By Andrew L. Rypel and Peter B. Moyle

It’s an odd, disturbing feeling – watching populations of native fish species collapse and then disappear. Sometimes it happens quickly, other times it’s a series of slowstep change events. The end result is the same though – smaller populations, extinctions, less biodiversity. We put up a little fight, and occasionally have moderate success. But by and large, the overall trend is down, the pace of change quickening, and it is relentless. We’ve watched it over our careers, and maybe some of you have too. Either as biologists or water professionals, or perhaps as long-time readers of this blog. This summer has been no different. It has been an avalanche of stories, all with variations on this theme. Here, we provide a synopsis of some recent events, along with wider thoughts on what watching this happen means. The following stories are by no means comprehensive, so if there are additional items we missed, feel free to discuss and link to them in the comments below.

California White Sturgeon Decision. On June 19, the California Fish & Game Commission voted that the petition to list White Sturgeon as “threatened” under the California Endangered Species Act was warranted. The species is not listed yet, but rather, now enters a one-year review period to determine a formal listing status. The data presented by CDFW to the Commission supports the need for increased protection. We wrote blogs about the sturgeon situation over the past two years as the situation worsened (Schreier et al. 2022, Moyle and Rypel 2023). Two major lines of evidence supporting listing include: 1) Massive decline in White Sturgeon numbers, as we have measured them over time; and 2) A mass die-off of sturgeon coincident with the red tide event two summers ago. This event killed a substantial fraction of the population, but we don’t really know how many, just a lot.

For years, the white sturgeon population in the San Francisco Estuary was regarded as a management success story because it supported a recreational and harvest fishery (Blackburn et al. 2019). By law, candidate listing of the white sturgeon means the fishery needs to be carefully examined. Under California Fish and Game Code 2084, it is possible an exception can be carved out to allow continued fishing on a candidate species in some form (e.g., restricted harvest, catch-and-release only). These kinds of exceptions were granted recently to allow fishing for California steelhead, but not harvest, in streams containing listed populations (California Fish and Game Commission 2022). Ultimately, the status change for the sturgeon will be yet another blow for fishing communities that have been hammered and dismantled by recent fisheries declines – most notably, two consecutive summers of closed salmon fishing. Another looming impact of the listing relates to potential construction and operation of Sites Reservoir. This planned off-channel impoundment is designed to draw water from the river to fill the reservoir during high water conditions and then use the water for agriculture during dry periods. Yet data for California white sturgeon clearly show that recruitment for this species only occurs during the wettest of years, and during the highest of flow conditions (Moyle 2002). According to the CDFW Species of Special Concern Report, the white sturgeon population is dominated by just a few strong year classes, especially from years with extraordinary spring flows (Kohlhorst et al. 1991, Schaffter and Kohlhorst 1999). One hypothesis is that high spring flows effectively move larval sturgeon downstream into key rearing areas (Stevens and Miller 1970) or somehow stimulate more sturgeon to spawn (Kohlhorst et al. 1991). These are hypotheses however, and the exact mechanism between sturgeon recruitment and flow remains unknown. Ultimately, sturgeon as a group have survived for hundreds of millions of years, but they don’t currently seem to be surviving us.

Longfin Smelt Listing. On July 30, the United States Fish and Wildlife Service published a rule in the Federal Register listing the San Francisco Bay-Delta distinct population segment of Longfin Smelt (Spirinchus thaleichthys) as endangered under the United States Endangered Species Act (US ESA). The Longfin Smelt is a close relative of the Delta Smelt (Hypomesus transpacificus), which has a long history of decline and political battles in California, but is essentially extinct in the wild. The Longfin Smelt differs from Delta Smelt in geographic distribution (occurs all the way north to Alaska, while Delta Smelt occur only in the San Francisco Estuary), but also life-history, feeding, and apparent patterns in anadromy (Hobbs et al. 2019, Lewis et al. 2020, Barros et al. 2022). San Francisco smelt populations have been in severe decline for years, primarily because the Delta ecosystem itself is in decline (Hobbs et al. 2017). Thus, formal listing of Longfin Smelt only confirms from a protective and regulatory standpoint, the tough reality that biologists have long struggled with. The listing likely harpoons any hope by some that extinction of the Delta Smelt may in some way ease restrictions on water exports. Many of the same water management actions taken to benefit Delta Smelt through e.g., through a Biological Opinion, also tend to benefit Longfin Smelt.

