New insights into Putah Creek salmon

by Malte Willmes, Anna Steel, Levi Lewis, Peter B. Moyle, and Andrew L. Rypel

It’s November 2016, and we’re out in canoes on Putah Creek as part of the annual salmon survey. Just as we navigate our watercraft through a narrow river section using push poles, thorny blackberry bushes and trees begin to close in from both sides of the channel. Finally, we reach a series of shallow riffles and spot our first salmon of the day. As we look it over, it’s easy to consider this fish, the ordeal it went through to get here, and how its journey symbolizes in some way the restoration of Putah Creek.

Putah Creek is a small stream originating on the East side of the Vaca Mountains. Flowing down-slope, water enters Lake Berryessa, a large impoundment created by Monticello dam. Below the dam, the creek flows to Putah Creek Diversion Dam, past the town of Winters, UC Davis, and dozens of farms and into the Yolo Bypass. From here it eventually flows into the San Francisco Estuary and the Pacific Ocean.

Chinook Salmon (Oncorhynchus tshawytscha) have become a welcome and familiar sight in recent years in Putah Creek. Considered a keystone species across the Pacific Northwest, Chinook Salmon hold a special place in our past and present as a cultural and food resource. This includes for indigenous peoples of California, such as the Patwin people, on whose land UC Davis is located. In California at the southern end of Chinook distribution, populations are in decline, due to combined effects of habitat degradation, water diversions, and climate change (Moyle et al. 2017). Putah Creek historically supported a population of fall-run Chinook Salmon (Yoshiyama et al. 1998). And while the creek had long been known to possess an intermittent hydrologic dynamic (Shapovalov 1940), reduced downstream flows after Monticello Dam was installed proved problematic. For example, areas of the creek dried more frequently during summer months, resulting in declines and extirpation of many anadromous and native fishes, including Chinook Salmon (Oncorhynchus tshawytscha). Their reappearance now is a direct result of ongoing restoration and water management efforts, particularly since ~2000.

Chinook Salmon are anadromous; they spawn in fresh water, migrate to the ocean to grow for 2-4 years (often 2 in CA), and return to natal rivers to spawn. They are also semelparous, which means they reproduce only once and die after spawning. Homing behavior of salmon allows for streams to develop evolutionarily-distinct populations with local adaptations, such as migration timing. The Central Valley Chinook Salmon population historically consisted of many smaller runs with local adaptations – this provided a critical buffer against California’s variable and unpredictable climate and ocean conditions, as it increased chances that some offspring would survive to return and reproduce under most environmental conditions. Yet a certain fraction of salmon, both historically and today, stray from their natal streams and disperse into new and previously disconnected habitats. In California, straying, especially of hatchery origin salmon, is sometimes viewed in a negative light. However straying reflects an important piece of salmon life-histories aimed at increasing fitness, and can create resilience for populations overall. Across the Pacific Rim, straying has allowed salmonids to adapt to changing habitat conditions, such as retreating glaciers in the past, or warming climates of the future.

Back to our canoe, we pass the shallow riffles, and follow the stream around a bend, where it widens and forms a series of deep pools. Carefully observing the bottom, Emily Jacinto spots a salmon carcass, and using a hook, deftly lofts it onboard the canoe. The salmon is already somewhat decayed, starting the release of valuable ocean nutrients into the creek, its smell placing a pungent twist on the peaceful and beautiful scenery (Fig. 1). We collect a few more carcasses, some in deep pools, others on the sides of the channel, and finally push the canoes onshore to process samples. Since 2016 UC Davis has been conducting annual carcass surveys in collaboration with the Solano County Water Agency, carefully tracking and counting the returning adults and collecting valuable information from the salmon carcasses.

Fig. 1. Chinook Salmon carcass survey on Putah Creek. Photo taken by Ken Davis.

Lots to say for a dead fish

Each carcass is carefully measured, its sex determined, and tissue samples taken for future DNA studies. We also check to see if the fish has its adipose fin intact; if the fin is missing, it’s an indication the fish originated from a hatchery, as about 25% of fall-run hatchery fish are marked this way. These marked fish also have been injected with a tiny wire tag engraved with a code, known as a Coded Wire Tag. Thus, when fish without an adipose fin are encountered, the head is sent to the CDFW Coded Wire Tag Laboratory in Sacramento to extract this valuable tag with information about the fish origin and brood year. In 2016, we recovered 23 of these marked fish, with 20 originating from the Mokelumne River Hatchery, two from the Nimbus Hatchery, and one from the Feather River Hatchery. The last step of the carcass survey is the trickiest. With a few skilled cuts with a sharp knife, Emily extracts both ear stones (otoliths) from the brain cavity of the fish (Fig. 2). Compared to the large decaying carcass next to us, these structures are tiny, but hold a wealth of information.

What can we learn from otoliths?

Fig. 2. Chinook Salmon ear stone (otolith) extraction. This tiny calcium carbonate structure holds information about age, growth, & movement histories of fish. Photo taken by Eric Chapman.

Otoliths (oto=ear, lithos=a stone) are calcium carbonate structures in the inner ear of most bony fishes, and they function to detect sound, water pressure, and depth. Otoliths grow continuously throughout the life of a fish and accrete daily layers, similar to the annual rings found in trees. The sequence of these layers can be used to estimate fish age, and their width can be used to reconstruct growth rates. In addition, distinct marks are visible in the otoliths, called ‘checks’, that were produced at hatching (hatch check), at the onset of exogenous feeding (exogenous feed check), and at ocean entry (ocean entry check). Finally, as the calcium carbonate structure grows, the chemical signature of the water surrounding the fish is incorporated as well, allowing us to reconstruct fish movement among different habitats.

One particularly useful chemical tracer in the Central Valley are strontium isotopes (87Sr/86Sr). This ratio varies among watersheds depending on the age and composition of the underlying geology, and can provide a unique geographic fingerprint (Johnson et al. 2016) as well as a tracer for migration from fresh to brackish to salt water. For our Putah Creek salmon otolith samples, we used a laser-ablation system at the ICPMS Center at UC Davis to analyze strontium isotopes across the entire otolith, reconstructing fish movements among habitats from the time the fish was born (core), across its time in freshwater (natal stream) to its time in the ocean and eventual return (edge of the otolith) (Fig. 3).

What did we find?

We recently published a paper (Willmes et al. 2020) applying this tool to 104 carcasses collected from Putah Creek in 2016 (Fig. 4). We found most Chinook Salmon returning to Putah Creek were 2 (44%) to 3 years (42%) old, with only a few 4 year old (14%) and no 5 year old fish present. This shift to a younger age distribution is not uncommon in the Central Valley and it might influence the number of juveniles being produced, as younger fish are generally smaller and produce fewer offspring. But juvenile surveys in 2017 and 2018 found large numbers (~33,000) of healthy juveniles leaving the river in spring, indicating Putah Creek supported successful spawning, and has the potential to maintain a salmon population (Miner et al. 2019).

Fig. 3. Top: Cross section of a Chinook Salmon otolith showing the position of check marks produced at hatching (hatch check), those produced by the onset of exogenous feeding (exogenous feed check), and ocean entry (ocean entry check). Fish ages were estimated based on the sequence of winter (translucent) and summer bands (opaque) and are noted in the image. The dotted white line shows the laser-ablation analysis transect. Bottom: Example 87Sr/86Sr profile of a Chinook Salmon otolith. The core forms using energy from the maternal yolk-sac, and thus has chemical signatures typical for the Pacific Ocean (red). This is followed by freshwater residence time and the start of exogenous feeding (yellow). Finally, a rapid transition to the ocean can be observed before the first annular ring forms. As with the otolith, this diagram appears semi-symmetrical since the core is at the center and otoliths grew in both directions.

One surprise finding from our otolith study was the diversity of origins of Putah Creek salmon. In 2016, fish came from at least seven different natal sources, overwhelmingly from hatcheries. Fall-run Chinook Salmon in the Central Valley are largely supported by hatcheries, which has increased straying rates and in turn created genetic and life-history homogenization. In addition, a high priority in hatchery operations is to increase fish survival to the ocean. This resulted in the trucking of juvenile salmon to downstream or estuary release sites during drought years with otherwise expected high migration mortality (Sturrock et al. 2019). However, this practice also increases straying rates (presumably because of a lack of natal stream imprinting), and appeared to be an important driver of fish straying into Putah Creek. While in many circumstances, high rates of straying can cause harm to salmon populations by reducing local adaptation, for Putah Creek the stray rates have been beneficial, as they bring added numbers and genetic diversity to the stream. Into the future, however, continued high stray rates may reduce the extent of new local adaptations to develop within this emerging run.

To date, we do not have enough information to determine whether Putah Creek Chinook Salmon represent the beginning of a newly established and self-sustaining run. In 2016, we found only one fish that originated in Putah Creek, and unfortunately our strontium isotope tracer was not able to distinguish it from wild Feather River origin fish. The fish returning in 2016 would represent juveniles migrating out in 2013 and 2014, before large numbers of Chinook returned to Putah Creek so finding a Putah Creek origin fish in 2016 was unlikely. Over time we expect to gather more evidence about reestablishment of the Putah Creek run.

Fig. 4. Natal origins of 104 Chinook Salmon analyzed from Putah Creek in 2016.

What does this mean for Putah Creek and Chinook Salmon in the Central Valley?

Rehabilitating a degraded and deeply incised stream ecosystem is a difficult proposition and a long process. Transitioning from small and shrinking salmon population to a robust and resilient one may take even longer. But by leveraging and restoring many small, spatially distinct systems, like Putah Creek, and restoring the core ecological processes that generate biological complexity, we may be able to achieve this goal over time. Locally-adapted salmon runs differ in susceptibility to natural and anthropogenic risks (Beechie et al. 2010). Furthermore, this work reveals an upside to straying salmon that is rarely discussed, but that upside is only realized if salmon have a good place to go. Reconnecting migratory pathways and restoring other degraded small streams like Putah Creek thus provides an opportunity to increase salmon life-history diversity and help strengthen and recover Chinook Salmon populations.

Putah Creek is a special place in many ways. It has a long history of habitat degradation, and the road to restoration has been a long and difficult one. Ongoing persistence of Chinook Salmon adds to this success story, and continued salmon returns may spark changes to the ecosystem overall. Because salmon die after spawning, carcasses nurish freshwater ecosystems with a supply of marine nutrients, connecting this small stream in our backyard to the expansive Pacific Ocean. As numbers increase, marine-derived nutrients will enrich vegetation, and enhance the productivity of all animals that feed on it. We are only at the beginning of our scientific program on Putah Creek and continued monitoring and the application of a vast toolset of scientific methods will be required to see if and how salmon establish a new population here.


We would like to thank the Solano County Water Agency (Roland Sanford and Rich Marovich) for funding and support of the study (Contract #03-00206VR). In addition, we thank the members of the Biotelemetry lab at UC Davis for assisting with carcass surveys in 2016: Tommy Agosta, Colby Hause, Christopher Bolte, Patrick Doughty, and Alexandra McInturf. Additional thanks to Kyle Brandt for his help during carcass surveys and rotary screw trapping and to Rick Fowler and Rick Poor for assistance with the preparation and deployment of the screw trap. Special thanks to John and Erin Hasbrook for graciously allowing us access to their property to deploy and tend the rotary screw trap.

