 s in Central San Francisco Bay, and 11 s in South San Francisco Bay (Table 1, Figures 1 and 2). Sites were surveyed 3 to 5 times by experienced permitted biologists using a point transect method, with 10 minutes per listening station. Listening stations were located primarily at marsh edges, levees bordering and within marshes, boardwalks, and boat-accessible channels within the marsh. Stations were placed meters apart. Locations of surveyed marshes are presented in Figures 1 and 2. All Clapper Rails (CLRA), as well as California Black Rail (Laterallus jamaicencis coturniculus), Virginia Rail (Rallus limicola), and Sora (Porzana carolina), detected from a listening station were recorded along with the time, direction and distance from the listening station. The actual number of rails detected was recorded, or if the detection was not heard clearly because of confounding circumstances (e.g., distance from observer or environmental conditions) a range in number of rails (e.g., 1 to 2, 2 to 4) was recorded. If no CLRA were detected within 200 meters of a listening station after 2 passive surveys, playback (up to 1 minute) of Clapper Rail vocalizations was used in an attempt to stimulate a response at the end of the third survey. Playback

2 2 surveys consisted of 5 minutes of passive listening (with no CLRA detected), then 1 minute of playback followed by 4 minutes of passive listening. Clapper Rails detected during transit between listening stations as well as before or after the 10-minute listening period were also recorded. Survey Summary We summarized our 2011 data by selecting the survey visit with the greatest number of detections, including detections outside of the official 10-minute survey period, at each area and taking the mean based on the minimum and maximum number of Clapper Rails detected for each survey. Trend Analysis We analyzed Clapper Rail survey data from years We divided the CLRA data from the San Francisco Bay Estuary into two regions for abundance estimation: North Bay (north of the San Francisco- Oakland Bay Bridge) and South Bay (south of the Bay Bridge), and excluded Suisun Bay because of the low number of detections. We only considered detections during the 10-minute survey period and within 200m of the survey point, as the ability of surveyors to detect rails diminishes beyond 200m (PRBO unpublished data). To further increase the chances of detection per point per season, we considered data only from points surveyed at least three times within each survey year. Zeroes in the dataset are both true (surveys of marshes where the species was not present) and false (the species was present but not detected). To improve our ability to estimate detection probability, we removed data from marshes with no CLRA detected in any of the survey years, as we would not be able to estimate detection probability at a marsh that never had any CLRA. Furthermore, the goal of this analysis was to describe trends in abundance which is not possible at marshes where rails were never detected. Filtered this way, the dataset still included a large number of true and false zeroes (53%). Therefore, we used a mixture model consisting of a negative binomial abundance model (generalized linear model with negative binomial link) and an intercept-only detection model (logistic regression) (i.e., zero-inflated model, Zuur et al. 2009). Negative binomial modeling accounts for increased variance in the data caused by true zeroes (species is not present). The zero-inflated model allows us to estimate the effect of false zeroes (the species is present but not detected), and thus we can estimate detection probability. For this zero-inflated negative binomial model we calculated an index of abundance at each point: the maximum count from all visits to the point within each year. Our statistical model therefore assumes that the variation in counts at each point is caused by year, Bay region, survey method (whether call playback was used), and probability of detection effects. Because the abundance equation of the mixture uses a negative binomial link, it also accounts for over-dispersion in the data. We found that detection probability varies with year; in some years individuals are more readily detected. Year effects were included as a discrete factor, thus not forcing the data to conform to a linear trend in time. This resulted in individual estimates of the abundance index for each year and Bay region independent from any trend effects and allowing the estimates to vary freely between years. For the purpose of illustrating the resulting pattern over the period , we fit a generalized additive model (GAM) to the predicted estimates of the abundance index vs. year for each Bay region separately, using a cubic spline with four degrees of freedom as the smoother. We did not include autoregressive effects for annual estimates (i.e., the effect of prior years abundance on each year s estimate), because the smoother naturally accounts for it. Abundance index estimates for each year and their standard errors were plotted along with the GAM curve showing the smoothed pattern. All analyses reported here were performed with the R statistical software (R Development Core Team 2011) and package pscl (Zeileis et al. 2008). Finalized results of the trend analysis will be in the July 1, 2012 report. Calling Rate Analysis In a separate analysis, we looked at the following factors as possible contributors to the variability among surveys: time of day, time of year, temperature, wind speed, moon phase, and tide height. We used surveys conducted 1 to 5 times per year between 19 December and 26 May from 2005 through. We included

