The Project: What We Are Doing And Why?

Previous studies of clapper rail ecology (Albertson 1995, Keldsen 1997, Schwarzbach et al. 2006) as well as ongoing population surveys provide some insight into the current status of clapper rails in San Francisco Bay, although new risks to clapper rails may now exist. Clapper rails inhabit multiple elevational tidal marsh zones throughout the San Francisco Bay Estuary. One of the greatest habitat threats to tidal wetlands in this region is the invasion of smooth cordgrass (Spartina alterniflora), a species native to the Atlantic coast. Invasive Spartina displaces and hybridizes with native Pacific cordgrass (Spartina foliosa) altering both the physical structure and biological composition of tidal marshes, mud flats, and creeks. These hybrids display increased vigor in both niche overlap (greater range of suitable substrates and salinities) and reproductive success (through pollen swamping and increased seed output; Anttila et al. 1998, Zaremba 2001). The combination of factors favoring invading Spartina hybrids suggests the potential for native Spartina extinction (Ayres et al. 2003). Invasive Spartina hybrids spread rapidly through marsh and mudflats often in circular clones leading to the vernacular term "hybrid swarms". Unlike native S. foliosa, S. alterniflora and its hybrids form dense monotypic stands (marsh plains), that have greatly increased sediment accretion rates (Daehler and Strong 1996). This enables dense stands to form rapidly, even on open mud flats, and engineer the local environment in a method that enables greater spread. The increasing rate of spread and potential ecological, and economic, consequences are of great concern (Ayres et al 2004).

Over the last 25 years, invasive Spartina has spread rapidly establishing in numerous wetland habitats and marsh restoration sites while threatening over 28,000 ha of native wetland habitats (Ayres et al. 2004). The CALFED Ecosystem Restoration Program (ERP), California Coastal Conservancy, and other federal, state, and local partners have invested heavily in eradication of invasive Spartina in San Francisco Bay via the Invasive Spartina Project (ISP). Most of the initial eradication efforts focused on smaller peripheral marshes, primarily because tidal marshes are characterized by protected endemic vertebrate species unique to the estuary. These include the endangered California clapper rail, one of the least numerous and most sensitive indicator species of tidal wetland health in the ecosystem. Clapper rails are found in all embayments of the San Francisco Bay estuary, but the largest populations are found in the South Bay, the region most heavily invaded by Spartina.

Invasive species have a long history of establishment and expansion in the complex environment of the San Francisco Bay and Estuary. The rate of new invasions and the ecological cost of invasions are increasing at the same time as extinction threatens native species, such as the clapper rail (Cohen and Carlton 1998). The ecological impact of Spartina invasion on California clapper rails is of particular concern. The predicted dense monotypic stands of S. alterniflora hybrids may reduce suitable rail habitat to the leading, Bay-ward, edge of invading clones (Baye 2004). In addition, due to the ecological engineering properties of S. alterniflora clones and their ability to establish at relatively low elevations on mud flats additional foraging habitat could be lost (Daehler and Strong 1996). Confounding the ecological consequences of invasive Spartina are the apparent habitat preferences of rails. Rails use Spartina, both native and invasive, for nesting and cover (De Groot 1927, Gould 1973, Rigney et al. 1989, Foerster et al. 1990, Baye 2004, J. Albertson USFWS pers. comm.). Invasive Spartina also maintains an earlier seasonal progression than S. foliosa (Callaway and Josselyn 1992). If this entices early nesting rails to use low-marsh Spartina over the more typical high-marsh Grindelia spp., nests may be more susceptible to early season high tides (De Groot 1927, Harvey 1988, Evens and Collins 1992). However, predation is typically lower in low marsh areas, both for adults and nests, in Spartina dominated habitats (Foin et al. 1997).

These factors create particular difficulties when considering invasive Spartina eradication in clapper rail habitats. The goals of invasive Spartina eradication and endangered species protection are consistent regarding long-term potential impacts of invasive Spartina. The current need however, is to assess the degree to which these goals are incongruent given the short-term suitability and use of invading Spartina clones by rails. To illustrate, a marsh invaded by invasive Spartina contains rails that use the Spartina for cover and nesting. Removal of invasive Spartina accomplishes the goal of Spartina eradication, but if rails fail to survive and reproduce, then the goal of species protection is unfulfilled. The ability for rails to respond to invasive Spartina eradication, through changes in habitat use or dispersal to suitable habitats, mitigates the potential impact on species protection goals. Currently, the potential for impact from invasive Spartina removal and the potential for mitigation by rail ecology and behavior remain poorly understood.