Malte Willmes is a Postdoc at University of California Santa Cruz in the Institute of Marine Sciences and NOAA Fisheries Collaborative Program.

Anna Steel is a Postdoc in the Department of Wildlife, Fish & Conservation Biology at the University of California, Davis, and works within the Ecophysiology Laboratory of Nann Fangue.

Levi Lewis is a Research Scientist in the Department of Wildlife, Fish & Conservation Biology at the University of California, Davis and leads the Otolith Geochemistry & Fish Ecology Laboratory.

Andrew Rypel is an Associate 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 Co-Director of the Center for Watershed Sciences

Peter Moyle is a Distinguished Professor Emeritus in the Department of Wildlife, Fish & Conservation Biology at the University of California, Davis and Associate Director of the Center for Watershed Sciences.

Further reading

Beechie, T.J., Sear, D.A., Olden, J.D., Pess, G.R., Buffington, J.M., Moir, H., Roni, P., and Pollock, M.M. 2010. Process-based Principles for Restoring River Ecosystems. Bioscience 60(3): 209–222. doi:10.1525/bio.2010.60.3.7.

Johnson, R.C., Garza, J.C., MacFarlane, R.B., Grimes, C.B., Phillis, C.C., Koch, P.L., Weber, P.K., and Carr, M.H. 2016. Isotopes and genes reveal freshwater origins of Chinook salmon Oncorhynchus tshawytscha aggregations in California’s coastal ocean. Mar. Ecol. Prog. Ser. 548: 181–196. doi:10.3354/meps11623.

Miner, M., Moyle, P.B., Jacinto, E., Steel, A.E., Cocherell, D.E., Fangue, N.A., and Rypel, A.L. 2019. Origin and Abundance of Chinook Salmon in Putah Creek. Annual Report to Solano County Water Agency.

Moyle, P.B., Lusardi, R., Samuel, P., and Trout, C. 2017. State of the Salmonids II: Fish in Hot Water.

Shapovalov, L. 1940. Report on the possibilities of establishment and maintenance of salmon and steelhead runs in Cache and Putah Creeks. Bureau of Fish Conservation, California Division of Fish and Game. Technical Report.

Sturrock, A., Satterthwaite, W.H., Cervantes‐Yoshida, K.M., Huber, E.R., Sturrock, H.J.W., Nusslé, S., and Carlson, S.M. 2019. Eight Decades of Hatchery Salmon Releases in the California Central Valley: Factors Influencing Straying and Resilience. Fisheries 44(9): 433–444. doi:10.1002/fsh.10267.

Willmes, M., Jacinto, E.E., Lewis, L.S., Fichman, R.A., Bess, Z., Singer, G., Steel, A., Moyle, P., Rypel, A.L., Fangue, N., Glessner, J.J.G., Hobbs, J.A., and Chapman, E.D. 2020. Geochemical tools identify the origins of Chinook Salmon returning to a restored creek. Fisheries: fsh.10516. doi:10.1002/fsh.10516.

Yoshiyama, R.M., Fisher, F.W., and Moyle, P.B. 1998. Historical Abundance and Decline of Chinook Salmon in the Central Valley Region of California. North Am. J. Fish. Manag. 18(3): 487–521. doi:10.1577/1548-8675(1998)018<0487:HAADOC>2.0.CO;2.

Putah Creek Council a community of nature enthusiasts and volunteers who enhance and restore the Putah Creek Watershed.

The Putah Creek Legacy: A five-part multimedia series by The Davis Enterprise and Climate Confidential.

Posted in Uncategorized | Leave a comment

Rockin’ with the Rockfish

By Andrew L. Rypel and Peter B. Moyle

Fig. 1. Black rockfish (Sebastes melanops) swimming in giant kelp. Photo credit: Eiko Jones Photography, downloaded from

California is a spoil of natural resource riches. Most times, our California waterblog busies itself with important freshwater resources issues. Yet every now and again, it is refreshing and worth turning our attention to the spectacular diversity and mysteries of our Pacific Ocean. But freshwater is important to the ocean too. For one, there are 1,350 km of California coastline, with 100s of streams and rivers dumping nutrients and sediment into the ocean. During geologic times when sea levels were much lower, big rivers helped carve out the rugged underwater topography that is so important for our native marine sea life, including rockfish. And some of California’s most cherished freshwater fishes, such as salmon, steelhead, sturgeon and smelt, divide their time between ocean and river. Some of these adults and subadults will even predate and rely on juvenile rockfishes. Thus, rockfish are a central aspect of the legendary “ocean conditions” so often cited as controlling salmon numbers. Here, we’d like to simply call attention to a fascinating group of marine fishes that have strong interactions with salmon and similar fishes: the abundant, diverse, and beautiful Californians – the rockfishes.

Rockfishes are members of the genus Sebastes, which translates from Latin to “magnificent” or “venerable”. The entire group is comprised of marine species. They are a comparatively young group of fishes dating back 23-34 million years before present (Hyde and Vetter 2007). For comparison, sharks are 450 million years old. Rockfishes range in habitats from the intertidal zone all the way down to ~3,000 m (9,800 feet), making some rockfishes essentially deep sea fishes. By-and-large, they are benthic species that make their living in, on, and around benthic rock outcroppings. Not surprisingly, then, a favorite ‘hangout’ for rockfish (and salmon) is the Farallon Islands, a complex reef system just off the mouth of San Francisco Bay.

There are 109 recognized rockfish species. And while the geographic range of rockfishes encompasses many parts of the globe, the diversity of species is notably concentrated along the Pacific Coast. And California is the direct epicenter of that diversity. Coastal regions of Santa Barbara (the biggest hotspot) harbor up to 60 rockfish species. That’s 55% of all global rockfish diversity! Parts of the coast in northern California (e.g., Bodega Bay) regularly contain 45-55 species.

Fig. 2. Reproduction boom of rockfish at Browning Passage, British Columbia, Canada. Photo credit: Jett Britnell,

Rockfish are a vital component of the California Current Ecosystem. Salmon, lingcod, killer whales, sharks and shorebirds all eat rockfish. There have been anecdotal observations that some of the biggest salmon runs follow years of very high rockfish reproduction. And people of course eat rockfish too. Rockfish sandwiches and tacos are popular seaside fare. Rockfish are also notoriously mislabeled in grocery stores and fish markets – sometimes referred to as “rockcod” or “red snapper” even though that species is native to the Gulf of Mexico.

Their reproduction is on the notably bizarre side for fishes. Rockfish have internal fertilization, high fecundity (number of eggs), and give birth to larval fish rather than laying eggs (aka viviparity). Some rockfish species have fecundities that approach 3M eggs per individual (!). Even for highly fecund fishes, this is high, and again – all those baby fish are born alive. As just one comparison, Tule Perch (Hysterocarpus traskii, another native California live bearer) has fecundities of just 20-60. And finally, female rockfish can store sperm. This allows female fish to engage in reproduction with multiple male mates and utilize stored sperm from males they mated with long ago (Muñoz et al. 2000).

The age and longevity of adult rockfishes can only be described as impressive. While some rockfish species have longevities that approach 20 years, many are notably longer. Species with longevities regularly over 80 years of age include the yelloweye rockfish (Sebastes ruberrimus), the darkblotched rockfish (Sebastes crameri), splitnose rockfish (Sebastes diploproa) and the rosethorn rockfish (Sebastes helvomaculatus) (Love 2002). A 205 year old rockfish was recently captured in Alaska. This individual (that was only recently captured) was apparently born in 1808, five years after the Louisiana Purchase.

Despite the long-lived ecology and life-history described above, rockfish do support commercial and recreational harvest fisheries in California. However, populations are notably vulnerable to effects of fishing and have a tendency to be serially over-harvested in the absence of science-based fisheries management (Wetzel and Punt 2016). On the commercial end, rockfishes are managed as “groundfish”. This classification includes rockfishes, but also flatfishes of various types and other fishes, like the lingcods.

Recreational fisheries management for rockfish in California is tricky. One of the hardest aspects of this challenge is that many rockfishes are exceedingly difficult to distinguish, even by the experts. For example, here are two quotes by Butler et al 2012. that illuminates the crux of the challenge:

“Even today, after a collective century of experience, one or another of the authors will pass around a crisp, sharp image of some rockfish peeking out of a crevice, or worse, just sitting right out in the open, and we will all agree that we don’t know what species we are looking at. Oh, we will have our theories. And we will back it up with chatter about the number of pectoral fin rays, or the absence of some blotch or smudge on the back or head, or the shape of the spine under the eye. But really, after all of this time working on these animals, when we view these fishes underwater, we are still sometimes mystified.”

“The ~84 species of scorpaenid fishes (i.e., rockfishes, thronyheads, and scorpionfishes) inhabiting the northeast Pacific help insure that the lives of many fish biologists will be exercises in decades-long humility.”

Ultimately, when even the experts struggle with field identification, you can’t reasonably expect anglers and fishers to be equally or better skilled. As such, California’s recreational fishery is mostly managed via aggregate bag limits (i.e., rockfish species are grouped together). The season is open year-round to shore anglers, but restricted to march-December for boats, presumably to protect large fecund females on spawning grounds. However, the regulations do require anglers to know how to identify some of the more obvious species, including the long-lived ones. This includes yelloweye rockfish, bronzespotted rockfish, and cowcod.

Barotrauma is another concern (Parker et al. 2006, Jarvis and Lowe 2008). Given the depths at which rockfish reside, when fish are quickly brought up from depth they are quickly decompressed, which expands the gases in their swim bladder. Fish released with inflated swim bladders (often expelled out of their mouths) cannot resubmerge and will die. Deepwater release or descender devices assist in recompression of fishes like rockfish such that they can be released safely. A recent study in Alaska found that survival of yelloweye rockfish (one of the more long-lived species) was 98% when released using descender devices; however only 22% of fish released at the surface survived. Descender devices are not mandatory in California, but many anglers do use them and are encouraged to do so. All things considered, these seem like reasonable fishing regulations for a group of fishes that present some significant challenges to management.

Fig. 3. Global map of Marine Protected Areas (MPAs). Roughly 6.4% of global ocean habitat is covered by protected areas and only 1.9% is exclusively no-take. Image from

Marine Protected Areas or MPAs appear to be another useful tool. Numerous studies have been published on the potential benefit of MPAs on marine fish stocks, notably rockfishes (White et al. 2010; Nickols et al. 2019). Incidentally, MPAs also serve as a good model for considering how to propose and manage freshwater protected areas. Evidence of the benefits of MPAs is apparently so overwhelming that the American Fisheries Society (the principal scientific organization concerned with the study of fishes and fisheries in the USA and North America) issued a policy statement on management of Pacific rockfish (Parker et al. 2000). In the statement, the society recognized the need for conservation and robust management of Pacific rockfishes due to their low population growth rates, status of many populations as overfished, and the complex nature of mixed commercial and recreational fisheries. The also state:

“The AFS supports the establishment of systems of Marine Protected Areas to protect the habitat of Pacific rockfish and to promote the recovery of stocks. Such areas should be established along with traditional management measures to control fishing mortality. Regardless of the management strategy used, substantial decreases in fishing mortality must be achieved soon to avoid stock collapse.”

