Last week, long-billed dowitchers and godwits pecked at mudflats exposed by the receding tide. The elusive clapper rail did not appear along the watery channel known as "rail alley." But there were signs: Marks in the mud bank showed where the birds had scooted down to water's edge from hollows made in the pickleweed. A lone feather clung to a nearby plant.
Chances of seeing the rails are slim. Ruddy-breasted, with tan and black striping and sturdy legs, the chicken-sized California clapper was fairly common in the San Francisco Bay 50 years ago. But today, there are only an estimated 1,500 birds in the area — about 15 to 20 of them in the Palo Alto Baylands, according to the nonprofit organization Point Blue Conservation Science.
More elusive still is the tiny salt marsh harvest mouse, which weighs as much as a quarter and does not live anywhere else in the world except for San Francisco Bay's marshes. No one really knows their numbers, experts said.
Environmental groups are engaged in a battle to save these endangered species, focusing mostly on preserving the wetlands they and other species call home. Over the years, as much as 80 percent of the San Francisco Bay marshlands have disappeared, according to scientists. Development and salt-pond conversion are the chief culprits.
So far, the work of re-establishing the marshes appears to be helping. Birds and mice are increasing in numbers where some habitat restoration has occurred, scientists said.
But it is a long-term and ever-changing fight. A predicted rise in sea levels due to climate change will, in future years, flood the marshes, washing away nests and making the habitat unsuitable for clapper rails and other species, according to a Point Blue study of projected sea-level-rise impacts.
The best time to spot clapper rails and harvest mice is during the highest solstice tides, said Richard Bicknell, a City of Palo Alto supervising ranger. The mice and rails emerge from their thickets of pickleweed and cord grass and seek higher ground. The rails climb onto the boardwalk or perch on driftwood; the mice cling to the tops of the plants.
In his four years of working at the Baylands, Bicknell thinks he saw a harvest mouse once, hanging from the pickleweed. He has seen clapper rails twice, he said.
Howard Shellhammer, emeritus professor of biology at San Jose State University, has studied the salt marsh harvest mouse since 1961. He said the loss of tidal marshes has forced species that used to live in the lower half to lower third of the marsh zone to higher land. And that leaves them more at risk of running into predators.
"The upper part of the high marsh zone is where the salt marsh harvest mouse, various shrews and other small mammals, plus a variety of birds, escape to during the highest tides ... when the larger birds feast on all those cover-dependent animals forced out of cover," Shellhammer said.
Though endangered, clapper rails aren't the only birds whose numbers have dropped. The populations of black-crowned night herons and snowy egrets, which nest in the trees near the duck pond during the spring, have decreased dramatically in the past two to three years, Bicknell said.
The showy herons, which sport red eyes and two long head feathers on their greenish-black caps, are known to soar gracefully through the sky, while the snow-white egrets glide like prehistoric creatures, making unearthly gargling noises as they flap their wings in the trees.
No one knows why there have been fewer of the herons and egrets, Bicknell said. Perhaps the habitat has changed in some way to make it less favorable; perhaps the much-loved birds sought a more favorable locale where they don't have to put up with human onlookers pointing oversized camera lenses at their nests.
The Point Blue "State of the Birds: San Francisco Bay 2011" report asserts that the primary threats to both birds are the loss or disturbance of nesting sites and noise from construction, which scares the birds away.
Several species of ducks — such as the canvasback, greater scaup, a diving duck, and surf scoter, a deeper-water duck — are also decreasing in population, the report found. Those losses could be significant. The San Francisco Bay populations of scaup and scoters represent between 40 and 50 percent of all scaup and scoters counted in the Pacific Flyway.
There is some good news in the report: Populations of some birds, including the black rail, are increasing.
It's not only the loss of marshes but the invasion of the wrong type of plants that threaten the clapper rails and salt marsh harvest mice. A nonnative, invasive species of cord grass, Spartina alterniflora, is pushing out the native variety, Spartina foliosa, Bicknell said. The aggressive weed is replacing plants on which the rail and mouse depend.
But volunteers, including from the nonprofit organizations Acterra and Save The Bay are working to remove the invasive plant, he said.
Lynn Hori, a retired Palo Alto High School teacher, started working with students on science research projects at the Baylands in 1997. Students took a raft and collected samples of the cord grasses, which were genetically tested at U.C. Davis. The tests showed which plants were nonnative Spartina, she said.
The invasive plant was discovered west of the sailing station and in Charleston Slough and Hooks Island, a flat, arrowhead-shaped spit of land at the preserve's easternmost edge. It hybridized with the native cord grass, making it harder to tell one from the other, she said.
