Methods

Objective 1 - We will examine habitat use and movement patterns using radio telemetry techniques on rails within marshes containing variation in Spartina density and configuration. Selected sites will include at least two of the three marshes identified with potential impacts resulting from invasive Spartina eradication (Colma Creek, Cogswell Marsh, and the San Leandro Bay Complex; USFWS 2005). These three sites all contain large areas of invasive Spartina and high densities of clapper rails. The remaining treatment site(s) will include less Spartina density, lower rail density or smaller marsh size. We will attempt to represent the range of conditions present in marshes occupied by rails, including matrix habitat types, marsh vegetative composition, isolation, and size. However, we will limit proposed sites to the Central and Southern portions of San Francisco Bay to represent the region with the most intense invasive Spartina eradication efforts and minimize the variability observed in habitat use and vegetation type patterns (Gill 1979).

We will capture rails from airboats or at night using spotlights in dip nets, cloverleaf traps, tanglefoot traps, or drop door traps (Zembal and Massey 1983, Conway et al. 1993, Albertson 1995, Tsao-Melcer and J. Takekawa, USGS, unpubl. data). Backpack harness transmitters weighing less than 10g will be attached to birds (Albertson 1995). Some birds may be marked using 3g leg band transmitters (ATS Inc., Isanti, MN). Marking will occur between December and February, at least one month prior to the onset of breeding. We will address both daily and seasonal space-use patterns with two separate tracking protocols. To achieve sufficient sample size for seasonal kernel home range analysis, we will attempt to obtain locations daily, representing a variety of tidal cycle periods, during each of five seasons (Worton 1989, Albertson 1995). Within each week, we will obtain two locations during high tide and low low tide slack water periods and two locations during ebb or flow tides. Nocturnal movements of rails are minor, therefore; evening telemetry is likely unnecessary but will be verified early in the project (Zembal et al. 1989). To address daily movement patterns, once per week within each marsh, we will locate all individuals during successive low/flow/high/ebb cycles. We will use fixed survey locations, minimize distance to the bird, and obtain multiple bearings during triangulation, and/or direct observation whenever possible to maximize accuracy of locations. We may also deploy automated tracking systems in suitable areas.

Specific movement patterns of interest include change in use of core areas, moderate range migration (>1km), increased daily movement rates, increased home range size, and overlap with adjacent territories relative to quantity and configuration of invasive Spartina. All of these measures have implications on survivability and suitability of habitat. Movement and space-use parameters will be estimated using univariate statistics and assessed using hypotheses developed during informal research team/cooperator meetings prior to data collection. These hypotheses will generate unique models representing factors affecting the parameter of interest.

Underlying theory used to develop hypotheses include: a) higher population density results in smaller movements and home range and greater territory overlap, abandonment, and rates of migration; b) larger marshes result in larger movements, and home range size and less abandonment, and migration; and c) population densities are typically greater in larger marshes (Evens and Collins 1992); therefore, decoupling the effect of marsh size and population density may not be possible; and d) marshes more distant from adjacent suitable habitat have lower rates of migration and less territory abandonment.

We will use space use information developed from telemetry methods and marsh composition and hydromorphology to develop models to describe and test multiple hypotheses regarding clapper rail habitat and space use patterns. We will develop digital maps of habitat and geomorphology in each marsh using existing data and field measurements. Existing data sources may include but are not limited to aerial photographs, LIDAR imagery, satellite imagery, and paper and digital information used by the Invasive Spartina Project. Local field measurements will incorporate sampling protocol designed for salt marsh vegetation (Garcia 1995, Roman et al. 2001, Spautz and Nur 2004). These include 1m2 quadrat sampling at permanent and temporary sites, permanent and temporary transects, and stratification among marsh zones. Sampling will occur following the nesting season to avoid disruption to rails. Otherwise, all conservation measures for clapper rails and salt marsh harvest mouse (Reithrodontomys raviventris) outlined in the 2005 Biological Opinion will be followed (USFWS 2005). Temporary sampling locations will be determined randomly during the first year of study. Subsequent years will incorporate space use information to locate one-half of temporary locations within home ranges. Remaining locations will be located randomly throughout the marsh. These field measurements will validate and improve thematic and positional accuracy of GIS habitat maps.