So in summary, rockfish are an extremely interesting and unique California resource. A number of fundamental ecological questions arise from just the limited information covered in this blog. For example: How do all those rockfish species coexist? What is it about California and the Santa Barbara region that has given rise to such speciation of rockfishes? Why are there 96 rockfish species in the north Pacific Ocean and only 2 in the north Atlantic Ocean? What is the relationship between rockfish abundance and that of salmon and steelhead? And finally, how can we conserve and manage these populations for future generations of Californian’s to enjoy?

Andrew Rypel is an Associate 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 Co-Director of the Center for Watershed Sciences

Peter B. Moyle is a Distinguished Professor Emeritus in the Department of Wildlife, Fish & Conservation Biology at the University of California, Davis and Associate Director of the Center for Watershed Sciences.

Fig 4. Blue rockfish (Sebastes mystinus) Blue rockfish off Cannery Point, photographed off of Point Lobos State Natural Reserve, CA. Photo Credit: Daniel Williford, downloaded from

Further Reading

Butler, J.L., M.S. Love, and T.E. Laidig. 2012. A Guide to the Rockfishes, Thornyheads, and Scorpionfishes of the Northeast Pacific. University of California Press.

Hyde, J.R., and R.D. Vetter. 2007. The origin, evolution, and diversification of rockfishes of the genus Sebastes (Cuvier). Molecular Phylogenetics and Evolution 44: 790-811.

Jarvis, E.T., and C.G. Lowe. 2008. The effects of barotrauma on the catch-and-release survival of southern California nearshore and shelf rockfish (Scorpaenidae, Sebastes spp.). Canadian Journal of Fisheries and Aquatic Sciences 65: 1286-1296.

Love, M.S. 2002. The Rockfishes of the Northeast Pacific. University of California Press.

Love, M.S. 2011. Certainly More Than You Want to Know About the Fishes of the Pacific Coast: A Postmodern Experience. Really Big Press.

Muñoz, M., M. Casadevall, S. Bonet, and I. Quagio-Grassiotto. 2000. Sperm Storage Structures in the Ovary of Helicolenus dactylopterus dactylopterus (Teleostei: Scorpaenidae): an Ultrastructural Study. Environmental Biology of Fishes 58: 53-59.

Nickols, K.J., J.W. White, D. Malone, M.H. Carr, R.M. Starr, M.L. Baskett, A. Hastings, L.W. Botsford. 2019. Setting ecological expectations for adaptive management of marine protected areas. Journal of Applied Ecology 56: 2376-2385.

Parker, S.J., S.A. Berkeley, J.T. Golden, D.R. Gunderson, J. Heifetz, M.A. Hixon, R. Larson, B.M. Leaman, M.S. Love, J.A. Musick, V.M. O’Connell, S. Ralston, H.J. Weeks, and M.M. Yoklavich. 2000. Management of Pacific Rockfish: American Fisheries Society Policy Statement Fisheries 25: 22-30.

Parker, S.J., H.I. McElderry, P.S. Rankin, and R.W. Hannah. 2006. Buoyancy regulation and barotrauma in two species of nearshore rockfish. Transactions of the American Fisheries Society 135: 1213-1223.

Wetzel, C.R., and A.E. Punt. 2016. The impact of alternative rebuilding strategies to rebuild overfished stocks. ICES Journal of Marine Science 73: 2190–2207.

White, J.W., L.W. Botsford, E.A. Moffitt, and D.T. Fischer. 2010. Decision analysis for designing marine protected areas for multiple species with uncertain fishery status. Ecological Applications 20: 1523-1541.

Posted in Uncategorized | Leave a comment

Happy 2021! Here’s to a New Water Year!

by Jay Lund

2020 was terrible, and as a water year (WY), October 2019 – September 2020, it is over.  A dry winter (drier than 2014-2015 in Sac. Valley), COVID-19, deep recession and unemployment, wildfires, racial violence and unrest, extreme high temperatures, water documents disappearing from State of California websites, and finally a very unpresidential debate.  (Fortunately, no major earthquakes.)

We happily ring out this year and hope for a better 2021! (… although it doesn’t seem to be improving just yet)

As we leave 2020, the soils are dry (and ashen) and most reservoirs and aquifers have been somewhat drawn down by the dry year.  Most major water storage reservoirs have below average storage, but some are above average.  We enter WY 2021 with less stored water than when we entered 2020.

What should we look forward to in the new Water Year 2021?

  1. Will 2021 be wetter?  Wetter would be better.
    1. If the new water year begins wet, it will be a great relief for folks living in rural areas, and all Californians who breathe.  A wetter year overall should bring a shorter and hopefully less intense fire season for the year. 
    2. Wetter years also better refill reservoirs and aquifers for use in the coming year, and future droughts.  Some refilling of aquifers is essential for many critically-overdrafted aquifers to comply with California’s Sustainable Groundwater Management Act and soften future reductions in groundwater pumping.
  2. Water, wind, and fire?  During WY 2020, we saw unusually tight and varied connections between water and wildfire conditions.  Tighter connections between precipitation and fire potential seem likely to persist until forest conditions change.  Fire budgets, preparations, and insurance might be usefully contingent on annual water conditions.
  3. Will 2021 be the year of voluntary environmental flow agreements?  If some of 2020’s major distractions subside, perhaps there is more hope.  A second dry year might further focus attention. Ecosystems don’t seem to be getting any healthier.  Regulatory uncertainty without such agreements might hinder or skew some water infrastructure investments might be insufficient without agreements or more certain regulations on environmental flows.
  4. Will 2021 be another dry year?  We have already had one dry year.  California’s larger water system usually needs at two dry years for a drought.  A single dry year can usually be accommodated with reservoir storage and some additional groundwater pumping, but longer droughts require more groundwater pumping, and increase shortages to human and ecosystem uses.  Additional dry years deepen shortages for ecosystems and humans, and increase risks of species extirpations, with warmer conditions exacerbating this situation. It might be time to dust off or prepare drought management plans for agencies, water projects, and ecosystems.
  5. How is SGMA going?  As SGMA deadlines get close, it becomes less likely that overdrafted basins will be rescued by a series of wet years, resulting in more need to curtail groundwater pumping to achieve SGMA goals. Is SGMA implementation moving forward sufficiently?
  6. How are the fish and native ecosystems?  The conditions of native fishes have not greatly improved since the end of the last drought.  This weak condition makes ecosystem impacts more likely if we have additional dry years and raises the importance of more aggressively improving ecosystem conditions in wetter (and all) years. (Durand et al 2020)
  7. How many rural community residents receive improved drinking water supplies?  This will be a continuing problem, and probably a worsening problem if 2021 is dry.
  8. Continued distractions?  Perhaps the greatest uncertainty for the new water year is whether the many distractions to effective science and policy-making will continue.  With the onset of deeper drought conditions, COVID and political disruptions could damage the water system’s usually effective abilities to respond and adapt to drought.

2020 demonstrates the diverse and changing challenges facing California, with deep implications for water and environmental management.  In 2021, we need to better organize how we will learn and explore how to manage water and ecosystems in California with profoundly changing conditions for decades to come.  We need to prepare for this future.

Further Reading

CDEC, Reservoir storages,

Durand, J., et al., Drought and the Sacramento–San Joaquin Delta, 2012–2016: Environmental Review and Lessons,, August 2, 2020

Escriva-Bou, A., J. Lund, J. Medellin-Azuara, and T. Harter,How reliable are Groundwater Sustainability Plans?,,May 10, 2020

Horberry, M. (2020), “After Wildfires Stop Burning, a Danger in the Drinking Water,” New York Times, 2 October 2020.

Sommer, T., Schreier, B., Conrad, J. L, Takata, L., Serup, B., Titus, R., Jeffres, C., Holmes, E. and Katz, J. (2020). Farm to Fish: Lessons from a Multi-Year Study on Agricultural Floodplain Habitat. San Francisco Estuary and Watershed Science, 18(3). doi:

Stone, K. and R. Gailey, Economic Tradeoffs in Groundwater Management During Drought,, June 10, 2019

Jay Lund is Co-Director of UC Davis’ Center for Watershed Sciences, where he is also a Professor of Civil and Environmental Engineering.

Posted in Uncategorized | Leave a comment

How will climate change affect the economic value of water in California?

by Lorie Srivastava

Climate change is affecting natural resources in California, with water being one of the most important in the state. Water source is critical for municipalities, agriculture, industry, and habitat/environmental purposes. Will future supply meet future demand? How will the economic value of water change over this century?

The economic value of raw – or untreated water – fluctuates over time, depending on prevailing supply and demand conditions. Over future decades from 2030 to 2090, average economic value of water on federal public lands – specifically on national forests – will range from about $4 per hundred cubic feet (HCF) to about $53 per HCF, depending on future climate conditions (note that all presented values are in 2018 dollars). The value of raw water will, on average, be highest when supply is scarcest at $53 per HCF, under the hot-dry future, and lowest over the decades when all possible climate scenarios are averaged (known as the ensemble mean), at $4 per HCF. If the future will be wet and warm, average economic value of water will be $20 per HCF

Fig. 1. Average Economic Value of Raw Water from Public Forests, by Climate Scenario.

Calculating the Economic Value of Water from Public Forests

The economic value of water from San Bernardino National Forest is calculated based on the dynamics of supply and demand change for urban residents over the years. We focus on urban residents who obtain water from water retailers who in turn get their water from San Bernardino National Forest. On the supply side, water from national forests managed by the United States Forest Service (USFS) are subject to drought conditions, wildfires, and changing temperatures associated with climate change. We use a dynamic vegetation model, MC2, to generate the supply of water from San Bernardino National Forest. Having endured droughts and wildfires for decades, Californians have devised policies and institutions to adapt and reduce their exposure to dynamic environmental stressors that affect watersheds and water supply. On the demand side, a variety of policies throughout California have been developed and implemented to reduce water use, including:

  • technological mandates such as low flow toilets,
  • tiered water pricing, and
  • mandated per capita daily limits since the last drought.

Because supply and demand varies over time, we focus on estimating raw water values – regardless of the end use – by decade until the end of the 21st century. To account for uncertainty with respect to future climate conditions, we evaluate water supply from the San Bernardino National Forest under 28 different possible climates. We then forecast water demand in each decade accounting for population, water rate changes, and assume per capita limits will be enforced as mandated under AB 1668 and SB 606.

Fig. 2. Trajectory of Economic Value of Untreated Water, Warm-Wet Climate 2030-2090.
Fig. 3. Trajectory of Economic Value of Untreated Water, Ensemble Mean of Climates 2030-2090.
Fig. 4. Trajectory of Economic Value of Untreated Water, Hot-Dry Climate 2030-2090.

Once we understand supply and demand for water from this public forest, we can then calculate whether there is a water shortage – when supply does not meet demand – or a water surplus – when supply exceeds demand. If the former circumstances prevails, intended recipients of the water are made worse off – they experience a decrease in economic welfare; conversely, if the there is a surplus of water, then recipients of water enjoy an improvement in their economic welfare since they are made better off by having water available that exceeds their demand.

