October 23, 2017
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Facing Extinction: California Fish Close to the Brink

Delta smelt and winter-run Chinook salmon are facing extinction in the wild, which raises questions about a lack of policy for declaring species extinct and the role of captive populations, write two U.C. Davis scientists.

By Peter Moyle, Jason Baumsteiger


AT LEAST TWO species of California fish appear to be facing imminent extinction in the wild: delta smelt and winter-run Chinook salmon. These species could join about 57 other North American fish declared extinct. If we are fortunate, these species will continue to scrape by with small populations, maintained through considerable human effort. But if we are unfortunate, these fish, and likely other species, will disappear in the near future. This likelihood suggests we need answers to the following questions:

  1. How do we know when a species is extinct? How long do we have to wait from the time the apparent last individual is captured to declaration of extinction?
  2. Who makes the official determination that a species is extinct?
  3. What role do captive populations play in the extinction process?
  4. Why is there a need to have an extinction policy in place?

Rather than answering these questions, we start by answering another question: What do previous fish extinctions tell us about preparing for future extinctions? Seven species of fish have gone extinct in California, eight if the eulachon (an anadromous smelt that has largely disappeared over the past two decades in California) is counted. The Tecopa pupfish disappeared in 1970, after Tecopa Hot Springs was converted to a resort. The High Rock Spring tui chub disappeared in 1989 when the spring was turned into a fish farm. Two Colorado River fish, Colorado pikeminnow and bonytail, are extirpated from the highly altered and polluted portion of the river in California but are present in habitats upstream, maintained largely by hatchery production. The last bull trout in California was caught in 1975 by U.C. Davis graduate student Jamie Sturgess after two fruitless summers spent searching for the fish in the McCloud River. Attempts to reintroduce bull trout into the river in the 1980s failed. The Clear Lake splittail was not described as a species until 1973, by which time it was probably already extinct. Finally, the last recorded thicktail chub was caught in Steamboat Slough in the Delta in 1957.

As far as we know, none of these fish was ever officially declared extinct for the first time by state or federal agencies. Extinction was usually recorded in an academic publication and thereafter largely ignored. An exception may be the thicktail chub, which was declared extinct by Terry Mills and Kathy Mamika in an administrative report by the California Department of Fish and Game, 23 years after the last fish was caught. Part of the delay in declaring extinction stems from the fact that the seven species became extinct before the Endangered Species Act (ESA) was written or widely used; there was no endangered status declared to warn of potential extinction. Let us now address the questions posed at the beginning of this article.

The second-to-last known bull trout, caught in California in 1975. (P. Moyle)

1. How do we know when a species is extinct? How long do we have to wait from the time the last individual is captured to declaration of extinction?

It would be easier to declare a species extinct if the last individual had a name, like Martha, the last passenger pigeon – or if all of a species habitat was destroyed, like the Tecopa pupfish and High Rock Spring tui chub, although even pupfish thought to be extinct have been rediscovered.

Extinction of fish in big waters, such as the Delta or Clear Lake, is especially hard to pin down. There always seems to be the potential for a small population to be hidden somewhere – missed by sampling efforts, as happened with the Miller Lake lamprey in Oregon, once declared extinct. Delta smelt have been unexpectedly discovered spending their entire life in fresh water in places like the Sacramento Deepwater Ship Channel. And the small numbers caught by sampling programs in recent years probably still represent a population of several hundred or thousand. So hope springs eternal.

But when regular sampling programs cease catching any smelt and targeted efforts to capture them fail, then extinction is a likely conclusion. When/if that happens to delta smelt, we recommend that targeted sampling cease (to avoid killing the last fish by sampling) and that biologists wait for individuals to reappear or not in the regular sampling programs for 10 generations (20 years, assuming some smelt live two years). The same general protocol would apply to other species as well, with sampling efforts based on generation time, not years.

2. Who makes the official determination that a species is extinct?

This is not clear. State and federal Endangered Species Acts are designed to prevent extinction, not to assess it. For species like delta smelt and winter-run Chinook salmon, there will be considerable pressure to declare them extinct because maintaining even small populations requires releases of water from dams. One possibility would be to have the agency responsible for listing a species convene a panel of 5–10 individuals representing all regional fisheries agencies and/or possessing real expertise on the species to make the determination.

Another possibility is to convene a panel of fish biologists from outside the state to review the data and make a recommendation to the heads of the California Department of Fish and Wildlife, the U.S. Fish and Wildlife Service and the National Marine Fisheries Service (NMFS), who would make the actual determination of extinction.

3. What role do captive populations play in the extinction process?

Both winter-run Chinook salmon and delta smelt have populations in captivity, under careful genetic management to maintain genetic diversity. If wild fish disappear, then a successful release of hatchery fish into the wild to reestablish wild populations depends on (a) the presence of natural conditions that will allow introduced individuals to thrive and reproduce, (b) hatchery fish not having become highly domesticated through “natural” selection for survival in a hatchery environment and (c) whether fish reared in artificial conditions are able to avoid predators, find food and engage in reproductive activities once released.

The first condition is problematic for delta smelt because it would presumably require large increases in Delta outflow and the control of several invasive species that compete with or prey on smelt. This condition is the reason why trap and haul of winter-run Chinook adults to, and juveniles from, the McCloud River is being proposed by NMFS as a way to save the species, a controversial proposition.

The second condition is being handled by genetic management that allows controlled mating of individuals, with preference given to mating fish taken from the wild. How well that will work if wild fish are gone is not clear. Assuming the first two conditions are met, meeting the third condition will require creative rearing and reintroduction strategies where fish learn how to survive in a natural environment.

4. Why is there a need to have an extinction policy in place?

Extinction is increasingly becoming a reality for many species. Noel Burkheadindicates that 57 fish taxa were driven to extinction in North America between 1898 and 2006, a rate 877 times greater than the natural background rate. They estimated that, conservatively, 53–86 more fish taxa will be extinct worldwide by 2050. This fits with the projections of Peter Moyle et al. that climate change will accelerate extinctions of California fishes. Anthony Ricciardi and Joseph Rasmussen modeled the extinction trajectories for all the aquatic fauna in North America and estimated extinction rates of 4 percent per decade, “which suggests that North American freshwater ecosystems are being depleted of species as rapidly as tropical forests.”

Further studies by Jeanette Howard et al. on the aquatic fauna of California support this conclusion, as does the study of Theodore Grantham et al., which shows a disconnect between fish needing protection and protected areas. Thus the evidence is growing that extinctions in freshwater ecosystems of California will become commonplace unless systematic action is taken to prevent them. No doubt there are similar trends in terrestrial organisms.

In conclusion, the best strategy is not to let any fish species go extinct. If a fish species does go extinct, despite our best efforts, then funds and water used to keep the species going should be redirected toward keeping other species from following the same extinction trajectory. But to avoid spending scarce conservation dollars on species that have already gone extinct, we need a policy in place that provides a pathway for declaring a species officially extinct.


This story first appeared on California Water Blog, published by the U.C. Davis Center for Watershed Sciences.