We will analyze habitat use using compositional analysis and MANOVA or ANOSIM tests using space use information and digital habitat maps (Clark and Green 1988, Aebischer et al 1993). We will include habitat components, such as species or plant assemblage occurrence, stem density, hydromorphology, and patch metrics identified in previous studies. Appropriate spatial scales for habitat analyses will be determined from rail movement patterns, data availability, data quality, and the ability to discern homogenous habitat types. Each year we will develop a predictive rail distribution using multiple logistic regression models and digital habitat maps. We will incorporate results from multiple hypotheses tests and use model averaged results to develop a single predictive map. In subsequent years, we will validate this map using updated space use and habitat information.

Objective 2 - Currently, effects of the control program are monitored with ground-based call surveys conducted at winter high tides (ISP unpubl. data). Call counts have three inherent problems when trying to interpret the impact of invasive Spartina removal on populations. First, surveys vary by habitat within and among sites, reducing the ability to quantify impacts of control efforts. Second, marsh-specific numbers do not reflect changes in population dynamics without information on dispersal rates, which may be particularly high following large-scale habitat alteration. Third, call counts require accurate accounting of individuals and consistent calling rates, both which are known to vary with habitat structure (Conway et al. 1993). Thus, increased dispersal or decreased calling following invasive Spartina removal will result in a bias tending toward lower counts (i.e. declining populations), even if numbers remain constant. Subsequent inference may inaccurately represent demographic responses to habitat change (survival and recruitment).

We will assess the impact of Spartina control on the dispersal rate and resource use of clapper rails using telemetry to identify location, movement and habitat selection patterns. We will contrast space use and resource selection with respect to the degree of Spartina control activities and resulting change in habitat composition and configuration. Specific movement patterns of interest include change in use of core areas, moderate range migration (>1km), increased daily movement rates, increased home range size, and overlap with adjacent territories. All of these measures have implications on survivability and suitability of habitat. Movement and space-use parameters will be estimated using univariate statistics and assessed using hypotheses developed during informal research team/cooperator meetings prior to data collection. These hypotheses will generate unique models representing factors affecting the parameter of interest.

We will also use space-use patterns to assess clapper rail detection rate during call count and winter high tide surveys. We will contrast the impact of habitat on calling or call-response rate between individuals, which will provide a useful assessment of current survey design and analysis.

Objective 3 - Both male and female California clapper rails incubate eggs and maintain young throughout the nesting-fledging cycle (Eddleman and Conway 1998). Radio telemetry therefore, provides a useful mechanism to identify nesting behavior and enable detailed observation of nests and success rates. We will evaluate the timing of nest initiation and nest placement relative to marsh habitat and habitat change following Spartina control. Furthermore, we will contrast nest survival rates and overall reproductive output between marshes, with respect to rail density and Spartina control activities.

Nest initiation will be analyzed using univariate statistics. We will analyze habitat differences in nest placement with MANOVA or Multivariate regression. We will incorporate individual and group (marsh) habitat and demographic metrics into analysis of nest success data using Program MARK (Cooch and White 2004).

Objective 4 - We will analyze clapper rail survival from radio telemetry data using the Kaplan-Meier and Known Fate models in Program MARK (Cooch and White 2004). Individual and group covariates, including Spartina control information and population demographics will be included in modeling from a suite of hypotheses useful in evaluating the impact of control activities.

Objective 5 - We will combine results from the preceding objectives, current composition of marsh vegetation, and proposed control activities into a spatially explicit model demonstrating both the ecology and demographics of California clapper rails and potential impacts of continuing Spartina control. This model will represent the estimated population trends derived from annual surveys and/or population growth rate derived from the demographic vital rates obtained in Objectives 1-4. The estimated impact of Spartina control activities on these derived parameters, population trend or growth rate, will be incorporated and provide the basis for management recommendations.

Objective 6 - Landscape theory relates the impact of Spartina control on California clapper rails to the impact of this control on rail habitat and the amount of disturbance associated with control activities. However, additional factors such as available habitat, population density, and local demographic processes also govern population trends. We will use the spatially explicit model of clapper rail demographics derived for Objective 5, and information obtained from the ISP regarding the effectiveness and methods used during Spartina control efforts to develop alternative management practices that offset or mitigate site-specific impacts from Spartina control. This information will provide the U.S. Fish and Wildlife Service, landowners, and ISP staff with an adaptive management toolset for use in the conservation and management of California clapper rails.

