Presumed Extinct: By Serendipity


Presumed Extinct: sooty crayfish, San Francisco horseshoe shrimp

As with the presumed extinct ivory-billed woodpecker reported in Arkansas in 2004, there is always the chance that a long-lost plant or animal will be rediscovered, thanks to persistent searching and luck. That’s true even in a busy metropolitan area like the San Francisco Bay Area. In May 2005, botanist Michael Park stumbled upon a population of Mount Diablo buckwheat (Eriogonum truncatum) on the slopes of Mount Diablo. The buckwheat was a  species long thought extinct, last seen in 1936 by UC Berkeley botany graduate student (and later Save Mount Diablo cofounder) Mary Bowerman. 

Spurred by the rediscovery of the buckwheat, it bears asking today which plants and animals endemic to – but presumed extinct in – the San Francisco Bay Area scientists continue to search for in the hope they may still be hanging on by a thread, waiting to be found and protected.

sooty crayfish (Pacifastacus nigrescens)

San Francisco horseshoe shrimp (Lightiella serendipita)

Illustration based on Shasta crayfish photo by B. Moose Peterson/WRP. Illustration by Cecil Devin-Wishing.

On one weekend every June, deep in the heart of the Sacramento-San Joaquin Delta, the town of Isleton comes alive to celebrate its annual Crawdad Festival. Curiously enough, amid the crawdad sausages and jambalayas, the only thing missing is the native crawdad that once inhabited local streams: the sooty crayfish (Pacifastacus nigrescens). Only two other crayfish are native to California’s waters: the Shasta crayfish (P. fortis), a state and federally endangered species found only in Shasta County, and the Klamath signal crayfish (P. leniusculus klamathensis) of far Northern California. From the original 1857 description by marine biologist William Stimpson, we know only that the sooty crayfish was four inches long, blackish, and “common in the vicinity of San Francisco.” It otherwise closely resembled the Shasta crayfish. In the late 1800s the species was reportedly common in Central California streams, including Alameda and Coyote creeks, turning up on occasion in San Francisco markets.

Since the sooty crayfish has vanished without a trace, we can only guess that invasive crayfish introduced for bait and food out-competed their sooty cousins. But that hasn’t stopped ecologist Robert Leidy from looking along the upper reaches of Coyote and Alameda creeks, much of which is pristine land with a native wildlife assemblage. “People rediscover species with periodic regularity in places that are fairly well studied,” says Leidy, “As a field biologist, there’s always that sexy idea of finding something long thought extinct.”

Illustration by Devin Cecil-Wishing

The Bay’s miniature San Francisco horseshoe shrimp (Lightiella serendipita)—one of just five Lightiella species known worldwide—is a cephalocarid, among the most primitive of crustaceans, harkening back 500 million years to the Cambrian period. In 1961, Meredith L. Jones, from New York’s American Museum of Natural History, dredged four of these tiny, eyeless shrimp from the muddy sand bottom of the Bay off Point Richmond, making it the only known benthic (bottom dwelling), non-fish species endemic to the Bay. Five more were found in 1987 and 1988 off Brooks Island and Coyote Point, but none have been seen since, despite a California Academy of Sciences “bio-blitz” in search of bottom-dwelling Bay creatures in 2000. Academy curator Rich Mooi says mud samples were taken throughout the Bay where Lightiella had been reported. “I would have expected that if they were there, we would have seen them,” says Mooi. But, he adds, “[the shrimp] are tiny, they’re hard to see, and people hate going through mud.” Then Mooi hints that Lightiella just might be lurking, overlooked, in one of the academy’s many jars of Bay mud, awaiting another sifting. Any takers?