The averages presented in Fig. 1 are based on economic values in each decade for each climate scenario. The trajectories of forecasted values for each climate scenario are illustrated in Figs. 2-4. Each reported climate scenario, or general circulation model (GCM), simulates representative pathway 4.5 (RCP 4.5), which is an overall framework that assumes globally high population growth, limited climate policy initiatives, and limited technological advances. We chose RCP 4.5 since it reflects the current limited state of global action with respect to climate change.

These economic values reflect changes in economic welfare, and their trajectories vary widely, largely due to changes in the supply of water from San Bernardino National Forest, which in turn is determined by temperature, precipitation, and wildfires. Value peaks under the warm-wet GCM (Figure 2) in 2040, at about $98/HCF, but declines thereafter. Under the hot-dry GCM (Figure 4), however, the economic value initially reaches $50/HCF in 2030, but then dramatically declines; it increases through the middle of the century, and is forecasted to be highest in 2080 at $204/HCF. Interestingly, the lowest value is $8/HCF in 2040, the decade with the highest value under a warm-wet GCM.

We derive the ensemble mean by averaging values across all 28 GCMs. As shown in Fig. 3, the economic value of raw water initially drops from $2/HCF to $0.01/HCF, then jumps to about $8/HCF, but decreases and by the end of the century again approximates $2/HCF. Note once more that this is a value estimate for raw, untreated water, regardless of how it is used – either for habitat, municipal, industrial, or agricultural.

We arrive at these economic values by initially starting with water rates for municipal households served by four water retailers that receive all their water from San Bernardino National Forest, located in Riverside, San Jacinto, Redlands, and Colton. Starting with their water rates to single family households, we work to remove costs for treating and distributing water; we then forecast how demand for water by these households will vary as water rates change and populations flux (i.e., number of single family households, while also accounting for per capita consumption limits). The initial starting point for the water rates is taken from the 2015 urban water management plan for each of the four retailers; we also use their forecasted demand changes, and the proportion of their water deliveries that go to single family households versus their other customers.

Policy Implications

As Californians and the rest of the nation adapt to climate challenges over the course of the 21st century, a better understanding of the economic value of water may help planners and policy makers by informing them of the value of scarce resources and public preferences via demand. Multiple uses of raw water from public lands – whether by municipal residents, agricultural and industrial purposes, ecological needs such as fish habitat, or recreation – coupled with the projected effects of climate change, will likely exacerbate water shortages in the future, especially in arid and semiarid Mediterranean-type areas such as southern California.

The most recent drought in California – from 2011 to 2017 – continues to linger in the public memory are droughts remain an ongoing concern for policy makers. Given these stressors to the supply of water in southern California and challenges associated with climate change, understanding welfare impacts of changes in the supply of water for downstream users may help public forest managers weigh actions that affect water supply and inform water retail agencies’ future investments.

For example, suppose land managers pursue vegetation restoration projects over the next decade. Due to increased vegetation cover and corresponding evapotranspiration, we would expect a decrease in surface water flows by 250,000 HCF per year from 2030–2039 (just under 15 percent of the projected surplus from the ensemble mean in that decade). Given the effect on welfare of the supply shortage ($2/HCF based on the ensemble mean), managers could conclude that the benefits of the restoration project must exceed about $500,000, plus the cost of the restoration, to offset welfare losses due to reduced water supply ($2/HCF x 250,000 HCF).

Water and its related services are among the most tangible benefits supplied by national forests in southern California, and its value will vary over the coming decades. Policy makers, industries, agriculture, residents, and consumers will better adapt, manage, and comprehensively weigh trade-offs of the associated price risks if they are armed with key information such as the long-term trend of the economic value of water.

Dr. Srivastava is a Research Associate in the Department of Environmental Science and Policy at University of California, Davis.

Posted in Uncategorized | Leave a comment

Crawdads: Naturalized Californians

Sandy, a 4+ year old red swamp crayfish, raised from a newly hatched egg by Marilyn Moyle.

By Peter Moyle

Crayfish, crawdads, crawfish: whatever you call them, they are everywhere in California’s waters and are as tasty as their lobster relatives. They are especially familiar to anglers who peer into the maw of a bass or pikeminnow or flush their stomachs to see what prey caused the bulging belly. Crawdads are familiar to kids wading in streams, who dare each other to catch one without being pinched. River otters love them as food too. I have watched otters dive in Putah Creek and repeatedly come up with one. With each capture, the otter rolls on its back and crunches the crayfish down. The otters appear to be smiling with satisfaction, smacking their lips.  People eating crayfish have the same general appearance.

Crayfish are so integrated into California’s aquatic ecosystems that they might be considered as native if you didn’t know their history. But most are the result of introductions as food for people or as forage or bait for game fish. And most California crayfish live in novel ecosystems. These ecosystems have a biota that is a mixture of native and non-native species living in habitats that are highly altered by the continuous actions of people. Crayfish therefore fit right in, feeding on organic matter, algae, dead fish or anything else they can process, and then being eaten themselves by native predators such as otters, herons and pikeminnows, or by non-native predators such as centrarchid (sunfish family) basses and bullfrogs. However, this integration comes at a cost, especially in less-altered waterways. Non-native crayfish, regardless of species, can (a) displace fish and native crayfish from cover, making them more vulnerable to predation, (b) reduce aquatic plant densities, making water clearer, (c) compete with fish for aquatic invertebrates as food, especially snails, and (d) displace native crayfish from their habitats. How much of all this they do in California ecosystems, however, is not well understood.

The situation with crayfish in California is actually complex because there are three native species and three non-native species. Their status ranges from extinct, to endangered, to being abundant enough to be sustainably harvested. Confusion is further generated by the tendency of many fish biologists (like me), when sampling aquatic habitats, to just refer to crayfish captured as “crayfish” with no reference to species. A second forthcoming crayfish blog will describe how to identify crayfish in California.

California crayfish

Sooty crayfish. The extinct species is the sooty crayfish (Pacifastacus nigrescens) which was found only in a few streams in San Francisco. They disappeared after only a few specimens were collected in the 19th century, presumably victims of rapid urbanization. The story of sooty crayfish is a mystery because if these crayfish were present in the Bay area streams, why weren’t they found throughout streams of the Central Valley, as non-native species are today? But there is no evidence, archeological or otherwise, that crayfish were ever present in most areas that support non-native crayfish today.

Pilose crayfish. An apparent victim of poor field notes is the pilose crayfish (P. gambelii). The species was described from specimens collected in “California” (the complete locality information on the type specimen) by Charles Girard in 1852. While the pilose crayfish is widely distributed across western states, it is not found in California, indicating Girard made a mistake in noting the vague locality (Larson and Olden 2011).

Shasta crayfish. This crayfish (P. fortis) is native to cold, spring-fed streams and rivers of the Pit River system, including Fall River and Hat Creek in northeastern California.  When graduate students from my lab were studying this crayfish in the 1980s and 90s, I was impressed with how different they were in their behavior from other crayfish: they were not aggressive. If there was bucket of live Shasta crayfish being measured, I could stick my hand in the bucket to grab one without looking. Representatives of any other crayfish would grab my fingers or hand with a big claw and hold on until shaken off.  Shasta crayfish did not appear to have the well-developed defensive mechanism of waving their large front claws around while backing into cover. Unfortunately, this lack of aggression has made them an endangered species. Larger, much more aggressive signal crayfish have invaded their habitat. Shasta crayfish now persist only where signal crayfish have not invaded or have been removed.

Signal crayfish (left) vs Shasta crayfish. The more robust, aggressive signal crayfish causes extirpation of Shasta crayfish when it invades their spring habitats. Photo by P. Moyle.

Klamath signal crayfish. This crayfish (P. leniusculus klamathensis) is native to the Klamath River, where it is abundant and widespread. It is possible that crayfish in the Eel River also belong to this subspecies and are native (Riegal 1959). The Klamath signal crayfish is considered to be a subspecies because it can be distinguished by both morphology and genetics from the widespread Columbia signal crayfish. The subspecies itself was introduced into Lake Tahoe and the Truckee River in 1895 where it is thriving, although it has hybridized with non-native Colombia river signal crayfish, so is no longer a distinct taxon in the eastern Sierra Nevada. A 1970 study (Abrahamsson et al. 1970) estimated that Lake Tahoe supported over 5.5. million crayfish; a more recent estimate is over 220 million crayfish, which dominate benthic production and affect everything from water clarity to native fish abundance (S. Chandra, unpublished data). Because these crayfish are resistant to crayfish fungal plague (Aphanomyces astaci), which had destroyed the crayfish fisheries in Sweden, Sweden stocked many of their lakes with crayfish from Lake Tahoe. While crayfish fisheries have been tried in Lake Tahoe, they have not been sustained (S. Chandra, personal communication). It would be an interesting experiment to subsidize a fishery for 10-20 years to see if such a fishery could have a positive effect on the ecology of the lake, including native fish, fisheries, and water chemistry.

These crayfish are now integrated into the ecosystems of Sierra Nevada streams and lakes, for better or worse. Light (2003) found that populations of signal crayfish in Sierra Nevada streams were regulated in part by flow, similar to trout and native fish populations. However, presence of a downstream reservoir that served as a refuge was necessary for recolonization following extreme flow events. Light (2005) also investigated the effects of signal crayfish on the biology of native Paiute sculpin in a small Sierra Nevada stream. While she found some evidence of competition, effects were minor, demonstrating coexistence was possible; presumably flow was more important to regulating crayfish populations than other factors.

(Left) Signal crayfish. USGS photo. and (Right) Shasta crayfish. USFWS photo.  

Columbia signal crayfish. Wide-spread the huge Columbia River basin, this crayfish (P. l. lenuisculus) was introduced into California in the early 1900s by fisheries agencies. Generally, when biologists talk about the signal crayfish, this is the form they are referring to, assuming the two subspecies do not have any ecological differences. The signal crayfish was introduced into Europe as a large, edible crayfish. Unfortunately, the introduced crayfish carried crayfish plague, a disease that pretty much wiped out the native European crayfish (Astacus astacus). This meant that in countries like Sweden, where crayfish are a traditional winter holiday food, crayfish had to be imported. For a while (1970s and 80s), a fishery for signal crayfish in the Delta helped to satisfy the demand. At its peak, the fishery involved an average of 32 boats. But the fishery has apparently disappeared or become small, presumably because cheaper crayfish from other countries or from aquaculture operations have entered the market. However, it is likely environmental change also played a role. Today, signal crayfish appear to be uncommon in the Delta, replaced by red swamp crayfish. When the Delta fishery was doing well, the town of Isleton held an annual crawdad festival. The last time it was held (2008?), the crawdads served were pond-raised and imported frozen from China.

Red swamp crayfish, Natural History of Orange County. Peter Bryant.