3 3 surveys where playbacks of Clapper Rail vocalizations were used on the third visit. Only surveys in San Pablo and San Francisco Bays were included in this analysis, and the survey effort was divided at the San Francisco- Oakland Bay Bridge into North Bay and South Bay regions. All Clapper Rail detections, including those outside the official listening period, were included in this analysis. In total, 1155 listening stations were used from The analyses all included a random effect for each survey station, and included as fixed effects: year and bay (North vs. South) and the interaction between year and Bay. The assumption is that detections differ by year in North Bay independently of how they differ by year in South Bay. Having controlled for survey station, bay, year, and bay x year, we are thus comparing surveys at the same station within and among years. The analysis was conducted on log-transformed counts. RESULTS 2011 Survey Summary PRBO detected 647 (range: 585 to 708) Clapper Rails at the 50 survey s in 2011 (Table 1). In San Pablo Bay, we detected 307 (range: 281 to 333) CLRA. In Central San Francisco Bay, we detected 122 (range: 113 to 130) CLRA. In South San Francisco Bay, we detected 218 (range: 191 to 245) CLRA. These summaries do not represent our population estimates for these s, as we did not attempt to calculate abundances or densities based on the detections. Nor did we apply the densities to non-surveyed suitable habitat at the s. These summaries do not represent the Bay-wide population estimate as not all suitable habitat was surveyed. No nests were incidentally discovered during surveys, nor were any Clapper Rails harmed or killed. San Pablo Bay Richmond/Pinole complex The number of detections along the north Richmond shoreline, which has the 3 rd largest population of Clapper Rails in San Pablo Bay, was stable between and There has been a slight decline in detections for the period , with small increases at San Pablo Creek marsh and decreases at Wildcat Marsh. A red fox (Vulpes vulpes) kit was photographed denning in the log pile at the wood recycling yard at the southern edge of San Pablo Creek marsh. We presented documentation to the City of Richmond of an ongoing threat to tidal marsh habitat in the area; two wood recycling operations have been dumping building debris and asphalt into the marsh and have depod trash at the edge of the marsh. San Pablo Bay National Wildlife Refuge There were 6 Clapper Rails detected during the highest mean survey at Sonoma Baylands, and 4 in Sonoma Baylands restoration to the north. The number of detections at Sonoma Baylands was about half of. Thirteen to fourteen Black Rails were detected in Sonoma Baylands. China Camp State Park Detections of Clapper Rails increased to 27 on the highest mean survey at the China Camp marsh (range 24 to 30) from 11 in. This is the highest number of detections we have had at China Camp, surpassing the previous high count in 2006 of 17 to 22 CLRA. A maximum of 3 to 4 California Black Rails (BLRA) were detected during the rail surveys. Central San Francisco Bay Corte Madera Creek complex In Central San Francisco Bay (Bay Bridge to Pt. San Pedro/Pt. San Pablo), we surveyed 6 s in The number of detections from the highest minimum survey increased at both Corte Madera Ecological Reserve and at Muzzi Marsh. This marsh complex remains one of the highest density locations in the Estuary.

4 South San Francisco Bay Don Edwards SFBNWR There was an increase in annual detections at the Faber-Laumeister tracts in 2011, with mean detections rising to 106 (range: 94 to 118) in 2011 from 76 in. We also for the first time detected CLRA in San Francisquito Creek, between Faber and the airport. At Outer Bair Island and Middle Bair East, mean detections increased to 44 (range: 36 to 51) CLRA in 2011 from 28 CLRA in. Mean detections at Dumbarton Pt. increased slightly from 16 in to 18 (range: 14 to 21) in We detected 9 to 10 CLRA at Goose Pt. and Triangle Marsh, north of Ponds A14 and A15. We detected a single CLRA at Charleston Slough in 2011, Palo Alto Baylands We detected fewer Clapper Rails at Palo Alto Baylands in 2011, 13 to 14 CLRA on the most productive survey, compared to 20 to 22 in. Mean detections at the adjacent Palo Alto Harbor/Hooks Island were also down slightly, from 18 CLRA in to 16 (range: 13 to 19) in Trends The combined North and South Bay CLRA population declined precipitously reaching a low in 2008 and 2009 then rebounded slightly in and 2011 (Figure 3). The largest between-year drop in abundance occurred between 2007 and In the North Bay, the pattern was similar, but the rebound, beginning in 2009, was more evident (Figure 4). In the South Bay rail abundance also declined with a sudden drop between 2007 and 2008 (Figure 5). Unlike the North Bay, rail abundance did not rebound after 2008 but appears to have leveled off. Calling Rate We found that time of day has a significant effect on detections during morning surveys (Figure 6). Detections peak rapidly about 20 minutes before sunrise, then for every 15 min later relative to sunrise, detection rate decreases by 11.9%, SE is about 1.2%). Time of day has a quadratic effect on detections during evening surveys, with detections peaking around 15 min after sunset (Figure 7). Time of year (Julian date) as a cubic is highly significant, but with different equations for morning and evening surveys (Figure 8). Once time relative to sunrise/sunset is controlled for, the difference between morning and evening surveys is eliminated. Temperature has a positive linear effect on detections only during evening surveys. For every 10 degree C increase, detection rate increases by 26.3%, after controlling for date. Wind has a negative linear effect on detections only during morning surveys. With an increase in wind speed of 10 km/h, detection rate decreases by 21.5%. Tide and moon phase were not found to be significant. DISCUSSION The California Clapper Rail population in the North Bay appears to be recovering from the decrease that occurred between the 2007 and 2008 surveys. However, the overall South Bay population has not been showing an increase in the last 3 years, although they are stable. While the removal of hybrid Spartina has been assumed to be a large part of the decline between 2007 and 2008, it remains unclear what the cause of the drop in North Bay abundance index in the same time period, where there was relatively little Spartina control compared to the South Bay. The Light-footed Clapper Rail population in Southern California also dropped dramatically between 2007 and 2008 (Zembal et al. ) indicating that weather-related effects may have been responsible for the decline observed for both subspecies. It is possible that Estuary-wide population levels are stabilizing after the significant decrease in population in , but with different trajectories in the North Bay and the South Bay. An earlier version of the combined North and South Bay CLRA trend analysis of survey data was presented in the State of the Birds San Francisco Bay 2011 ( Appendix 2). 4

