Estuary News

October 2022

Of Mice and Marshes: Surveying Salties to Save Them

It’s five in the morning, and Don Edwards San Francisco Bay National Wildlife Refuge remains in the tight velvet grip of night. All is peaceful and quiet, despite the fact that the toll plaza of the Dumbarton Bridge is less than a quarter-mile away.

By 5:15, car dome lights and slamming doors have transformed this lonely spot at the watery edge of Newark into a hub of activity. People are taking last sips of coffee, strapping headlamps to their foreheads, and swapping civilian footwear for rubber muck boots. The occasion that’s roused everyone from bed more than an hour before sunrise? The first survey of the salt marsh harvest mouse conducted across the rodent’s entire San Francisco Bay-centered range.

In 1970, Reithrodontomys raviventris became one of the first animals added to the federal endangered species list. Found along the damp fringes of San Francisco Bay, the salt marsh harvest mouse is the only mammal entirely restricted to coastal marshes—specifically, those found in the San Francisco Estuary. The loss of more than 90% of historical tidal marsh since Gold Rush times, compounded by future expected sea-level rise, puts the species in danger of extinction. Yet this tenacious rodent hangs on in remnant pickleweed-dominated marshes along the Petaluma River, Suisun and San Pablo bays, and Alviso north to Hayward and the Peninsula.

No one, however, has a good sense of how the species is faring. That includes the U.S. Fish and Wildlife Service, the agency responsible for managing the recovery of all listed species. This August 2022 expedition to Dumbarton Marsh and the north shore of Mowry Slough is part of a seven-week effort to obtain a comprehensive picture of the at-risk rodent’s entire population. The project would ultimately survey mice at 55 sites around the Bay, and collect scat samples from bait stations at an additional 29 sites to confirm the presence or absence of the species.

Leading today’s survey is biologist Katie Smith of WRA, Inc., an environmental consulting firm. Having trapped more than 4,000 “salties” since 2008—2,000 for her doctoral dissertation alone—Smith is the leading expert on a species she considers to be charismatic minifauna.

Critical Baywide Data

Surveys in previous decades have generally been one-offs, limited to a handful of sites on the rare occasion that scientists have had time and funding. But such a scattershot approach is inadequate to get a read on the population as a whole. “The populations can vary a lot from month to month and rain year to rain year,” Smith says. “If you trap here this year during this month, and a different spot next year in a different month, we can’t necessarily compare them.”

Image courtesy of Suisun Resource Conservation District

Surveying the entire Bay at one time is the only antidote. “The idea here is we trap everywhere all at once, and we can have a baseline. More mice here, less mice there,” Smith says.

Funding for the study comes from the National Fish and Wildlife Foundation, the nation’s largest private provider of conservation grants. One of the survey’s thorniest tasks proved to be gaining permission to trap. On top of his regular duties as operations manager of Suisun Resource Conservation District, John Takekawa helped coordinate the survey and spent nearly three years tracking down the myriad, often mysterious, landowners of tidal marsh properties, as well as petitioning government agencies for trapping permits.

Additional preparations included gathering records of as many previous trapping efforts as possible. Many of those accounts were missing basic data such as the date or numbers of traps set. Even so, the information has allowed Smith to start modeling habitat characteristics such as the marsh elevations where the highest numbers of mice were trapped.

Despite its complicated logistics, the survey finally promises to yield the baseline data to guide future salt marsh harvest mouse conservation. Determining where the species is present, absent, or struggling with problems such as low numbers or inbreeding is the first step toward finding solutions.

It’s still pitch-dark in the parking lot, but Smith wastes no time marshaling her seven volunteers into the field. All are biologists, from WRA as well as a variety of regional, state, and federal agencies. “We’re always racing the sun,” Smith explains while steering our convoy of three vehicles over a rutted levee road. Last night, Smith and colleagues left 100 Sherman traps baited with birdseed in these marshes. We need to get to any animals trapped inside before the aluminum boxes get too hot.

The sky has brightened to blush with a smear of tangerine over Mission Peak by the time we pull up at Dumbarton Marsh. Weathered plank walkways suspended over a sea of pickleweed will take us into the heart of the wetland. We climb rickety wooden ladders over massive decommissioned water supply pipes, pass beneath towering electric pylons, and step gingerly over exposed nails and rotted boards to reach the trap grids.

Before anyone touches a trap, Smith fills out the pre-survey site assessment. The form asks about types and height of vegetation and cover, whether the marsh is connected to nearby habitat, and the likelihood that competitor species such as rats and voles are present. The information will help reveal what features make some marshes better for salties than others. At present, that’s not entirely clear; Smith has seen plenty of places that look like lousy habitat yield many mice, and vice versa. “Having this large dataset will give us a lot more analysis power to say, for example, areas with this cover or pickleweed of a certain height consistently have more animals across the species range,” she says.

Complicating matters further, location also affects a site’s suitability as mouse habitat. For example, shorter pickleweed in Suisun Bay can offer good shelter because the tidal range there is smaller, while plants of the same height in the Central Bay could offer inadequate refuge against inundation. And though low marsh is more vulnerable to tides, “it’s kind of like a hideout for salties,” Smith says; other species are less competitive in areas subject to frequent inundation.

What Kind of Mouse?