Wild Spring-Run Chinook Salmon in the Sacramento Basin are on the Brink of Extinction. The collapse of wild spring-run Chinook salmon in the Sacramento Basin has been swift and scary. Spring-run Chinook salmon are one of four distinct varieties native to the Central Valley of California; the others being fall-, late fall-, and winter-run Chinook salmon. Winter-run and spring-run Chinook salmon are listed under the US ESA, as ‘endangered’ and ‘threatened’, respectively. Spring-run adults enter freshwater streams as sexually immature individuals and over-summer there, often in deep plunge pools and streams that stay cold all summer. When water levels rise in the fall, the salmon ascend upstream to spawn, with roughly similar timing as fall-run fish. This life-history historically allowed salmon to take advantage of the clean, cold, snowmelt streams throughout the Sierra Nevada Range. Some juveniles exit freshwater in spring, while others spend a year or more rearing in these cold ecosystems. It is a fascinating life-history, and an important one for California. Unsurprisingly, spring-run Chinook salmon populations in California were decimated by dams (Rypel et al. 2021). And because of their need for cold water during summer, they are highly threatened by climate change (Moyle et al. 2017).

The near-complete collapse of spring-run Chinook salmon in California is actually incredible. These fish were once codominant with fall-run Chinook salmon in the Central Valley (Yoshiyama et al. 1998). Total annual abundance of spawners was 600,000 adults during the late 1800s, but reduced to an average of around 10,000 fish in the 1960s. Numbers stayed near this level until just a few years ago (Rypel et al. 2021). Just three streams now sustain stronghold non-heterozygote populations of spring-run Chinook salmon: Deer Creek, Mill Creek, and Butte Creek. For many years, these streams (despite water diversion and other issues) were considered model ecosystems, resilient to effects of climate change and human impacts because of an abundance of cold water and forested watersheds. Yet numbers collapsed further in the last two years. According to numbers published in CDFW’s “GrandTab” Database, last summer the total number of adults in Deer, Mill, and Butte Creeks were just 23, 34, and 95 salmon, respectively (Azat 2024). This prompted a relocation of some of these juveniles to UC Davis in an emergency attempt to start a captive broodstock. And this year the adult numbers, currently unpublished, appear to be similar. A reintroduction effort of spring-run on the San Joaquin River is ongoing.

Why is this happening to spring-run now? Part of the answer is that these are fish born during the last drought; survival conditions are poor for California spring-run Chinook salmon when flows are low (Hause et al. 2022). Another issue is Thiamine (vitamin B1) deficiency, a major nutritional problem being observed in salmonids across California (Ward and Bell-Tilcock 2022) and the Pacific Coast (Reed et al. 2023). Yet perhaps most disturbing at this moment is the Park Fire, which raged through the Deer and Mill Creek watersheds. Several news stories in the LA Times, the Sac Bee, and CalMatters covered the peril these fish face now. Both adults and juveniles are in these systems currently. And while these fish are located higher in the watershed, the fire may still find them. And even if it doesn’t right now, ash and sediment runoff from burn scars will come this fall after rains and will impact both streams greatly. Managers had most likely been considering up-listing Central Valley spring-run Chinook from threatened to endangered and recent events now all but guarantee that. However, these fish could easily go extinct in a year or two, before any listing changes have a chance of doing any good. Our general impression is that we are collectively unprepared for that possibility. One thing is certain: this is a turning point, and a test of the viability of the salmon going forward in California.