"Some picked up the roots characteristics; some picked up the height or the flowers. You almost had to test it all to find out what was native or nonnative. It just comes in and takes over. It grows denser than the native species and makes it harder for animals to move around. It is interfering with the dynamics of the marsh," she said.
The students monitored various areas in search of the nonnative species, and they used tarpaulins to smother some of the plants. They replaced the invasive Spartina at Hooks Island with native cord grass, she said.
Groups have made major efforts to cull invasive Spartina throughout the bay region. Work by the California Coastal Conservancy's San Francisco Estuary Invasive Spartina Project reduced the weed from a high of 800 acres to 40 acres, said Amy Hutzel, coordinator for the project.
Save The Bay has removed invasive Spartina and added native cord grass plugs in Palo Alto, said Seth Chanin, the nonprofit's restoration program manager. The organization has restored 45,000 acres of wetlands around the bay over the past decade, with a goal of 100,000 acres.
Levees, which have poor, degraded soil and have been taken over by invasive European weeds such as wild fennel, mustard, radishes and ice plant, are also the focus of restoration work.
Volunteers collect local native seeds at the marshes in the fall and install plants in the winter during the rainy season. Save The Bay is propagating 40,000 plants at a nursery set up in the Palo Alto Baylands, Chanin said.
"We go into undisturbed transition zones (from one kind of plant habitat to another) and look at what's growing and try to replicate that," Chanin said. They use 25 to 30 plant types, including salt-tolerant grasses and low shrubs that provide cover for animals and a food source, he said.
Save The Bay, Acterra and the East Palo Alto nonprofit organization Collective Roots are working jointly on projects to restore habitats in East Palo Alto's Faber-Laumeister Tract. The project is paid for through a grant from the 2007 Cosco Busan oil spill, said Alex Von Feldt, Acterra's stewardship program director. The restoration also involves schoolchildren from the East Palo Alto Charter School and Youth Community Services. A Junior Bay Stewards program will teach East Palo Alto students about marshland ecology, she said. This past summer the project started a clapper-rail habitat restoration project, she said.
Save The Bay has planted half-mile stretches of native species at Palo Alto's 126-acre Byxbee Park. The plants line the edge of a levee overlooking the pickleweed and cord grass. Chanin has seen a clapper rail once in the three years he has worked there, but volunteers often hear its loud, distinctive call: keck keck keck keck keck keck keck keck.
The Bay Area's tidal marshes comprise an ever-shifting system, and the presence or absence of animals presage its future condition. The shorebird population in San Francisco Bay has shifted north, where their numbers have increased in the north bay, and away from the central and south bay, according to the State of the Birds report. The numbers of one of the more common species, the Western sandpiper, has declined Bay Area-wide, while two other common species, the least sandpiper and the willet, have increased greatly.
Burrowing owls that nested in the Palo Alto Baylands are gone, while along Mountain View's shoreline, habitat improvements have helped the species.
In 2008, the clapper rail population dropped, especially in the south bay.
"We suspect the entire Bay Area really crashed in 2008. Most likely, it was weather-related. Pressures could have caused poor reproduction. We really don't know," said Julian Wood, Point Blue's San Francisco Bay program manager.
Pollution can seriously upset the food supply, according to Joanne McFarlin, a senior ecologist with Acterra, who three years ago examined bugs at Stevens Creek. Endangered steelhead trout and clapper rails feast on invertebrates. When samples from the upper creek found only pollution-tolerant insects, such as black flies and midge flies, McFarlin suspected a pollution source in the surrounding neighborhood was emptying into the water.
Soil analysis found very high levels of pesticides known as pyrethroids, which are commonly used in backyard gardens, she said. An outreach program to educate residents by the City of Cupertino resulted in lower levels of pesticides, which in turn allowed insects that are important on the food chain to repopulate the waterway, she said.
Some restoration work covers large swaths of land. The South Bay Salt Pond Restoration Project, a massive plan by state and federal agencies and private foundations, purchased 15,100 acres from Cargill Inc., with plans to restore 50 to 90 percent of south bay ponds to a mix of tidal marsh and shallow, managed ponds.
Restoration has brought back large numbers of leopard sharks and native fish to south bay waters, Hutzel said. Restored areas include near the Dumbarton Bridge at Ravenswood Open Space Preserve, near Moffett Field in Mountain View, at Eden Landing near Hayward, in Alviso in the South Bay and at the Don Edwards San Francisco Bay National Wildlife Refuge.