Red swamp crayfish. This crayfish (Procambarus clarki) is typically red and does inhabit swamps, where it burrows into the mud. This behavior can cause distress to farmers if the ‘swamp’ happens to be a rice paddy or its levee. On the other hand, farmers who harvest the crayfish consider them to be a bonus crop (Brady 2013). This crayfish is also very versatile, abundant in streams with warm to cool water, variable water quality, and mud to rocky bottoms. It is aggressive and has apparently displaced other crayfish, and an occasional swimmer, in many places where introduced. Introduced into California in the 1930s, it is now the most commonly encountered crayfish in the central and southern parts of the state and subject of a trap fishery in the Delta and Central Valley, mostly for bait.

Buciarelli et al. (2018) demonstrated how red swamp crayfish can change stream ecosystems that historically lacked crayfish. They preyed on or displaced dragonfly larvae in low gradient streams. The dragonfly larvae were more efficient predators on mosquito larvae than crayfish, so fewer dragonflies resulted in more mosquitoes. Red swamp crayfish have also been shown to be aggressive to other crayfish species and appear to have displaced signal crayfish from some streams in Oregon, as well as in Spain (Pearl et al. 2013). This may account for the observation that signal crayfish in California are often confined to cold headwater (trout) streams) when red swamp crayfish are present in the warm lower reaches of the streams.

Virile crayfish, Wikipedia commons.

Virile (Northern) crayfish (Faxonius virilis) are native to much of northeastern and midwestern USA and are one of the most widely introduced crayfish worldwide. They are best known as Orconectes virilis but were recently reclassified as Faxonius virilis by Crandall and de Grave (2017). They have been widely introduced around the western USA, including California, apparently because of their popularity as bait. The first records from the Central Valley were of crayfish in ponds near Chico State College, where they were kept for teaching purposes starting in the early 1940s (Riegel 1959). Today they seem to be common in southern California and abundant in the Central Valley. Virile crayfish, however, can live in a wide variety of habitats including flowing streams, preferring warm water. Like the red swamp crayfish, they create burrows into which they can find refuge as their habitat dries up. The fact their broad habitat requirements are similar to those of red swamp crayfish suggests the two species co-occur and perhaps compete for food and space at times.

General observations

Crayfish had an easy time invading California.  Here are some reasons.

  • People like to eat them or use them as bait for game fish.
  • They are hardy and easy to transport with minimal water.
  • A population can be established by a single ‘berried’ female carrying 100-300 fertilized eggs or newly hatched young. The young can mature in 1-2 years and live up to 5 years, longer in captivity.
  • They can live in a wide variety of streams, reservoirs, and other aquatic habitats, with signal crayfish doing well in cold waters (e.g. trout streams) and red swamp crayfish and virile crayfish widespread in warmer waters.
  • They quickly spread once introduced into a new area, making them nearly impossible to eradicate once established.
  • We have a poor understanding of how crayfish affect aquatic ecosystems and native aquatic species in California.

Because crayfish, especially non-native crayfish, are so widespread and abundant in California, they tend to be taken for granted. They are present in habitats from warmwater ditches to coldwater mountain lakes and appear to be thoroughly integrated into our aquatic ecosystems, even waters like Lake Tahoe. They do especially well in habitats thoroughly altered by people, such as reservoirs, regulated streams, and rice fields. But there is much we don’t know about them. Some potential research questions include:

  • What is the distribution of crayfish species in California today, native and non-native? Such information could allow us to see if they are useful indicators of habitat quality and change. Sampling e-DNA might be a useful approach to this question.
  • Do the species replace one another in different habitats?  Is the red swamp crayfish today the dominant crayfish in most habitats?
  • Are dominant crayfish suppressing invertebrates and plants in streams, lakes, and sloughs throughout California, changing the nature of the ecosystems? This seems to be true in Lake Tahoe.
  • Would removal of crayfish return a given aquatic ecosystem to its original state, favoring native species?
  • Are other crayfish species likely to invade California? For example, the rusty crayfish (Faxonius rusticus) is an ecosystem damaging, aggressive crayfish that is spreading across North America.

Further Reading

Abrahamsson, S.A. and Goldman, C.R., 1970. Distribution, density and production of the crayfish Pacifastacus leniusculus Dana in Lake Tahoe, California-Nevada. Oikos, 21(1): 83-91.

Agerberg, A. and Jansson, H., 1995. Allozymic comparisons between three subspecies of the freshwater crayfish Pacifastacus leniusculus (Dana), and between populations introduced to Sweden. Hereditas122(1): 33-39.

Brady, S. 2013. Incidental aquaculture in California’s rice paddies: red swamp crawfish. Geographical Review, 103(3): 336-354, DOI: 10.1111/j.1931-0846.2013.00002.x

Crandall, K.A. and  S. De Grave, An updated classification of the freshwater crayfishes (Decapoda: Astacidea) of the world, with a complete species list. Journal of Crustacean Biology, 37(5):615–653,

Larson, E.R. & J. D. Olden. 2011. The state of crayfish in the Pacific Northwest, Fisheries 36(2): 60-73.

Light, T., 2003. Success and failure in a lotic crayfish invasion: the roles of hydrologic variability and habitat alteration. Freshwater Biology 48(10): 1886-1897.

Light, T., 2005. Behavioral effects of invaders: alien crayfish and native sculpin in a California stream. Biological Invasions 7(3): 353-367.

McGriff D. 1983. The commercial fishery for Pacifastacus leniusculus (Dana) in the Sacramento-San Joaquin delta. Freshwater Crayfish 5(1): 403-417. DOI: 10.5869/fc.1983.v5.403

Pearl, C., B. McCreary, and M. Adams. 2011. Invasive crayfish of the Pacific Northwest. USGS Fact Sheet 2011-3132. USGS, Corvallis, Oregon.

Riegel, J.A.  1959.The systematics and distribution of crayfishes in California. California Fish and Game 45(1): 29-50.

Rogers, D.C. 2005. Identification Manual to the Freshwater Crustacea of the Western United States and Adjacent Areas Encountered during Bioassessment. EcoAnalysts, Inc. Technical Publication #1. 78 pp.

Posted in Uncategorized | 2 Comments

Seven conservation lessons I learned in government work

By Andrew L. Rypel

Fig. 1. “Sampling” for bluegill on Lake Monona, Madison, Wisconsin.

Before joining the faculty at UC Davis, I spent the previous five years as a research scientist at the Wisconsin Department of Natural Resources in Madison, Wisconsin. Apparently this experience is somewhat rare among academics. A peer even once described me as “approximating a unicorn”, which I’m still not sure is a good thing or a bad thing! Ultimately, the experience of having lived in both spheres has provided useful perspectives, particularly on the anatomy of successful conservation efforts. So, I’d like to share with you a set of lessons I took from my government work.

  1. Look for questions only science can answer.  Perhaps this seems obvious, but there is much about organisms, habitats, and humans that remains unknown. This is where science is useful. Aldo Leopold (one of the great champions for science-based natural resource management) famously said, “One of the penalties of an ecological education is that one lives alone in a world of wounds.” Indeed this is true. And while it can be quite sad to look upon the ways that humans have violated the natural world, scientific studies shine the path towards novel solutions and futures. It is ultimately okay, if biologists and managers do not know all the answers to every conservation question right now. It is actually one of the exciting features of natural resource jobs – to make important decisions in the absence of complete information where uncertainty is high. Nonetheless, identifying which questions we know and do not know answers to is a key part of the process of building quality policy. Further, as a scientist, identifying high priority science questions in collaboration with decision makers can lead to more impactful and actionable science. This should be a central goal for managers and academics alike – to pursue science that will be useful in decision making.
  1. Long-term data is extremely important. Ecosystems are extraordinarily complicated and flux in unpredictable ways. Some ecological dynamics (like phosphorus-chlorophyll relationships in lakes) show few signs of change up until a threshold is crossed, after which point management is excruciatingly difficult and expensive (Carpenter and Lathrop 2008). Identifying and staying away from these thresholds is key. In other cases, change appears directional and operates in more of a relentless pattern. The warming of aquatic ecosystems over the last century due to climate change has more or less followed this type of dynamic (Sharma et al. 2019). Detecting change in ecosystems is ultimately a tricky proposition, and while there are increasingly better modeling tools available, they will never obviate the need for high quality long-term ecological data. These data are also needed to validate future models. Some of the best long-term ecological datasets available in the USA come from the NSF Long-Term Ecological Research Program (LTER) which tracks key aspects of ecological change at 28 sites across the country. A new NSF program, the National Ecological Observatory Network or NEON will soon also provide useful and standardized data on the heartbeat of ecosystems across the USA. However, other more local examples of long-term monitoring programs have existed for some time. They are more numerous, even coming down to just a single biologist doggedly sampling the same population or ecosystem year after year for the span of a career. These seemingly small efforts generate compound interest and turn enormous conservation profits over time. These are the datasets frequently used to uncover decline of populations and fisheries, the rise of an invasive species, effects of climate change, or impacts of watershed disturbance or water extraction.

As just one California example, if biologists only recently began monitoring the Delta, they might conclude that the Delta Smelt is a naturally rare species. Yet smelt have not always been rare (Börk et al. 2020). Delta Smelt became rare as humans increasingly modified the Sacramento-San Joaquin Rivers and the San Francisco Estuary. Long-term data, notably the fall midwater trawl carried out by an army of dedicated CDFW staff since the 1950s has provided the data necessary to track the decline of smelts, ultimately leading to important efforts to save the species.

Ironically, in tough budget times one of the first things that seems to get cut is monitoring work. It is inherently laborious, time-consuming and expensive. In this author’s opinion, collecting monitoring data is one of the best investments of precious public resources, and often yields some of the best returns on investment. Almost without exception, these activities should be amplified and encouraged rather than cut down.

  1. Money is (unsurprisingly) essential. Conservation activities (monitoring, permitting, grants, science, policy) require funds to conduct and complete. The funding landscape in California is quite different than Wisconsin. For example, fisheries work in Wisconsin is mostly funded through fishing license sales and Sportfish Restoration Act dollars (aka the Dingell-Johnson Act). Those funds are also available in California, but they make up a much smaller portion of the pie. Here, endangered species and water management projects generate the primary funding streams. While this reality is a testament to failed conservation of species (notably fishes) over time, it also provides exceptional opportunity for engaging in cutting-edge conservation practices. As biologists we should all be looking for novel and creative ways to leverage the unique conservation resources of California. However, my personal opinion is that as a collective, we need to get bigger and bolder with our ideas. It is becoming painfully obvious that the status quo in California is simply not working.
  1. Seize the momentum! Government work (but also conservation work is general) is frustratingly slow. It takes hard work, dedication, science and public engagement just to get traction and movement on any given issue. Momentum is an asset. As with any business, staff and leaders move on, budgets change, elections happen and priorities shift. I have seen many projects and teams slowly atrophy and break apart. And this isn’t always anyone’s fault – which make these situations all the more frustrating! The lesson is clear – the time is now. If you can act and move the ball forward on a good science-based conservation policy, you should. Never assume the opportunity to enact change will always be there.
  1. Become an equal opportunity collaborator and conservationist. Unfortunately, people will never agree with you 100% on everything. My experience has been that good policy is not made from getting people to agree with you on everything all the time. Rather, good policy always seems to be strategically built by getting people who don’t agree on everything, to agree on something. I have always been baffled by how birders and duck hunters seem to dislike one another and refuse to work together as much as they could. The arguments usually go something like this (note this is a heuristic and hyperbolic example and certainly not true of all bird people):

Duck hunter: “We buy the licenses and duck stamps that support all the habitat work that the birders are enjoying. They simply aren’t paying their fair share.”