Field Guide to the Lost Species of the Bay Area

: sooty crayfish (Pacifastacus nigrescens)


FIRST/LAST RECORDED: 1857/late 1800s

RANGE: reported specifically in Alameda Creek, Coyote Creek, Steamboat Slough, and other Bay tributary streams

HABITAT: freshwater Bay tributary streams

FIELD NOTES: the sooty crayfish hasn’t been seen in over 100 years; the sooty crayfish closely resembles its cousin the Shasta crayfish (Pacifastacus fortis) but is blackish, smaller in size (4 inches long), and has more slender, hairless hands (claws)


Crayfishes (Astacidae) of North and Middle America, by Horton H. Hobbs

Ask the Naturalist—All the Crawdads You Can Eat (Bay Nature), March 13, 1996, by Michael Ellis


SPECIES: San Francisco horseshoe shrimp (Lightiella serendipita)



RANGE: known only from San Francisco Bay at Point Richmond, Brooks Island, Coyote Point

HABITAT: muddy sand bottom

FIELD NOTES: although extensive sampling has been done to rediscover this shrimp at its type locality and other collection locations, “searching” for this species amounts to sorting through Bay mud; mud-raker Richard Mooi of the California Academy of Sciences has generously offered would-be shrimp seekers the opportunity to pick through jars of mud—with the proper training, of course—to make sure no horseshoe shrimp have been overlooked— Reach Mooi at (415)321-8270.


Animals of San Francisco Bay: A Field Guide to Its Common Benthic Species, by Rich Mooi, Victor G. Smith, Margaret Gould Burke, Terrence M. Gosliner, Christina N. Piotrowski, and Rebecca K. Ritger

The account excerpted above was originally featured in the October/December 2007 issue of Bay Nature magazine.

Illustrations by Devin Cecil-Wishing.

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  1. #1 by ntbronco on February 8, 2014 - 4:25 pm

    Mathew’s blog reminds us of two of California’s invertebrate creatures (crustaceans) presumed extinct—although we wish otherwise. While there may be nothing we can do for the San Francisco horseshoe shrimp or the sooty crayfish, there is something we can do about the Mohave Shoulderband snail (Helminthoglypta greggi). In the case of this gastropod, human beings are causing the threat, and human beings can intervene!

    Easily overlooked, this snail is approximately one-half inch tall with a light brown spiraling shell that is a pale pink underneath. Its soft body is generally dark brown. It claims three hills (Soledad Mountain, Standard Hill and Middle Butte) in southern Kern County as its home. Here’s the problem: in spite of the fact that the majority of the snail’s habitat is located on Soledad Mountain, a new open-pit gold mine, the Golden Queen, has been permitted, and construction there has already begun.

    Visitors to Soledad Mountain confirm that the distribution of H. greggi is restricted to the base of vertical rock outcrops, preferably north-facing, which have at least small patches of talus. This microhabitat offers the best shelter because it has the most hours of shade and best retention of soil moisture. During lengthy dry periods, the Mohave Shoulderband snail goes dormant in deep crevices under the soil; it favors, for example, wood rat (Neotoma spp.) nests, where it can burrow under several inches of rocks and moisture-retaining organic debris.

    Because they are hermaphroditic, both snails in a pairing are able to lay eggs following mating. (The biological term, hermaphrodite, is a combination of the names, Hermes and Aphrodite, male and female divinities from Greek mythology.) The eggs, which are gelatinous with a thin enclosing membrane, are laid deeply enough within the soil, to keep them continuously moist. Although neither clutch-size nor incubation-period figures are known for H.greggi, certainly, rapid egg development would enhance hatchling survival.

    Newly hatched juveniles consume egg remnants and unhatched eggs. This increases individual growth rate while preventing population expansion in an environment with limited food choices–decayed organic matter, lichens, and cryptobiotic soil crust. It takes at least four years for a hatchling H.greggi to reach sexual maturity. Thus, it difficult for snails to recover from environmental upsets—which this new gold mine certainly is! The Center for Biological Diversity just last month filed an emergency petition with the Secretary of the Interior through the Fish and Wildlife Service to list the Mohave Shoulderband snail as “threatened” or “endangered” and its habitat as “critical” under the Endangered Species Act.

    Why should we care about these tiny creatures? We need them! As primary consumers of plant, animal, and fungal matter, snails aid in decomposition processes and contribute to nutrient recycling, and soil formation. No soil, no life—for soil makes it possible for the plants to grow that the rest of us feed upon.

    The granting of emergency Endangered Species Act protection to this snail would give time for mitigation measures to be put in place; this would safeguard a sizable portion of the population from open-pit mining operations. A special part of California’s natural heritage, this little animal is also playing the role of “canary -in-the-coal-mine.” If our elected and appointed representatives in government cannot be bothered to intervene–if some species are deemed expendable–we are left wondering about the future, not only of our children, but also of every other species in the community of life.

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