The form completed, it’s time to check the traps. Walking across dense pickleweed takes some getting used to; the fluid-filled stems are just springy enough to affect balance. An occasional shout erupts from those who get mired in a hidden pothole or channel. For our all-female group, Smith considers these happenings “marsh maiden” initiations.

Volunteers preparing to check traps. Photo: Kathleen Wong

The first few traps are open. Then Smith picks up one that has its door sprung shut. Holding the trap inches over the bottom of a bucket, she carefully pushes the door open. A fuzzy ball roughly the size of a chicken egg tumbles out. Smith scoops up the zippy little animal up by the base of its tail and places it on her gloved hand.

With satisfaction, Smith declares it to be a salt marsh harvest mouse. Most people, however, couldn’t say that with certainty. To the untutored eye, salties look nearly identical to the common and plentiful Western harvest mouse, which can also live in tidal marshes. Dimensions of tail and body, plus hair length and color, are the best ways to distinguish the species by sight.

Smith flips the animal over to examine its reddish belly fur, a characteristic of South Bay mice, and records the number code for the matching hue and pattern. North Bay mice tend to have a lighter or white underside. “These ones in the South Bay, the coloration and the shape of their faces, are especially cute,” Smith says. With the deftness of long practice, she repositions the mouse to measure the length of its body and tail, determines its sex and breeding condition, and pops it into a plastic bag for a weighing.

After collecting samples for lab analysis—hair and a tiny snip of ear tissue—and attaching a numbered silver tag to its ear, Smith sets the little male on the ground. It freezes for a heartbeat before vanishing beneath the gray-green stalks of its pickleweed kingdom. By 9:30, Smith and the team have captured a respectable 16 salties and one house mouse at Dumbarton Marsh and Mowry Slough.

The ear tissue samples will be sent to Mark Statham, a UC Davis expert on salt marsh harvest mouse genetics. His analyses, also funded by the survey grant, will verify whether the rodents that were caught were salties or Western harvest mice, yielding more accurate population size estimates.

Hair samples are collected for lab analysis. Photo: Marisa Ishimatsu

Beyond confirming species identity for the survey, the DNA sequences will provide nuanced insight into population divisions and robustness. The most important factor is genetic diversity, says Statham: “Diversity is sort of a measure of genetic health. The lower the diversity, the fewer genetic tools the animals have to deal with whatever they’re getting hit with, such as climate change.”

Marshes where mice are especially distinctive might, for example, merit extra preservation efforts. Similarly, populations with substantially lower diversity might need an influx of new genes.

“The longer the genetic divergence between two populations, the more evolutionarily distinct they are. If we find populations that are very recently separated because of something humans have done, say a road, we can tell we have stopped the gene flow between them,” Statham says. Here, removing the physical barriers isolating marshes, or creating novel linkages, could enable them to breed with neighbors again, bolstering their genetic diversity.

Among the most interesting puzzles awaiting Statham’s attention is the geographic dividing line between the two recognized subspecies of the mouse. Currently, mice in Suisun and San Pablo bays are grouped into a northern subspecies, while those from Point Pinole to the southern end of San Francisco Bay belong to the southern subspecies.

“Looking at the genetics of these animals across the range, we’ll be able to figure out where the real break between the different subspecies is, and whether we have got additional distinct units within,” Statham says.

By the time the survey wrapped at the end of August, it had amassed an astonishing trove of mouse-oriented information. Out of 50 traps set out for three nights apiece at 55 sites, the survey netted about 575 salties (a number that awaits genetic confirmation). Such statistics on trapping success can serve as estimates of population density—necessary for the federal government to declare where, when, and if the species merits delisting.

As for Smith, she is beyond pleased with the results. “We hit almost every site we wanted to get to, a lot of people got to participate and learn about the mouse, and we know a lot more already than we did before the survey,” she says. “We will be able to do a lot of really cool analyses with the data, and answer some of the questions that we haven’t really been able to address over the past 50 years. It should go a long way toward helping the species recover.”

Top Image: A tagged mouse in pickleweed. Photo by Marisa Ishimatsu

Related Stories

About the author

Bay Area native Kathleen M. Wong is a science writer specializing in the natural history and environment of California and the West. With Ariel Rubissow Okamoto, she coauthored Natural History of San Francisco Bay (UC Press, 2011), for which she shared the 2013 Harold Gilliam Award for Excellence in Environmental Reporting. She reports on native species, climate change, and environmental conditions for Estuary, and is the science writer of the University of California Natural Reserve System.

Related Posts

American Avocet on managed, former salt ponds in the South Bay. Photo: Roopak Bhatt, USGS

One-of-a-Kind Stories

Our magazine’s media motto for many years has been “Where there’s an estuary, there’s a crowd.” The San Francisco Estuary is a place where people, wildlife, and commerce congregate, and where watersheds, rivers and the ocean meet and mix, creating a place of unusual diversity. In choosing to tell the...
dam spillway oroville

Supplying Water

Ever since the state and federal water projects were built in the 1930s and 1940s, California has captured snowmelt in foothill reservoirs, and moved the fresh water from dam releases and river outflows to parched parts of the state via aqueducts hundreds of miles long. A convoluted system of ancient...

Tackling Pollution

Though the Clean Water Act did an amazing job of reducing wastewater and stormwater pollution of the San Francisco Estuary, some contaminants remain thorny problems.  Legacy pollutants like mercury washed into the watershed from upstream gold mining, PCBs from old industrial sites, and selenium from agricultural drainage in the San...