Direct observation during control efforts (for which extensive and reasonable mitigation measures are developed; USFWS 2005) and analysis of population surveys provide assessments of the impact of invasive Spartina on rails. The USFWS uses standardized annual breeding season call counts and biannual winter high tide surveys to evaluate the California clapper rail population (Liu and Nur 2005, Duke et al. 2006, J. Albertson USFWS pers. comm.). Project partners, including PRBO Conservation Science, Avocet Research Associates, East Bay Regional Parks and others, conduct these surveys. However, comparisons between call counts and radio-telemetry locations for the Yuma clapper rail showed lower call response by rails in sparse habitats (Conway et al. 1993). Successful invasive Spartina control efforts would likely create less dense blocks of habitat that may confound call-count survey results. Emigration resulting from habitat change would also affect population surveys at individual marshes. Thus, relying on surveys alone to assess the impacts of invasive Spartina control may be problematic.

The perceived likelihood of adverse impact on rails has already resulted in phased treatment schedules for 3 of 22 sites, and incomplete treatment of 1 site (USFWS 2005). While these measures are justified and reasonable (USFWS 2005), delay or suspension of invasive Spartina removal resulting from perceived increased endangered species "take" will increase the cost of eradication and reduce or eliminate the effectiveness of efforts already completed. Large blocks of invasive Spartina are the primary treatment areas necessary for eradication (Taylor and Hastings 2004, C. Stenvall, Manager, Willapa NWR, pers. comm.) but are the most likely to be inhabited by large numbers of clapper rails. Thus, negative impacts are more likely to occur when treating the most important areas of Spartina invasion. Since the spread of invasive Spartina is subject to an Allee effect, annual treatment of small and isolated patches unoccupied by rails may be insufficient to reverse the spread throughout the San Francisco Estuary (Taylor and Hastings 2004, Davis et al. 2004).

The effects of invasive Spartina and eradication efforts operate in conjunction with additional biotic and abiotic factors to alter the regulatory mechanisms, which in turn determine California clapper rail vital demographic rates (i.e. survival, recruitment, and movements). Our conceptual model of clapper rail ecology recognizes the input of these three levels (ecological conditions, ecological constraints, and population dynamics) as factors determining the size and location of clapper rail population. In other words, the combined effects of the environment influence the attributes and interactions that change population (or individual) growth and location. One advantage of this model is that it allows a hierarchical investigation of clapper rail ecology including assessment of individual movements or reproduction, marsh specific survival rates and metapopulation dynamics for the San Francisco Bay-Delta region. Furthermore, this represents a conceptual template for a spatially explicit model of California clapper rail population dynamics and factors affecting vital demographic rates (including habitat and population stressors).

Control of invasive Spartina (Spartina alterniflora and hybrids) under the Invasive Spartina Project will have uncertain effects on the ecology of California clapper rails in San Francisco Bay. The behavior of individual clapper rails may be altered in response to control efforts and associated shifts in habitat composition, leading to changes in individual distribution or survival, and potentially even population viability of the species. Thus, the purpose of this study is to examine the ecological response of clapper rails to invasive Spartina control efforts, and to identify eradication strategies that minimize negative effects on their primary habitats and vital rates.

Objectives: We will quantify the impact of invasive Spartina and Spartina control on clapper rails and recommend control strategies that minimize negative effects. Our specific objectives to achieve this goal are to;

1. Estimate impact of invasive Spartina on clapper rail habitat and space use patterns relative to native vegetation.
2. Quantify the impact of invasive Spartina control on clapper rail resource and space use patterns.
3. Determine the effect of invasive Spartina control on clapper rail reproductive success.
4. Estimate clapper rail seasonal and annual survival, and investigate covariation between survival and invasive Spartina control.
5. Integrate results of objectives 1-4 into a model of population dynamics with estimated impacts resulting from invasive Spartina removal.
6. Assess invasive Spartina control methods and recommend solutions that reduce negative impacts to clapper rails.

• Methodology