Jen McBroom, clapper-rail monitoring manager at Berkeley-based habitat restoration and monitoring firm Olofson Environmental, Inc., has done hundreds of surveys of clapper rails all around the bay. Some hope is coming to the rails as a result of returning salt ponds to wetlands, she said. A 2012 Point Blue study found the number of clapper rails increases dramatically following restoration of tidal marshes, but the increase begins after 17 to 20 years, she noted.
"Currently, we don't have data on clapper rail response to restoration through planting. However, we do know that much of the depredation of clapper rails occurs during high tides, when clapper rails are forced to seek refuge on higher ground. Plantings adjacent to tidal wetlands can provide the cover that the clapper rails need to hide from predators during high tide," she said.
The effects of higher tides from climate change — and the human response to it — is a concern for many scientists.
Claire Elliott, a senior ecologist with Acterra, said there has been talk of raising the levees in response to sea-level rise. That will have an impact on what kind of plant refuges are available to the animals, she said.
"My fear is that the levees will isolate species from areas they need to access," she said.
Local officials are indeed planning for a sea-level rise — but they're also taking Baylands animals into account.
The San Francisquito Creek Joint Powers Authority, a coalition that includes Palo Alto, Menlo Park, East Palo Alto, the Santa Clara Valley Water District and the San Mateo County Flood Protection District, is in the midst of a major multi-year project to protect surrounding communities from flooding.
The work includes the widening of channels, reconstruction of levees and a complete reconfiguration of the Palo Alto Municipal Golf Course. Though flood control is the main objective, habitat restoration is also part of the plan. The Environmental Impact Report for the project lists as its first objective to provide a "golf course that has enhanced wildlife habitat, improved wetland areas and a more interesting course."
One of the goals, in fact, is to make the golf course feel more like the Baylands. The reconfiguration would reduce the area of "managed" turf from 135 acres to 81 acres. Rob de Geus, assistant director of the Community Services Department, noted that the project will "add over 50 acres of natural Bayland."
Former councilwoman Enid Pearson, who along with former councilwoman Emily Renzel was largely responsible for saving the Baylands in the 1960s, said she fears the marshes will be damaged by attempts to stem flooding.
The flood-control plan would direct overflowing water from the San Francisquito Creek, between the Baylands and U.S. Highway 101, toward the Faber Tract in East Palo Alto, where clapper rails and harvest mice live.
The U.S. Fish and Wildlife Service shares her concern. In July, the agency raised flags in a letter to the Creek Authority. The Wildlife Service stated that flood waters in the Faber Tract could result in the loss of refuge for the clapper rails and the mice, exposing them to predators. The project, the agency argued, "has the potential to have severe adverse effects to the California clapper rail and salt marsh harvest mouse."
Among the Creek Authority's plans, it is looking into ways to protect the species, including building mounds that harvest mice could climb, should flooding occur.
Rising sea levels pose challenges more widely, McBroom and Hutzel said.
"We've built communities up to the edge of the bay. If that wasn't there, the marshes could move upward and inland, but they will get squeezed between the communities and a rising bay," Hutzel said.
But Wood said computer modeling by Point Blue indicates that marshlands might have more resilience in the face of a sea-level rise than previously thought. Sediment deposits could increase in some areas, building up the marshland. As sediment builds, marsh plants start to grow.
"The sooner that happens, the more likely it is that the marsh can keep pace with sea-level rise," he said. But he added a caveat: "If there is a faster rise, will they be able to do it faster?"
The study, which is found at www.prbo.org/sfbayslr, shows that some areas currently under water will become mudflats in the Palo Alto Baylands by 2030, with low sediment deposits and a more than .52-meter sea-level rise. Under a scenario with higher sediment deposits, much of the lower marshes will fill in to become so-called "mid-marsh" zones. The Baylands would have a less-varied habitat, according to many of the models.
While that could portend big changes for wildlife that depend on varied zones for their survival, Wood said the models also offer tools for marshland managers to design habitats that could help species to survive.
McBroom agreed that humans, who have contributed significantly to the demise of the marshes, must have a hand in saving species. Clapper rails need large, round marshes with a range of elevations, from low marsh to forage in during low tides to high marsh in which to take cover during high tides, she said.
"Their habitat will shrink as the rising waters drown the tidal wetlands — unless we are able to increase the elevation of these marshes or allow them to expand landward," she said.
Daren Anderson, Palo Alto's manager of open space, parks and golf, said the city must consider the best ways to manage the competition between the rising tides, wildlife and community. In its search for ways to care for the Palo Alto Baylands, the city will seek ways to manage and preserve the tidal marshes for generations of wildlife and humans to come.