Birder: “That person is wearing camouflage. They must not believe in climate change and are killing birds! Why would anyone do that?!”

Ironically on conservation issues, these two groups are naturally aligned and should be partners. Both groups share a love for birds and waterfowl and are commendably devoted to the preservation and restoration of wetlands. If both camps came together, they would be a definitive force in advancing the conservation needs of declining fish and wildlife in our country. Bringing groups together enlarges the power that any one group might have individually. Uniting factions brings additional financial resources to bear on problems and majority politics suddenly become more realistic. However, such reconciliation necessitates people be open to “working with the other side” and having conversations that are not always totally comfortable.

  1. Get out there! It is exceedingly easy to stay in the office and busy oneself with meetings, reports, and various other administrative duties. However, some of the best experiences I had as a government scientist came from organizing and engaging in public meetings and having conversations with people at boat landings, gas stations and diners.

There was a hashtag that circulated on Twitter several years ago (#actuallivingscientist). It involved scientists introducing themselves as an “actual living scientist” because apparently, so few people know one. But unfortunately there was a twinge of condescension at play here. For example, it’s not really any one of the public’s fault they don’t know a scientist. And are we even reaching those people on social media where the proprietary algorithms tend to bin together people with similar interests? Ironically, the blame if any, should fall squarely with us scientists. As a group, we are simply not great at reaching out and talking plainly with folks. Even in our own families, this can be hard! Of course it would be wonderful if more people knew of the great diversity and talent of scientists and biologists, and I think this was the original intent of the hashtag. It helps reduce fear of science and government employees, and believe it or not, can enhance the science if we learn how to listen. But there is no shortcut (on Twitter or otherwise) to the really hard work of getting out there, meeting people and getting to know them and their lives. Hashtags don’t reach large blocks of the population, and I suspect it may stay that way for some time. For these reasons, in my classes at UC Davis I emphasize how important it is to learn to become excellent scientists AND science communicators. Elements of this topic were explored in a classic book, Escape the Ivory Tower, aimed at academics. However, many of these same principles also apply to government work. 

  1. Anyone can make a difference. Everyone’s work has value and dignity. Government employees do have latitude to make change, suggest change, do simple things, or work to redefine their role to be more effective. These are all opportunities to make a difference in conservation and the public sector. It can be excellent, fulfilling, and worthwhile work.

Furthermore, outside of the government, small groups of citizens can have an out-sized impact if they are motivated and well-organized. In fact, grass roots conservation efforts are often the seeds and engine for real change. In Wisconsin, no one thought about restricting harvest regulations on Muskellunge populations until a small group of concerned anglers and citizens pushed hard for it (Rypel et al. 2016). Government agencies should recognize the rightful and important place of these groups and encourage them as best possible. There are many grass roots conservation organizations in California that pursue excellent science-based natural resource management policies. These folks and their organizations are a treasure to the state and its ecosystems. Margaret Mead may have said it best, “Never doubt that a small group of thoughtful, committed citizens can change the world; indeed, it’s the only thing that ever has.”

For brevity, this is an incomplete list. Maybe some of you have important lessons from your own experiences. If so, please feel free to share them in the comments section below!

Andrew Rypel is an Associate 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 Acting Director of the Center for Watershed Sciences

Fig. 2. Peterson Lake at Dusk, Burnett County, Wisconsin

Further Reading

Baron, N. 2010. Escape from the ivory tower: A guide to making your science matter. Washington, DC: Island Press. 

Bik, H.M. and M.C. Goldstein. 2013. An introduction to social media for scientists. PLOS Biology. 11: e1001535.

Börk, K., A.L. Rypel, and P. Moyle. 2020. New science or just spin: science charade in the Delta,

Börk, K., P.B. Moyle, J. Durand, T.C. Hung, and A.L. Rypel. 2020. Small populations in jeopardy: a delta smelt case study. Environmental Law Reporter. Published Online. 

Carpenter, S.R., and R.C. Lathrop. 2008. Probabilistic Estimate of a Threshold for Eutrophication. Ecosystems 11: 601-613.

Magnuson, J.J. 1990. Long-term ecological research and the invisible present. Bioscience 40: 495-501.

Moyle, P., K. Börk, J. Durand, T. Hung, A.L. Rypel. 2019. Futures for Delta Smelt,

Rypel, A.L., J. Lyons, J.D.T. Griffin, and T.D. Simonson. 2016. Seventy year retrospective on size-structure changes in the recreational fisheries in Wisconsin. Fisheries 41: 230-243.

Sharma, S., K. Blagrave, J.J. Magnuson, C.M. O’Reilly, S. Oliver, M.R. Magee, D. Straile, G.A. Weyhenmeyer, L. Winslow, R. Iestyn Woolway. 2019. Widespread loss of lake ice around the Northern Hemisphere in a warming world. Nature Climate Change 9: 227–231.

Posted in Uncategorized | 5 Comments

Losing mussel mass – the silent extinction of freshwater mussels

by Andrew L. Rypel

Fig. 1. Sampling a healthy freshwater mussel population in the unregulated Sipsey River, Alabama. Photo credit: Andrew Rypel

Throughout my career I’ve spent some time studying the fascinating ecology and conservation issues of freshwater mussels (Fig. 1). For me, learning about mussels has fortified a recurring theme of the natural world – that everything is connected and that small changes in one part of a system can yield unexpected changes elsewhere, often many years later. More importantly, freshwater mussels are essentially threatened everywhere. And because we don’t often hear about them, it is hard to save them, because public will is so critical to generating change.

What is a freshwater mussel?

Some basics. Freshwater mussels, along with freshwater snails (another taxonomic group in major trouble) are varieties of molluscs. Most molluscs on Earth live in saltwater, however several families live in freshwater. Freshwater bivalves (order Unionidae) are one of the major clades of these species. This group’s fossil record extends back to the upper Devonian (416-365 million years ago or “mya”). In North America, first fossils appear to have emerged in the Triassic (250-200 mya). So these animals are not quite as old as fish (>400 mya), but certainly old.


Now here’s where it gets really interesting. [Caution…your mind may explode like mine once did!] With some exceptions, most juvenile freshwater mussels are obligate parasites on fishes. This means they cannot complete their life cycle without using fish as hosts. Baby mussels (glochidia) attach to the gills and fins of fish hosts. In some cases the host fish for a mussel is highly specific, e.g., mussel species x must use fish species y. In other cases, mussels are generalists which can use a range of fish species. By studying these obscure dynamics, a web of interactions begins to emerge between mussels and fishes that is ecologically vital.

Perhaps more interesting is how mussels transmit the glochidia to the fish. Because mussels are mostly sedentary, they have evolved lures to attract their fish hosts. The lures are often part of the mussel’s mantle and are loaded with magazines of baby glochidia. Once a fish bites the lure, the glochidia are ejected onto the host fish. Some lures are basic while others can be exceedingly ornate. Lures resemble all types of potential fish prey including bluegill, minnows, darters, sculpins, salmon, and aquatic insect larvae. Elaborate superconglutinate lures even emerge from the mussel as though on a mucus string, with the same goal of attracting a host fish to bite. In these cases, the mussel literally appears as though it is “going fishing”. Check out the following video of a mantle lure in action!

Ecosystem services

Freshwater mussels perform a variety of important functions in aquatic ecosystems, well-reviewed by Vaughn 2018. For example, mussels regulate water quality through biofiltration. They also process and store excess nutrients in ecosystems. An interesting thought experiment is to consider the role oysters (a similar group of animals) have in regulating water quality in Chesapeake Bay. According to the Chesapeake Bay Foundation, oysters once filtered the entire ecosystem (estimated ~19 trillion gallons of water) every week. However, with declining oyster abundance, it now takes oysters > 1 year to filter the Bay just once. To what extent do mussels similarly promote water quality in freshwater ecosystems? And what might their losses mean?

Freshwater mussels were important to Native American cultures. Mussels seemed to be highly central to mound-building societies of the midwestern and southern USA. However, shell mounds (or “middens”) were also common on the West Coast, notably in San Francisco – driving down “Shellmound Street” might be one major clue! Shell mounds were created by tribes as sacred ceremonial places and as burial sites. Most mussel shells in archaeological sites are “unworked”, meaning mussels were used as food. But, their low caloric value means mussels were probably supplementary food and used more frequently during times of food scarcity. In the Columbia River, mussels were harvested by tribes well into the 20th century and prepared for consumption mainly by steaming. Shells were also for pottery-making, utensils, and jewelry. Because shells are relatively well-preserved, middens can also reveal how mussels and aquatic ecosystems responded to human activities. For example, one genus of mussels in southeastern USA (Epioblasma spp.) showed relatively constant abundance at archaeological sites over a 5000 year period; but around 1000 years ago, mussel abundances declined rapidly with the rise of maize and bean cultivation. In the last 100 years, Epioblasma spp. have declined substantially further due to ecosystem alterations such that species are now listed under the US Endangered Species Act.

In addition to filtering, mussels support fish populations by engineering benthic habitats to be more suitable for fishes like darters, minnows, dace and sculpins that require firm and complex structures. Mussels also are useful in monitoring water quality because they are among the first species that disappear as water quality declines (Augspurger et al. 2003). Because mussel organs are exposed constantly to ambient environmental conditions, they are figurative “canaries in the coal mine” for aquatic environmental change. Mussels support aquatic and terrestrial foodwebs by providing energy to diverse species including fishes, otters, muskrats, raccoons, waterfowl, crayfish, turtles, frogs, salamanders and people. 

Fig. 2. (Left) Loading mussels on scows along the Mississippi River, IA for use in the pearl button industry. Photo by Hugh M. Smith (1899) in Mussel Fishery and Pearl-Button Industry of the Mississippi River, Bulletin of the United States Fish Commission. (Right) Common cutting technique used in pearl-button manufacturing. Photo from Coker (1921) Fresh-water Mussels and Mussel Industries of the United States, Bulletin of the United States Bureau of Fisheries, vol. 36, 1917-1918.

The market for mother-of-pearl buttons was a leading factor in initial mussels declines and extirpations in North America (Fig. 2). Another factor was pearl hunting, even though pearls from native freshwater mussels are mostly rare and imperfect. Gossip in Rome during the 1st century speculated that one reason Julius Caesar invaded England was to search for pearls in mussels from local streams, and that he returned with a piece of armor decorated in pearls (Haag 2012). In the USA, there were two “pearl rushes” – one in the mid-late 19th century, and a second round in the 1950s related to a new process of culturing pearls in Japan. These rushes had horrible consequences for mussel populations, particularly long-lived species.

Diversity, California & Decline

While Class Bivalvia contains ~20,000 living species worldwide, only ~1000 species are known to live in freshwater, and 850 of these species are in the Order Unionida. Estimates suggest there are ~300 species of freshwater mussels in North America. Like many North American taxa, a diversity hotspot for freshwater mussels is the southeastern USA where a lack of glaciation and a correspondingly old evolutionary landscape promote local evolution and high diversity. 

