Monthly Archives: May 2014

California Clapper Rail

Clapper rail

Photo Credit: Robert Floerke, CDFW

By Tim Dodson

The California clapper rail (Rallus longirostris obsoletus) is the focus of this edition’s “Species Spotlight.” The California clapper rail belongs to the order Gruiformes, in the family Rallidae, which includes rails, gallinules, and coots. The genus Rallus consists primarily of marsh-dwelling birds with short rounded wings, large feet, and long toes.

California clapper rails are fully dependent on salt marsh habitat and occur almost exclusively in tidal salt and brackish marshes with unrestricted daily tidal flows, adequate invertebrate prey food supply, well developed tidal channel networks, and suitable nesting and escape cover that can be used as refugia during extreme high tides.

California clapper rails eat spiders, amphipods, yellow and striped shore crabs, clams (Macoma balthica), and the introduced horse mussel. These birds nest from mid-March into July with nesting peaks in late April–early May and late June–early July. The second peak may include late nesters and pairs attempting to overcome initial nesting failure.

Historically, the range of the California clapper rail may have extended from Humboldt Bay to Morro Bay. Thousands of California clapper rails were eliminated by market hunters from the time of the Gold Rush until the passage of the Weeks-McLean Law in 1913, which was a precursor to the Migratory Bird Treaty Act (MBTA). The MBTA was designed to stop commercial hunting and illegal shipment of migratory birds from one state to another.

The current distribution is limited to the salt marsh habitats in the San Francisco Bay Delta (SFBD) Ecoregion. California clapper rail is a true endemic to this area meaning

Bay Delta Marsh

CDFW photo

it occurs here and nowhere else. Originally, the salt marshes of South San Francisco Bay had the largest populations of California clapper rails. Now, remaining populations are found in remnant salt marshes such as those on Bair and Greco Islands, along Coyote Creek, and throughout the marshes in the Don Edwards San Francisco Bay National Wildlife Refuge. Smaller populations are located in western Contra Costa, eastern Marin, and northern Alameda Counties.

California clapper rails are also found in northern San Pablo Bay, along the Petaluma River as far north as Schultz Creek, along major creeks and marshes in both Sonoma and Napa Counties and on Bull Island on the Napa River. The extension of range further east in Suisun Marsh and northern Contra Costa County may bear some relationship to reductions in Sacramento-San Joaquin Delta freshwater outflow and concomitant increases in salinity.

California clapper rails typically utilize salt marshes dominated by both pickleweed (Salicornia virginica) and pacific cordgrass (Spartina foliosa). California clapper rails use a network of small tidal sloughs for foraging and quick escape. They construct nests near tidal sloughs (within 10 meters), canopied with either pickleweed or cordgrass, sometimes gum-plant, salt grass, or drift materials. Density of cover, floatability of materials, height above tides, and annual weather changes are all variables of successful nesting. California clapper rails also construct “brood nests” on higher ground to protect nests and young from storm influenced tides. These are usually simple floatable, platforms of twigs or stems, without a canopy.

The California clapper rail is listed as an Endangered Species under the Federal and State Endangered Species Act and as a Fully Protected Species under the California Fish and Game Code. As described in the 2010 U.S. Fish and Wildlife Service Draft Recovery Plan for Tidal Marsh Ecosystems of Northern and Central California, lack of extensive blocks of tidal marsh with functional habitat structure is the ultimate limiting factor for the species’ recovery. In addition, vulnerability to predation by native and non-native predators is exacerbated by reduction of California clapper rail habitat now occurring predominately as narrow and fragmented patches close to expanding urban areas.

Bay Delta marsh

CDFW photo

Diking, dredging and filling the marsh for conversion to agriculture, urban development and salt production have reduced total marshes in the San Francisco Bay by 84% or more. Levees provide artificial access for terrestrial predators displacing optimal cover of high marsh vegetation. The predators of adult rails include cats, other mammals, northern harriers, red-tailed hawks, and peregrine falcons. The presence of non-native red foxes is further impacting the rail. Norway rats prey upon young rails. In addition, contaminants, particularly methylmercury, have been identified as a significant factor affecting viability of California clapper rail eggs.