Speckled Dace Listings. On 8/7, the USFWS published in the Federal Register that the Long Valley Speckled Dace is now a candidate species for listing under US ESA. For many years, Speckled Dace was considered to be a single species from Canada to Mexico, but research at UC Davis Center for Watershed Sciences revealed that there was great cryptic diversity within these fishes (Moyle et al. 2023). There are three Speckled Dace species now recognized in California. These include the Santa Ana Speckled Dace (Rhinichthys gabrielino, described in more detail below), the Desert Speckled Dace (Rhinichthys nevadensis), and the Western Speckled Dace (Rhinichthys klamathensis). The Long Valley Speckled Dace is a subspecies of Desert Speckled Dace (Rhinichthys nevadensis caldera) (Moyle et al. 2023). This fish is currently found in just one spring east of Mammoth Lakes – uniquely enough, in the direct outflow from a public swimming pool that is fed by a hot spring. It is one of the rarest and most vulnerable endemic fishes in California. We know very little about its biology and life-history, and its continued existence hinges on attention to the water supply and to the population recently established in an artificial pond where old tires are the principal cover provided for the fish.

Days later, the USFWS proposed listing the Santa Ana Speckled Dace as ‘threatened’ under the US ESA. This species was formally described only one year ago (Moyle et al. 2023), and is estimated to be missing from at least half of its historical habitats in the Los Angeles, San Gabriel, and Santa Ana Rivers. These findings prompted the petition by the Center for Biological Diversity to USFWS to list the species. It is feared that, if nothing is done, the species may go extinct in 50 years or less.

Conclusion: An Unambiguous Signal. None of these recent developments are surprising. Freshwater biodiversity is collapsing globally, and extinction rates are far higher in freshwater ecosystems versus terrestrial ones (Ricciardi and Rasmussen 1999). This pattern has been playing out for some time in California, with the number of stable species declining and the number of endangered species increasing (Fig. 4). At least 83% of California’s native fishes are currently at risk of extinction (Moyle et al. 2011). 78% of salmonids are projected to go extinct in the next century (Katz et al. 2013, Moyle et al. 2017). These losses are harmful to Indigenous cultures in multiple ways, and the loss of salmon changes the ecology of our riparian forests, which were historically fertilized by salmon carcasses.

When we lose species, it speaks volumes about our inability to prevent ecosystem decline, and to constantly borrow from nature without repayment (Rypel 2023). The pattern is especially sobering with charismatic species such as Chinook salmon, which receive large amounts of conservation funding and attention. This is a clear and unambiguous signal that cannot be ignored. But what should we do about it? A good start might be the development and implementation of a comprehensive fish management plan for California. We provided some scaffolding for what such a plan might look like in a previous blog. The 30×30 conservation goal of the Resources Agency can boldly protect many declining fishes if fully implemented. This initiative seeks to directly protect entire watersheds, including where many declining fish occur.

For these two fish biologists, however, declines and extinctions never get easier to observe or accept. They are a pox on our species and reveal some of the unsightly costs to our progress. Every time a species is listed, or worse, goes extinct, it is another indicator of how the environment in which we live is becoming less suitable for people and fish overall. It shows that despite our best intentions and previous efforts to manage fallout, we have not solved the grand challenge of how to pursue economic growth while also sustaining ecosystems. California is a globally important biodiversity hot spot, and fish are just one part of its highly distinctive biota. Our goal should be to lead the world in showing how we can make our distinctive, rich economy compatible with our astonishing biotic heritage.

Peter B. Moyle is a Distinguished Professor Emeritus at the University of California, Davis and is Associate Director of the Center for Watershed Sciences. Andrew Rypel is a Professor and the Peter B. Moyle and California Trout Chair of coldwater fish ecology at the University of California, Davis. He is a faculty member in the Department of Wildlife, Fish & Conservation Biology and Director of the Center for Watershed Sciences.