While freshwater mussel diversity is low in California (3-4 native species), these organisms can be locally abundant. Mussels therefore play underappreciated roles in our ecosystems, and in many locations are apparently in significant decline. Native California mussels include the Western Pearlshell (Margaritifera falcata), the Western Ridged Mussel (Gonidea angulata), the California Floater (Anodonta californiensis), and possibly the Oregon Floater (Anodonta oregonensis) (Fig. 3). The Western Pearlshell is notable for its long life, often exceeding 60 years. These mussels are so old, they can be used to reconstruct past climates, parallel to the ways tree-rings can be used (Black et al. 2015). Ecologically, their host fishes are likely trouts and/or salmon. As recently as 1942, Western Pearlshells were a dominant species in the Truckee River with at least 20,000 individuals surveyed; however only 120 mussels were found recently (Murphy 1942, Howard 2008). Today, the only known populations of Western Pearlshell Mussel in the Tahoe basin are in the Upper Truckee River, Trout Creek, and the Truckee River. Western Ridged Mussels are also native to California and are the dominant native mussel species in the Rocky Mountains and to the West. This species is also in decline across the western USA and sculpins might be a host fish. Finally, the California Floater is common in large rivers and pools of streams. Floaters of the genus Anodonta are frequent specialists on floodplain lakes and pools. We frequently encounter floater shells on banks in the Yolo Bypass and in farm ponds. Speckled dace and sculpin are known host fishes for the California floater (Main et al. 2016), but it is likely that this mussel is a generalist species.

Fig. 3. Photos of native freshwater mussels in California. (Upper Left) Adult and juvenile Western Pearlshells alongside invasive Asian clam. Picture from (Lower Left) Adult specimen of California Floater, photo from (Right) External, internal and hinge of the Western Ridge Shell. Photo from

There is great variation in the life-histories of different freshwater mussel species (Haag and Rypel 2011). Some species are exceptionally long-lived. The freshwater pearl mussel (Margaritifera margaritifera) regularly lives >100 years of age. One specimen from Finland had an estimated age of 162 years – this individual was born 37 years before California became a US State. If you go marine, some bivalves live even longer; a specimen of Arctica islandica from the coast of Iceland in 2006 lived 507 years!

In a classic examination of the conservation status of freshwater mussels in North America, Williams et al. 1993 noted 72% (213 of 297) of species are endangered, threatened or of special concern 21, and 7.1% of species had probably gone extinct. These are the highest rates of imperilment of any other known group of freshwater taxa. According to the Xerces Society, crayfishes, freshwater fishes, amphibians, dragonflies have imperilment rates of 51%, 37%, 36%, and 18% respectively. As another contrast, imperilment rates for flowering plants, mammals and birds are 33%, 16% and 14%, respectively. Mussels are…uniquely endangered.

California problem – California solution?

While mussels are declining globally, the mussel problem is also a California problem. Studies in the Truckee River showed a 99.4% decline in abundances of a long-lived mussel (Murphy 1942, Howard 2008). Howard et al. 2015 re-surveyed 450 historical records from 116 sites throughout California,  showing freshwater mussels re-occured at only 47% of these sites. Mussel losses were especially acute in southern California, with 13 of 14 streams having lost their mussels. Yet while loss of native mussels is occurring in many ecosystems, the addition of invasive mussels is simultaneously wreaking havoc on others. Invasion of the Sacramento-San Joaquin Delta by Asiatic clams (Corbicula spp.) is a commonly-studied mechanism for changing zooplankton and fish communities. The ecology of invasive mussels in California and the West will be a good topic for a future blog post.

Like many natural resource issues, we have inherited and contributed to the freshwater mussel problem, which will require hard and focused work to correct. The mechanisms for losses remain elusive. Commonly cited factors include loss of fish hosts, poaching and overharvest, pollution, invasive species and climate change (Haag 2012). Substantially more basic information is needed on the status and distribution of native mussels in California. Where are our mussels? What are their host fishes? Is there cryptic diversity? What are trends in diversity and abundance? What are the impacts of water and riparian land management and invasive species? How have native fish declines impacted mussels? 

A “mussel-building program” in California could take many shapes. I suggest a draft 4-point plan that might be useful to consider:

1. A statewide inventory: A statewide inventory of freshwater mussel abundance and diversity is long overdue. Currently no native California mussel is listed at the state or federal level as threatened or endangered, even though some of these species are already identified as in jeopardy or extirpated from other Western states. A statewide inventory could occur with a series of targeted grants or directed actions, or using a special research unit within one of the relevant state agencies. These data are needed to assess if some of our native mussel species, populations, and ecosystems should be protected. New environmental DNA (eDNA) tools hold promise for such an endeavor.

2. Sentinel sites: Long-term data shows trends over time. Without these data, scientists have little hope of adequately investigating hypotheses of species declines or developing models for testing potential conservation solutions. A series of sentinel sites (e.g., 10-15) strategically located around the state could monitor freshwater mussel populations over time. Sentinel sites/data would give an immediate benefit to scientists struggling to understand mussel dynamics across our large and complex landscape.

3. Conservation hatcheries?: Some eastern US states are developing mussel hatcheries to recover rare species after habitat issues are corrected. In many cases, older decommissioned hatcheries and aquaculture facilities are being repurposed for conservation aquaculture. Are mussel hatcheries a possibility in California? If mussel species were to become listed at some point, hatcheries may be needed to achieve goals. While hatcheries are never intended to replace natural reproduction, they can be an emergency back-up plan for populations and species.

4. Look for win-wins: Strategic prioritization is needed to locate restoration opportunities that would benefit fishes and freshwater mussels. Because mussels rely on suitable fish hosts, loss of fish hosts from habitats will eventually crash mussel populations. Yet because mussels live long lives, mature adults can subsist for decades without host fishes following landscape fragmentation by dams and other structures. This pattern is often referenced in the ecological literature as a “extinction debt” (Timan et al. 1994). Restarting natural mussel recruitment necessitates recolonization by native fishes. Ecosystems with a high potential for boosting native mussel populations could then be prioritized for restoration. Rehabilitation might include large dam removals, but also could be as simple as adjusting the myriad in-stream culverts that also block fish passage to headwater streams, some of which contain mussels. Strategic prioritization along these lines also ties in with existing mechanisms for restoration funding and climate resilience (e.g., through Propositions 1 and 68). In short, the future of mussels is closely tied to the future of fishes – we need to save them together.

Key lessons can be found when examining the demise of mussels. Healthy lands = healthy watersheds = healthy rivers and lakes often = healthy mussels (and fishes and amphibians and plants) = healthy societies. California has so often been a leader in environmental conservation efforts, and needs to be once again.

Andrew Rypel is an Associate 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 Acting Director of the Center for Watershed Sciences

Fig. 4. Freshwater mussels sampled on a survey of the Marais des Cygnes National Wildlife Refuge 2011. Photo by Tim Menard, USFWS. Downloaded from

Further Reading

America’s freshwater mussels are going extinct — Here’s why that sucks

A freshwater mussel apocalypse is underway – and no one knows why

California floater mussel take fish for an epic joyride

Nature’s britta filter is dying and nobody knows why

Oyster fact sheet

The tiny clams that ate the Bay-Delta

There Were Once More Than 425 Shellmounds in the Bay Area. Where Did They Go?

Scientists find 507-year-old clam. Are older ones out there?

Black, B.A. J.B. Dunham, B.W. Blundon, M.F. Raggon, and D. Zima. Spatial variability in growth-increment chronologies of long-lived freshwater mussels: Implications for climate impacts and reconstructions. Ecoscience 17: 240-250.

Haag, W. R., 2012. North American freshwater mussels: Natural history, ecology, and conservation. Cambridge University Press, Cambridge UK.

Helama, A., and I. Valovirta. The oldest recorded animal in Finland: ontogenetic age and growth in Margaritifera margaritifera (L. 1758) based on internal shell increments. Memoranda Soc. Fauna Fennica 84: 20-30.

Augspurger, T., A.E. Keller, M.C. Black, W.G. Cope, and F.J. Dwyer. Water quality guidance for protection of freshwater mussels (Unionidae) from ammonia exposure. Environmental Toxicology and Chemistry 22: 2569-2575.

Howard, J. K. 2008. Strategic inventory of freshwater mussels in the northern Sierra Nevada Province. Final Report by Western Mollusk Sciences, San Francisco, CA to US Forest Service PSW Regional Office, Vallejo, CA. 65 pp.

Howard, J.K., J.L. Furnish, J.B. Box, and S. Jepsen. 2015. The decline of native freshwater mussels (Bivalvia: Unionidae) in California as determined from historical and current surveys. California FIsh and Game 101: 8-23.

Haag, W.R., and A.L. Rypel. Growth and longevity in freshwater mussels: evolutionary and conservation implications. Biological Reviews 86: 225-247.

Maine, A., C. Arango, and C. O’Brien. Host Fish Associations of the California Floater (Anodonta californiensis) in the Yakima River Basin, Washington. Northwest Science 90: 290-300.

Murphy, G. 1942. Relationship of the fresh-water mussel to trout in the Truckee River. California Fish and Game 28: 89-102.

Timan, D., R.M. May, C.L. Lehman, and M.A. Nowak. Habitat destruction and the extinction debt. Nature 371: 65-66.

Vaughn, C.C. 2018. Ecosystem services provided by freshwater mussels. Hydrobiologia 810: 15-27. 

Williams, J.D. M.L. Warren, K.S. Cummings, J.L. Harris, and R.J. Neves. Conservation Status of Freshwater Mussels of the United States and Canada. Fisheries 18: 6-22.

Posted in Uncategorized | Leave a comment

Old Readings on California Water

by Jay Lund

1957_map.tiff 2

The California Water Plan. State Dept. of Water Resources, 1957

Today’s water struggles have deep roots.

In our shared summer confinement, we hopefully have some time for some deeper reading on California water.  Here is a small collection of older writings on California water, the youngest of which is still older than me.  Beyond historical interest, these early writings have useful perspectives on water problems today, in the future, and outside California.

These writings illustrate how a society of poor disorganized immigrants experienced abrupt climate change when they moved to California and had to change how they did agriculture, built cities and water systems, and organized water laws and institutions in a new (to them) climate and land.  We still struggle with this condition today, and will in the future.  California society is mostly much richer today, and somewhat more organized.