The rapid invasion of San Francisco Bay by exotic Spartina alterniflora (smooth cord grass) and its hybrids with the native S. foliosa (Pacific cordgrass) has presented a unique challenge. Since the Invasive Spartina Project (ISP) began in 2000 with the intent of eliminating introduced species of Spartina from the San Francisco Bay Estuary, more than 75 ISP partners have successfully reduced the infestations by 96% from the peak of over 800 net acres in 2006. Clapper rail population trends are stable at sites where non-native Spartina has undergone continuous control and where non-native Spartina has been reduced to insignificant levels.

In the long run, the control of Spartina should benefit the rail by creating a more natural native marsh. However in the near-term, eradication poses a severe threat to California clapper rails and their habitat because of the temporal loss of cover due to the lag time between eradication of exotic cordgrass and regrowth of native cordgrass. The ISP is undergoing active revegetation at treatment sites that is designed to enhance foraging, nesting and high tide refuge habitat for the California clapper rail by carefully considering this timing issue.

As described in the another article in this current newsletter, under the SWAP 2015 Update, the SFBD Conservation Unit team has developed conservation strategies that protect existing marshes, streamline restoration projects, control invasive species, as well as that support education program to enhance the public’s appreciation of the marsh and the California clapper rail, all of which are meant to benefit this important and unique species.

 NOTE: the following were used as references for this article:

The United States Fish and Wildlife Service’s 5-Year Review: Summary and Evaluation for the California Clapper Rail

United States Environmental Protection Agency’s Endangered Species Fact Sheet for the California Clapper Rail

J. McBroom’s California Clapper Rail Surveys for the San Francisco Estuary Invasive Spartina Project 2013

Overton et al. Tidal and seasonal effects on survival rates of the endangered California clapper rail: does invasive Spartina facilitate greater survival in a dynamic environment?



San Francisco Bay Delta Conservation Unit

Map of San Francisco Bay Delta Conservation Unit

San Francisco Bay Delta Conservation Unit

By Terry Tillman and Tim Dodson

The San Francisco Bay Delta is unmistakably one of the largest estuaries on the Pacific Coast. This region includes the San Francisco Bay – a vast inlet where the Pacific Ocean ultimately joins freshwater in-flows originating in the Sierra Nevada Mountains, creating the dynamic mixing zone we refer to as the Delta.

While being an epicenter of commerce and recreation for millions of Californians, the San Francisco Bay Delta is also an essential habitat to a host of plants and animals. Where salt water and fresh water occur together in the mixing area or brackish zone, a unique and crucial environment has evolved over time. The State Wildlife Action Plan (SWAP) 2015 Update has identified this area as the greater San Francisco Bay Delta (SFBD) Conservation Unit.

The SFBD Conservation Unit offers diverse tidally influenced habitat types such as open deep water, shallow water, tidal wetlands, salt marsh, freshwater wetlands, riparian, managed wetlands, grasslands, and cultivated lands. It is home to over 130 species of fish and a retreat for over one million migrating birds who find sanctuary in its open waters, sloughs, rivers, marshes and tidelands as they traverse the Pacific Flyway. A broad spectrum of wildlife, including marine mammals, invertebrates, and shellfish, as well as plants inhabit this estuarine ecosystem. In addition to supporting a critical food web and rearing grounds for many species, the Bay and Delta also provides important aesthetic, economic, and recreational benefits for neighboring communities.

San Francisco Bay Delta

CDFW Photo (2004)

One of the most important habitat types found in the SFBD Conservation Unit is salt marsh habitat. Salt marsh habitat occurs as a narrow band of vegetation around the bay and delta where fresh and salt waters mix in areas that are generally at or below 6.5 feet in elevation. Salt marsh habitat is important because it provides rearing, foraging, and nesting habitats for numerous species, many of which are protected under the state and/or federal endangered species acts.

Species such as the salt-marsh harvest mouse, clapper rail, and Suisun thistle depend on healthy salt marsh habitats for survival. The salt marsh also provides ecosystem services including pollution amelioration, nutrient cycling, water storage and aquifer recharge, carbon sequestration, flood protection and shore line protection.