Further Reading 

Azat, J. 2024. GrandTab 2024.05.20 California Central Valley Chinook Escapement Database Report. California Department of Fish and Wildlife. Available from https://www.calfish.org/ProgramsData/Species/CDFWAnadromousResourceAssessment.aspx

Barros, A., J.A. Hobbs, M. Willmes, C.M. Parker, M. Bisson, N.A. Fangue, A.L. Rypel, and L.S. Lewis. 2022. Spatial heterogeneity in prey availability, feeding success, and dietary selectivity for the threatened longfin smelt. Estuaries and Coasts 45: 1766-1779.

Blackburn, S.E., M.L. Gingras, J. DuBois, Z.J. Jackson, and M.C. Quist. 2019. Population dynamics and evaluation of management scenarios for white sturgeon in the Sacramento-San Joaquin River basin. North American Journal of Fisheries Management 39: 896-912.

California Fish and Game Commission. 2022. Findings of Emergency and Statement of Proposed Emergency Regulatory Action. Emergency Action to  Re-adopt Section 749.13 Title 14, California Code of Regulations Re: Incidental Take of Southern California Steelhead.

Hause, C.L., G.P. Singer, R.A. Buchanan, D.E. Cocherell, N.A. Fangue, and A.L. Rypel. 2022. Survival of a threatened salmon is linked to spatial variability in river conditions. Canadian Journal of Fisheries and Aquatic Sciences 79: 2056-2071.

Hobbs, J.A., P.B. Moyle, N. Fangue, and R.E. Connon. 2017. Is extinction inevitable for delta smelt and longfin smelt? An opinion and recommendations for recovery. San Francisco Estuary and Watershed Science 15: 1-19.

Hobbs, J.A., L.S. Lewis, M. Willmes, C. Denney, and E. Bush. 2019. Complex life-histories discovered in a critically endangered fish. Scientific Reports 9: 16772.

Katz, J., P.B. Moyle, R.M. Quiñones, J. Isreal, and S. Purdy. 2013. Impending extinction of salmon, steelhead, and trout (Salmonidae) in California. Environmental Biology of Fishes 96: 1169-1186.

Kohlhorst, D.W., L.W. Botsford, J.S. Brennan, and G.M. Cailliet. 1991. Aspects of the structure and dynamics of an exploited central California population of white sturgeon (Acipenser transmontanus). In: P. Williot ed. Proceedings of the First International Symposium on the Sturgeon. CEMAGREF, Bordeaux, France. pp. 277-293.

Lewis, L.S., M. Willmes, A. Barros, P.K. Crain, and J.A. Hobbs. 2020. Newly discovered spawning and recruitment of threatened Longfin Smelt in restored and underexplored tidal wetlands. Ecology 101: e02868.

Moyle, P., R. Lusardi, P. Samuel, and J. Katz. 2017. State of the Salmonids: Status of California’s Emblematic Fishes 2017. Center for Watershed Sciences, University of California, Davis and California Trout, San Francisco, CA. 579 pp. https://watershed.ucdavis.edu/files/content/news/SOS%20II_Final.pdf

Moyle, P.B. 2002. Inland Fishes of California, revised and expanded. University of California Press, Berkeley, CA USA.

Moyle, P.B., J.V. Katz, and R.M. Quiñones. 2011. Rapid decline of California’s native inland fishes: a status assessment. Biological Conservation 144(10):2414-2423.