LITERATURE CITED

Aebischer, N. J., P. A. Robertson, and R. E. Kenward. 1993. Compositional analysis of habitat use from radio-tracking data. Ecology. 74:1313-1325.

Albertson, J. D. 1995. Ecology of the California clapper rail in South San Francisco Bay. M.A. thesis. San Francisco State University, San Francisco, CA.

Antilla, C. K., C. C. Daehler, N. E. Rank, and D. R. Strong. 1998. Greater male fitness of a rare invader (Spartina alterniflora, Poaceae) threatens a common native (Spartina foliosa) with hybridization. American Journal of Botany. 85:1597-1601.

Applegarth, J. H. 1938. The ecology of the California Clapper Rail on the south arm of San Francisco Bay. M.S. thesis, Stanford Univ., Palo Alto, CA.

Ayres D.R., D. R. Strong, and P. Baye. 2003. Spartina foliosa - a common species on the road to rarity? Madrono 50: 209-213.

Aryes, D. R., D. L. Smith, K. Zaremba, S. Klohr, and D. R. Strong. 2004. Spread of exotic cordgrass and hybrids (Spartina sp.) in the tidal marshes of San Francisco Bay, California, USA. Biological Invasions 6:221-231.

Baye, P. R. 2004. A review and assessment of potential long-term ecological consequences of the introduced cordgrass Spartina alterniflora in the San Francisco Estuary - Draft Technical Report. San Francisco Estuary Invasive Spartina Project. Berkeley, CA.

Callaway, J. C., and M. N. Josselyn. 1992. The introduction and spread of smooth cordgrass (Spartina alterniflora) in South San Francisco Bay. Estuaries 15:218-226.

Clarke, K.R., and R.H. Green. 1988. Statistical design and analysis for a 'biological effects' study. Marine Ecology Progress Series. 46:213-226.

Cohen, A. N, and J. T. Carlton. 1998. Accelerating invasion rate in a highly invaded estuary. Science 279: 555-558.

Conway, C. J., W. R. Eddleman, S. H. Anderson, and L. R. Hanebury. 1993. Seasonal changes in Yuma clapper rail vocalization rate and habitat use. Journal of Wildlife Management 57(2): 282-290.

Cooch E., and G. White. 2004. Program MARK: a gentle introduction. Third edition. URL:http://www.phidot.org/software/mark/docs/book/.

Daehler C. C., and D. R. Strong. 1996. Status, prediction and prevention of introduced cordgrass Spartina spp. invasions in Pacific estuaries, USA. Biological Conservation 78: 51-58.

Davis, H. G., C. M. Taylor, and D. R. Strong. 2004. pollen limitation causes an Allee effect in a wind pollinated invasive grass (Spartina alterniflora). Proceedings of the National Academy of Sciences. 101:13804-13807.

De Groot, D. S. 1927. The California clapper rail: its nesting habits, enemies and habitat. Condor 29: 259-270.

Duke, R., P. Boursier, J. Bourgeois, S. Terrill, H. Shellhammer, M. Orland, and L. Henkel. 2006. Marsh studies in South San Francisco Bay 2005-2008: California clapper rail and salt marsh harvest mouse survey work plan. H. T. Harvey and Associates. Project: #477-28. Unpublished report prepared for City of San Jose, CA.

Eddleman, W. R. and C. J. Conway. 1998. Clapper rail (Rallus longirostris). In The Birds of North America. No. 340 A. Poole and F. Gill, eds. The Birds of North America, Inc., Philadelphia, PA.

Evens, J. G., and J. N. Collins. 1992. Distribution, abundance, and habitat affinities of the California clapper rail Rallus longirostris obsoletus in the northern reaches of the San Francisco estuary during the 1992 breeding season. Final report to Carl Wilcox, California Department of Fish and Game, Yountville, CA.

Foerster, K. S., J. E. Takekawa, and J. D. Albertson. 1990. Breeding density, nesting habitat, and predators of the California clapper rail. Unpubl. Rpt. No. SFBNWR-116400-90-1, prep. For San Francisco Bay Natl. Wildl. Refuge, Fremont, Cailfornia. 46 pp.