The interaction of past, present, and future land uses, combined with changing and uncertain climatic conditions, shapes the future ecological landscape in the SFBD. Besides climate change impacts such as higher annual temperatures, less snow pack and snow period, and sea level rise, other stresses believed to be affecting salt marsh habitats are sediment erosion, pollution, extreme events and flooding, changes in groundwater levels, and invasive species. Human activities likely impacting salt marsh habitat are housing and commercial development, incompatible livestock grazing and farming pracitces, roads and railroads, illegal activities, and water management among others.

San Francisco Bay Delta

CDFW photo (2004)

The SWAP update has developed conservation strategies intended to be implemented over the next decade. Several of these address restoring, protecting, and enhancing salt marsh habitat. Strategic actions also include conducting research and monitoring. Some of the interests under this strategy are to decipher population trends of sensitive species that occur in the area, and to provide a regional framework to better integrate and share data with conservation collaborators. One key strategy considers educational programs to better inform the public about the impacts affecting salt marsh habitats, its importance, and the role it plays within the sphere of the entire SFBD Conservation Unit.

Other strategic actions will include the identification, management, and control of invasive species as well as advocacy for laws and policies that will protect existing habitats and streamline restoration projects. These conservation strategies are meant to benefit the habitat, species, and the ecosystem services that salt marsh offers. They are interrelated and incorporated within a high-level program that focuses on integrated resource management and joint advocacy partnerships.







Phase II of the SWAP 2015 Update is underway. Phase II includes: actual writing of the SWAP document for the regional conservation strategies developed under Phase I; evaluating our performance in meeting the objectives of SWAP 2005 and those of State Wildlife Grant (SWG) funded projects; identifying lessons learned through these SWG projects; developing a draft and final SWAP 2015 Update document; and conducting public review for these documents.

Ascent Environmental was selected as our contractor to assist with the Phase II process. Once under contract, they are tasked to:

  • Review and standardize the Miradi files created to document and model the regional conservation strategies.
  • Upload Miradi files to Miradi Share – a newly developed cloud-based data system that enables us to integrate the regional data into statewide information.
  • Complete regional strategy development especially for the targeted habitats that span over multiple conservation units.
  • Review all the SWG funded projects between 2005 and 2013 and identify progress, results, challenges, area for improvement and future recommendations.
  • Update the SWAP 2005 Plan and create the draft and final SWAP 2015 Update.
  • Provide for public review and conduct public meetings for those documents.

CDFW is also working with University of California, Davis, to assess vegetation vulnerability to the climate change. The analysis will complement the taxa specific vulnerability assessments that were completed, or are in near completion, as part of the updates to the Species of Special Concern reports issued by the Department. The targeted conservation species under a state wildlife action plan (of any state) are called as “Species of Greatest Conservation Need (SGCN)”, and in the case of California, it is the Department’s responsibility to identify these priority species. For the SWAP 2015 Update, the list of SGCN is comprised of the Species of Special Concern along with CA state and federally listed and candidate species.

We are finalizing schedule for two additional scoping meetings that will be presented for tribal communities via WebEx on June 17th and 18th, 2014. Nearly two hundred invitation letters were sent to tribal members identified by the Department. Coordination and strengthening partnerships with tribes and First Nations is a priority for this project as expressed in the SWAP 2015 Update vision document.

We are planning to begin Phase III (the last phase) of the SWAP 2015 Update later this year. Phase III will involve developing eight companion plans associated with the main SWAP 2015 document. Companion plans focus on actions that can be better undertaken in collaboration with other agencies, organizations, private landowners and other partners. These actions complement the SWAP 2015 Update and expand implementation of conservation strategies beyond the Department. The benefit is increased coordination, improved resources and data sharing, and better alignment of planning, policies, and regulations – which all contribute to improve conservation effectiveness. The companion plans will be organized by the following focal topics: Agriculture; Commercial & Recreational Uses; Energy Development; Forests & Rangelands; Land Use Planning; Transportation Planning; Tribal Lands; and Water Management.

We are continuing to make progress and are pleased to report that we are on schedule to finalize the SWAP 2015 Update by October 2015.