Moyle, P., R. Lusardi, P. Samuel, and J. Katz. 2017. State of the Salmonids: Status of California’s Emblematic Fishes 2017.  Center for Watershed Sciences, University of California, Davis and California Trout, San Francisco, CA. 579 pp. https://watershed.ucdavis.edu/files/content/news/SOS%20II_Final.pdf

Moyle, P.B., N. Buckmaster, and Yingxin Su. 2023. Hiding in plain sight: newly described freshwater fishes from the Los Angelas area and elsewhere in California. https://californiawaterblog.com/2023/03/05/hiding-in-plain-sight-newly-described-freshwater-fishes-from-the-los-angeles-area-and-elsewhere-in-california/

Moyle, P.B., Buckmaster, N. and Su, Y. 2023. Taxonomy of the Speckled Dace species complex (Cypriniformes: Leuciscidae, Rhinichthys) in California, USA. Zootaxa https://doi.org/10.11646/zootaxa.5249.5.1

Moyle, P.B., and A.L. Rypel. 2023. Monster fish: lessons for sturgeon management in California. https://californiawaterblog.com/2023/05/14/monster-fish-lessons-for-sturgeon-management-in-california/

Quiñones, R.M., and P.B. Moyle. 2015. California’s freshwater fishes: status and management. FiSHMED: Fishes in Mediterranean Environments 1:1-20.

Ricciardi, A., and J.B. Rasmussen. 1999. Extinction rates of North America freshwater fauna. Conservation Biology 13: 1220-1222.

Reed, A.N., F.E. Rowland, J.A. Krajcik, and D.E. Tillitt. 2023. Thiamine supplementation improves survival and body condition of hatchery-reared steelhead (Oncorhynchus mykiss) in Oregon. Veterinary Sciences 10: 156.

Rypel, A.L., P.B. Moyle, and J. Lund. 2021. A swiss cheese model for fish conservation in California. https://californiawaterblog.com/2021/01/24/a-swiss-cheese-model-for-fish-conservation-in-california/

Rypel, A.L., G. Singer, and N.A. Fangue. 2021. Science of an underdog: the improbable comeback of spring-run Chinook salmon in the San Joaquin River, https://californiawaterblog.com/2021/12/05/science-of-an-underdog-the-improbable-comeback-of-spring-run-chinook-salmon-in-the-san-joaquin-river/

Rypel, A.L. 2023. Facing the dragon: California’s nasty ecological debts. https://californiawaterblog.com/2023/06/11/facing-the-dragon-californias-nasty-ecological-debts/

Schaffter, R.G. and D.W. Kohlhorst. 1999. Status of white sturgeon in the Sacramento-San Joaquin Estuary. California Fish and Game 85:37-41.

Schreier, A., P.B. Moyle, N.J. Demetras, S. Baird, D. Cocherell, N.A. Fangue, K. Sellheim, J. Walter, M. Johnston, S. Colborne, L.S. Lewis, and A.L. Rypel. 2022. White sturgeon: is an ancient survivor facing extinction in California? https://californiawaterblog.com/2022/11/06/white-sturgeon-is-an-ancient-survivor-facing-extinction-in-california/

Stevens, D.E. and L.W. Miller. 1970. Distribution of sturgeon larvae in the Sacramento-San Joaquin River system. California Fish and Game 56:2 80-86.

Yoshiyama, R.M., F.W. Fisher, and P.B. Moyle. 1998. Historical abundance and decline of Chinook salmon in the Central Valley region of California. North American Journal of Fisheries Management 18: 487-521.

https://www.fws.gov/press-release/2024-07/us-fish-and-wildlife-service-lists-bay-delta-longfin-smelt-endangered

https://wildlife.ca.gov/News/Archive/fish-and-game-commission-approves-white-sturgeon-as-a-candidate-species-for-listing-as-threatened

https://calmatters.org/environment/water/2024/04/california-salmon-fishing-banned-again

https://www.sacbee.com/news/politics-government/capitol-alert/article289005314.html

https://www.latimes.com/environment/story/2024-08-06/park-fire-threatens-critical-california-salmon-habitat

https://www.sacbee.com/news/california/article290848619.html?utm_campaign=trueanthem&utm_medium=social&utm_source=twitter

https://calmatters.org/environment/water/2024/07/california-wildfires-salmon-park-fire

https://www.californianature.ca.gov

Feds eye rare California fish for endangered species protections