Foin, T. C., E. J. Garcia, R. E. Gill, S. D. Culberson, and J. N. Collins. 1997. Recovery strategies for the California clapper rail (Rallus longirostris obsoletus) in the heavily urbanized San Francisco estuarine ecosystem. Landscape and Urban Planning 38: 229-243.

Garcia, E. J. 1995. Conservation of the California clapper rail: An analysis of survey methods and habitat use in Marin County, California. Thesis. University of California Davis.

Gill, R. 1979. Status and distribution of the California clapper rail (Rallus longirostris obsoletus). California Fish and Game 65(1): 36-49.

Gould, G. 1973. California clapper rail survey - 1973. California Dept. of Fish and Game. Sacramento, CA.

Harvey, T. E. 1988. Breeding biology of the California clapper rail in South San Francisco Bay. Trans. Western Section the Wildlife Society 24: 98-104.

Keldsen, T. J. 1997. Potential impacts of climate change on California clapper rail habitat of south San Francisco Bay. M. S. Thesis. Colorado State University, Fort Collins, CO. 88pp.

Liu, L., and N. Nur. 2005. Restoring a Tidal Marsh, One Step at a Time. Quarterly Journal of PRBO Conservation Science, Number 139. Point Reyes Bird Observatory. San Francisco, CA.

Lonzarich D. G., T. E. Harvey, J. E. Takekawa. 1992. Trace element and organochlorine concentrations in California Clapper Rail (Rallus longirostris obsoletus) eggs. Archives of Environmental Contamination and Toxicology. 23:147-153.

Morrissey, C. A., L. I. Bendell-Young, and J. E. Elliott. 2004. Linking contaminant profiles to the diet and breeding location of American dippers using stable isotopes. Journal of Applied Ecology 41:502-512.

Rigney, M., P. Delevoryas, R. A. Hopkins, R. R. Duke, and H. T. Harvey. 1989. California clapper rail breeding survey, South San Francisco Bay. Technical report. Alviso, CA.

Robert, M, L. Cloutier, and P. Laporte. 1997. The summer diet of the yellow rail in Southern Quebec. Wilson Bulletin 109:702-710.

Roman, C. T., MJ. James-Pirri, and J. F. Heltshe. 2001. Monitoring salt marsh vegetation - A protocol for the long-term coastal ecosystem monitoring program at Cape Cod National Seashore. Cape Cod National Seashore, National Park Service, Wellfleet, MA.

Schwarzbach, S. E., J. D. Albertson, and C. M Thomas. 2006. Effects of predation, flooding, and contamination on the reproductive success of California Clapper Rails (Rallus longirostris obsoletus) in San Francisco Bay. Auk 123:45-60.

Spautz, H. and N. Nur. 2004. Impacts of Non-native perennial Pepperweed (Lepidium latifolium) on Abundance Distribution and Reproductive Success of San Francisco Bay Tidal marsh birds. A report to the US Fish and Wildlife Service, Coastal Program. URL: http://www.prbo.org/cms/docs/wetlands/lepidium04.pdf Last Accessed 8/28/2006.

Taylor, C. M., and A. Hastings. 2004. Finding optimal control strategies for invasive species: a density-structured model for Spartina alterniflora. Journal of Applied Ecology 41:1049-1057.

U.S. Fish and Wildlife Service. 2005. Formal intra-service endangered species consultation on implementation of the San Francisco Estuary Invasive Spartina Project: Spartina Control Program, as detailed in the 2005 to 2007 Invasive Spartina Control Plans. Memorandum 1-1-05-F-0243. Sacramento, California.

Worton, B.J. 1989. Kernel methods for estimating the utilization distribution in home-range studies. Ecology. 70:164-168.

Zaremba, K. 2001. Hybridization and control of a native-non native Spartina complex in San Francisco Bay. M.A. Thesis. San Francisco State University, San Francisco, CA.

Zembal, R., and B. W. Massey. 1983. To catch a clapper rail - twice. North American Bird Bander 8: 144-148.

Zembal, R., B. W. Massey, and J. M. Fancher. 1989. Movements and Activity Patterns of the Light-Footed Clapper Rail. Journal of Wildlife Management 53: 39-42.