USGS Western Ecological Research Center

Home Who We Are Where We Are What We Do Products Search Outreach Jobs Contacts

Ecology of California Clapper Rails in the San Francisco Bay/Delta Region

Clapper rail moving through the marsh at Colma Creek --Photographer: USGS

The California Clapper Rail (Rallus longirostris obsoletus) is a federal and state listed endangered species restricted primarily to San Francisco Bay, Suisun Bay, and wetlands near the mouth of San Francisco Bay. The historical distribution of rails ranged from Morro Bay northward to Tomales Bay and possibly Humboldt Bay.   The US Fish and Wildlife Service is currently revising the species recovery plan for California clapper rails while critical information on this species’ movements, habitat use and survival are not well understood.  Widespread habitat conversion, nonnative predators, and contaminants have been implicated in the dramatic decline of Clapper Rails, whose populations may have been in the tens of thousands.  By the early 1990s, Clapper Rails may have numbered as few as 200 and are currently thought to number around 1,800. 

Project Details

Clapper rail fitted with a radio transmitter. --Photographer: USGSPrevious studies of clapper rail ecology, as well as ongoing population surveys, provide some insight into the current status of clapper rails in San Francisco Bay. 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. The increasing rate of spread and potential ecological and economic consequences are of great concern. The endangered California clapper rail, one of the least numerous and most sensitive indicator species of tidal wetland health in the ecosystem, 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

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. Invasive Spartina also maintains an earlier seasonal progression than S. foliosa.  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.  However, predation is typically lesser in low marsh areas, both for adults and nests, in Spartina dominated habitats.

Marked rail.
Clapper Rail Under Cover 

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. 

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.


A Banded Clapper Rail 

Links to Other Projects

Floating Island Project


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.

7.  Evaluate linkages between mercury concentrations and clapper rail diet using multistage (cross-seasonal vs. intra-seasonal) stable isotope analysis.

USGS Contact For This Project
Michael Casazza
(530) 669-5075
Dixon Field Station
800 Business Park Drive, Suite D
Dixon, CA 95620
View this person's Details


Accessibility FOIA Privacy Policies and Notices

Take Pride in America logo logo U.S. Department of the Interior | U.S. Geological Survey
Page Contact Information:

References to non-U.S. Department of Interior (DOI) products do not constitute an endorsement by the DOI.

* DOI and USGS link policies apply.