5 In addition, the report lists the major threats facing CLRA and recommended actions for planning, management, and restoration. The results of the detection probability analysis confirm that the current survey protocol for California Clapper Rails includes an appropriate time period (15 January to 15 April), although surveys later in the season show reduced detectability. The timing of daily peak detections generally corresponds to qualitative surveyor observations. The positive relationship between higher temperatures during evening surveys and not morning surveys is harder to interpret, but may be related to a circadian rhythm commonly found in birds, or less temperature variation with morning surveys. The lack of effect of tide on detections is a bit surprising, but may be related to most surveys being conducted on low to medium tides, with an absence of data on higher tides. Next Steps In 2012, we plan to conduct call-count surveys in areas not previously surveyed, including areas of Petaluma Marsh and the upper Petaluma River, and the Napa-Sonoma marshes. We plan to incorporate the results of the calling rate analysis, along with habitat variables, into an analysis of detection probability that will produce a more accurate Estuary-wide population and distribution estimates in the final CDFG report this year. The report will also compare the current distribution and abundance with the results of the surveys, and identify population trends within and among marshes as well as regionally. We also plan to develop an information base to help inform management decisions regarding this endangered species in the face of challenges that will inevitably arise as changes in habitat values occur due to marsh restoration efforts, invasive Spartina, sea level rise, substrate contamination, and other influences. Also in 2012, we will implement a pilot protocol study to test a revised marsh bird monitoring protocol that is compatible with the Standardized North American Marsh Bird Monitoring Protocol. The pilot protocol will be conducted at selected marshes and will not influence our planned effort in 2012 using the standard San Francisco Bay survey protocol. The pilot protocol study will be led by the USFWS Inventory and Monitoring Program with PRBO and ISP and including assistance from CDFG and USGS. 5

6 REFERENCES R Development Core Team R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN Zeileis, A., C. Kleiber, and S. Jackman Regression Models for Count Data in R. Journal of Statistical Software 27(8). Zembal, R., S. M. Hoffman, and J. Konecny.. Status and Distribution of the Light-footed Clapper Rail in California. Final report to State of California Department of Fish and Game. Zuur, A. F., E. N. Ieno, N. J. Walker, A. A. Saveliev, and G. M. Smith Mixed Effects Models and Extensions in Ecology with R. Springer-Verlag, New York. ACKNOWLEDGEMENTS Data were collected under TE from USFWS and a Memorandum of Understanding between CDFG and PRBO (4/23/). Bayland Habitats in Figures 1 and 2 are from San Francisco Estuary Institute s Bay Area EcoAtlas Version 1.50b4. We thank PRBO staff biologist Megan Elrod for her help in conducting Clapper Rail surveys at numerous s throughout San Francisco Bay. During 2011 surveys, PRBO benefited greatly from collaboration with a number of other organizations and agencies: California Coastal Conservancy s Invasive Spartina Project, U.S. Fish and Wildlife Service, Don Edwards San Francisco Bay National Wildlife Refuge, San Pablo Bay National Wildlife Refuge, California Department of Fish and Game, California Department of Parks and Recreation, East Bay Regional Parks District, City of Palo Alto, and City of Petaluma. We also thank Craig Cummings, Natasha Dvorak, Joe Eaton, Beth Huning, Robin Leong, Molly McNamara, Orien Richmond, John Robeson, Christina Sloop, Ron Sullivan, Laura Valoppi, and Erika Walther for their valuable assistance. 6

7 Table 1. Highest mean survey results of PRBO s 2011 rail surveys, with results where available. 7 Complex Map # Site Name min mean max* surveyor 2011 min 2011 mean San Pablo Bay Gallinas Creek 6 China Camp PRBO BLRA 19 Mitchell Fragment# ARA Gallinas Creek- north branch ARA Gallinas Creekmiddle reach# PRBO BLRA 69 Santa Venetia# PRBO BLRA 20 McInnis Marsh# PRBO BLRA 21 Hamilton South# PRBO BLRA Upper Petaluma River 91 Ellis Creek ISP BLRA 315 Gray s Ranch ISP Petaluma Marsh 60 Miramonte Slough n/a n/a n/a BLRA 58 San Antonio Creek n/a n/a n/a BLRA lower Petaluma River 71 Black John Slough north PRBO BLRA Petaluma River mouth 4 Novato Creek Sonoma Baylands upper Napa River lower Napa River NE San Pablo Bay 2011 max notes 2 Black John A** PRBO BLRA Green Point area marshes PRBO BLRA 129, 87, Carl's Marsh PRBO Petaluma River east PRBO BLRA Day Island Wildlife Area PRBO BLRA 110 Novato Creek mouth PRBO BLRA BLRA 27 Sonoma Baylands PRBO Sonoma Baylands 66 restoration PRBO Sonoma Marina PRBO Sonoma Baylands east n/a n/a n/a BLRA 35 Lower Tubbs Island n/a n/a n/a BLRA 31 Tolay Creek n/a n/a n/a BLRA Coon Island DFG BLRA 97 White Slough Marsh n/a n/a n/a BLRA Mare Island A n/a n/a n/a BLRA 18 Mare Island B n/a n/a n/a BLRA Richmond-Pinole 26 San Pablo Creek PRBO BLRA 108 Rheem Creek area PRBO Wildcat Marsh/Castro Creek PRBO BLRA * - ARA and ISP method of collecting detection maximums differs from PRBO method # - 5 rounds of surveys ** - different areas of surveyed in and 2011

8 Table 1 continued. Highest mean survey results of PRBO s 2011 rail surveys, with results where available. 8 min mean max* surveyor 2011 min 2011 mean Complex Map # Site Name notes Central San Francisco Bay Richardson Bay Bothin Marsh/Tam High 32 Fragment PRBO Corte Madera 184 Piper Park PRBO Corte Madera Ecological Reserve (Heerdt 78 Marsh)# PRBO Muzzi Marsh# PRBO Marta s Marsh# ARA San Clemente Creek# PRBO South San Francisco Bay Bair-Greco 239 Middle Bair Southeast PRBO Middle Bair East PRBO BLRA PRBO-ISP PRBO-ISP Outer Bair Is. joint survey joint survey Dumbarton 274 Dumbarton Pt PRBO BLRA Alviso 257 Charleston Slough** ISP Coyote Creek Goose Point/Triangle 263 Marsh n/a n/a n/a BLRA Palo Alto 249 Faber Tract# PRBO Laumeister Tract# PRBO San Francisquito Ck.# PRBO Palo Alto Baylands PRBO max Palo Alto Harbor/Hooks Island PRBO * - ARA and ISP method of collecting detection maximums differs from PRBO method # - 5 rounds of surveys ** - different areas of surveyed in and 2011

9 Figure 1. San Pablo and Central San Francisco Bay marshes. Numbers on map correspond to s listed in Table 1; not all marshes were surveyed in

10 10 Figure South San Francisco Bay Clapper Rail marshes. Numbers on map correspond to s listed in Table 1; not all marshes were surveyed in 2011.

11 11 Figure 3. Trend in Clapper Rail abundance in North and South Bay combined (San Francisco Bay and San Pablo Bay) from Error bars represent one standard error. Figure 4. Trend in Clapper Rail abundance in South Bay (south of Bay Bridge) from Error bars represent one standard error.

12 12 Figure 5. Trend in Clapper Rail abundance in North Bay (San Pablo Bay) from Error bars represent one standard error. Figure 6. Detection rate in relation to sunrise.

13 Figure 7. Detection rate in relation to sunset. 13 Figure 8. Detection rate in relation to time of year.