  1. Alexander, B.S., George H. Mendell, George Davidson (1873) Report of the Board of Commissioners on the Irrigation of the San Joaquin, Tulare, and Sacramento Valleys of the State of California, Washington: G.P.0. Report on irrigation development for the Central Valley, including a wonderful global survey of irrigation projects from around the world.
  2. Austin, Mary (1903), The Land of Little Rain, Houghton, Mifflin and Company, New York, 280 pp. (Text version) On water, life, cultures, landscape, and Native Americans in the Eastern Sierra/Owens Basin.  Includes some early water and irrigation management conflicts.  A very pleasant read.
  3. DWR (1930), California Water Plan, Division of Water Resources, California Department of Public Works, Sacramento, CA.  An excellent strategic presentation, reflecting more than a decade of systematic state studies and discussions, this plan during the Great Depression, shaped the CVP and SWP.  [This document seems to be no long available on a State of California web site.]
  4. Goldschmidt, Walter (1947). As You Sow: Three Studies in the Social Consequences of Agribusiness. Montclair, N.J: Allanheld, Osmun and Co. Publishers, Inc. Excellent readable early work on the anthropology and sociology of rural irrigation-based communities in the Tulare basin – many issues and findings remain relevant.  See recent blog post on this one.
  5. Montgomery, Mary and Marion Clawson (1946), History of Legislation and Policy Formation of the Central Valley Project, United States Department of Agriculture Bureau of Agricultural Economics, Berkeley, CA, March, 264 pp. An excellent history of the early CVP, from a state water project to a federal water project, with struggles over public versus private interests, state projects to supplement declining groundwater and expand irrigated area, and the state’s struggles to regain control of the CVP (while retaining federal funding). [So far, you need to visit a library for this one.]
  6. Banks, Harvey (1953), “Utilization of Underground Storage Reservoirs,” Transactions of the American Society of Civil Engineers, Vol. 118, No. 1, January, pp. 220-234. One of the State Water Project’s main engineers began with excellent analyses and discussions of groundwater.
  7. DWR (1957), The California Water Plan, Bulletin No. 3. Sacramento, California. California Department of Water Resources, May, 1957. This plan could have the subtitle – leave no valley undammed, and set the direction of state water planning until 1983.  [This document seems to be no long available on a State of California web site.]

Many excellent writings on California water are more than 50 years old (pre-dating the popular Cadillac Desert!).

Please suggest additional writings in the comments section, including a web link where available.

Read old to stay sharp.

Jay Lund is a Professor of Civil and Environmental Engineering and Director of the Center for Watershed Sciences at the University of California – Davis.

Posted in Uncategorized | 5 Comments

Fish surveys in the estuary: the whole is greater than the sum of its parts

by Dylan K. Stompe, Peter Moyle, Avery Kruger, John Durand

Fig. 1. Measuring a Sacramento splittail caught in a bottom trawl, Suisun Marsh. Photo: Peter Moyle

The San Francisco Estuary is a dynamic and altered estuary that supports a high diversity of fishes, both native and non-native. These species have substantial recreational, commercial, and intrinsic value to people. Since the 1950s, various agencies and UC Davis have established long-term surveys to track the status of fish populations. These surveys help scientists understand how fishes are responding to natural- and human-caused changes to the Estuary.

Each survey has strengths and weaknesses due to differences in sampling gear and effort, program duration, consistency of sampling, and area sampled. Because of this, it is challenging to understand drivers of change when looking at only a single survey. For example, when considering a single survey with limited sampling area, a decline in catch may be associated with either A) change in the distribution of a species within the Estuary, B) change in characteristics of sampling sites (e.g., deepening or shallowing, invasion of submersed aquatic vegetation) that affects gear efficiency, or C) a true decline in the Estuary-wide abundance of a species.

Surveys are designed to catch different species based on the question under investigation.  Common gear types include midwater trawls, bottom trawls, and beach seines, and each one is better at catching certain species than others (Figure 2). Midwater trawls are generally best at catching pelagic fishes such as juvenile salmon, striped bass, and smelt; bottom trawls do a better job of catching benthic fishes such as Sacramento splittail and gobies; and beach seines are best at catching fishes associated with shallow or weedy-edge habitats, such as largemouth bass and Mississippi silverside.

Fig. 2. Illustration of gear types used in San Francisco Estuary fish surveys.

One of the oldest and most widely cited surveys in the Estuary is the California Department of Fish and Wildlife Fall Midwater Trawl Survey, which was designed primarily to identify trends in striped bass populations. Thankfully, other fish species captured in this and other surveys are recorded as well. As a result, numerous papers have been published identifying periods of declining catch of native and non-native pelagic fishes leveraging the Fall Midwater Trawl data set. However, when data from other surveys are considered, different stories emerge.

We combined data from 14 long-term surveys (Table 1) in a way that allows for basic analysis of trends for up to 167 fish species in a much more spatially and temporally rich manner than could be done with a single survey (Stompe et al. 2020). These surveys use different methods and sample different areas so the total number of fish that they catch is not comparable. However, the trends in catch are comparable among surveys. Using data from multiple surveys in combination shows that some trends for fishes that are present in some surveys are absent or even contradicted by others (Figure 3, 4).

Fig. 3. Trends in pelagic fish catch per unit effort (CPUE) as show by the CDFW Fall Midwater Trawl (right) and aggregative data (left). Notice wide fluctuations in longfin smelt CPUE in the Fall Midwater Trawl versus consistent decline in aggregative data, as well as the steep decline in threadfin shad catch around the year 2001 in Fall Midwater Trawl versus consistent catch in aggregative data. Note that both sets of data show a decline in pelagic fishes in general starting around 1980, followed by a partial recovery, and then another decline starting in about 2001.  Mean annual CPUE calculate as the average catch per trawl or seine pull every year. The blue line denotes the approximate year of invasion by overbite clam, while the red line represents the initiation of the Pelagic Organism Decline (POD, Sommer et al. 2007, Thomson et al. 2010). The horizontal black bars show periods of drought.

For example, average catch per trawl of threadfin shad by the Fall Midwater Trawl declines drastically between 2001 and 2002 (Figure 3, panel B). However, aggregated data revealed that the population did not decline during this time period, and in fact remained relatively stable up until 2007 (Figure 3, panel A; see Stompe et al. 2020 for aggregation methods). The expanded data suggest that the decline in catch per trawl by the Fall Midwater Trawl between 2001 and 2002 was likely the result of changes in threadfin shad distribution or behavior, or changes in sampling station characteristics.

Similarly, if we consider catch per trawl of striped bass in two dissimilar surveys within the Estuary, very different trends appear. Average catch of striped bass per trawl by the Fall Midwater Trawl declines to near zero by the year 2000, while average catch per trawl remains relatively high throughout this same time period in the Suisun Marsh Otter Trawl (Figure 4). The Suisun Marsh Otter Trawl primarily samples shallow and marshy habitats as opposed to many of the deeper and less productive waters sampled by the Fall Midwater Trawl. This differential indicates productive areas such as Suisun Marsh are likely functioning as important and resilient refuges for the fishes of the Estuary.

Fig. 4. Average catch per trawl, by year, of striped bass in the Fall Midwater Trawl (FMWT) and the Suisun Marsh Otter Trawl (SMOT) surveys. Notice how catch by the FMWT declines to near zero by the year 2000 but remains relatively high (yet variable) in the SMOT.

Knowing how species move within the Estuary and what habitats become productive or unproductive over time allows us to make better-informed and more effective management decisions. Each unique survey of the Estuary is an important key to our understanding of fish populations. While certain surveys may appear to have more utility right now, it is impossible to predict which surveys will become invaluable as the Estuary continues to change, new fish species are inevitably listed under the state and federal endangered species acts, and new alien species invade.

Further Reading:

Stompe D.K., Moyle P.B., Kruger A., Durand J.R. 2020. Comparing and Integrating Fish Surveys in the San Francisco Estuary: Why Diverse Long-Term Monitoring Programs are Important. San Francisco Estuary and Watershed Science, 18(2).

Sommer T., Armor C., Baxter R., Breuer R., Brown L., Chotkowski M., Culberson S., Feyrer F., Gingras M., Herbold B., Kimmerer W. 2007. The collapse of pelagic fishes in the upper San Francisco Estuary. Fisheries, 32(6):270-277.

Thomson J.R., Kimmerer W.J., Brown L.R., Newman K.B., Nally R.M., Bennett W.A., Feyrer F., Fleishman, E. 2010. Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary. Ecological Applications, 20(5):1431-14

This work came from a recently published paper comparing and integrating fish surveys in the SF Estuary (Stompe et al. 2020). It is part of a larger project to evaluate striped bass demography and natural history in the Estuary, funded by California Department of Water Resources.

Posted in Uncategorized | Leave a comment

SGMA and the Human Right to Water: How do submitted Groundwater Sustainability Plans address drinking water?

by Kristin Dobbin, Darcy Bostic, Michael Kuo and Jessica Mendoza

In 2012 California passed the Human Right to Water (AB 685) which declares all Californians have the right to safe, clean, affordable and accessible drinking water. Two years later during a record-breaking drought, California passed another piece of historic legislation known as the Sustainable Groundwater Management Act (SGMA). To prevent undesirable results from groundwater overdraft, SGMA requires the development of regional Groundwater Sustainability Plans (GSPs) in high and medium priority groundwater basins.

Although only five of 41 GSPs submitted to the Department of Water Resources for review in January mention the human right to water, and only one of those affirmed it as a consideration in their plan, these two policies are closely related. Groundwater contamination and overdraft are both primary factors that limit universal access to safe water in California today. As we look to a future of increased drought under climate change, our ability to maintain adequate groundwater levels is also a grave concern for sustaining the tenuous access of rural residents reliant on single, shallow domestic or public supply wells.

How might SGMA implementation affect environmental justice priorities at this policy intersection? To probe this question our UC Davis research team examined the distribution and extent of drinking water users in critically overdrafted groundwater basins. We then reviewed each of the 41 GSPs posted for public comment to assess how the plans reflect engagement with, and consideration of, those drinking water stakeholders.

We found that critically overdrafted groundwater basins in California cover many different drinking water users including nearly 250 communities and more than 40,000 drinking water supply wells (domestic and municipal). We also found that many submitted GSPs share several major gaps when it comes to drinking water, these include:

  1. Many GSPs lacked Minimum Thresholds for key contaminants that affect public health. For plans that do set thresholds for these constituents, their thresholds are often not aligned with drinking water standards. Many plans failed to discuss the potential impact of these policy decisions on drinking water users.
  2. The Minimum Thresholds for groundwater levels set in submitted GSPs have water levels continuing to decline nearly everywhere. Again, the role of drinking water stakeholders in establishing these minimum standards and their impact on domestic and municipal users is unclear in many GSPs.
  3. GSPs often lacked descriptions of drinking water users in their area. This was particularly true for domestic wells, for which 66% of submitted plans omitted information about the number and/or locations of these beneficial users.
  4. Stakeholder engagement and participation was addressed in most plans yet discussion of how feedback was incorporated into final plans was often lacking. Few plans addressed stakeholder engagement for plan implementation with any detail.
  5. Very few plans (15%) mentioned drinking water affordability, a central tenant to California’s human right to water.
  6. Most plans do not propose projects or management actions with drinking water or Disadvantaged Community (DAC) benefits.

Nonetheless, across these plans we also found important instances where drinking water was thoroughly incorporated. Examples from specific GSPs include aligning Minimum Thresholds for water quality with state drinking water standards; proposing projects that foster water supply reliability for DACs; assessing the risk of, and developing mitigation plans for, negative impacts to shallow domestic wells; and ensuring the integration of drinking water stakeholder voices in decision-making through voting board representation and stakeholder committees. These examples are a clear starting place for further integrating groundwater planning efforts and state environmental justice priorities.

To prevent disproportionate impacts and promote human right to water implementation in the state, current and future GSPs need to more fully address drinking water uses and users. While a growing arsenal of tools can help address drinking water needs in sustainable groundwater planning, doing so will likely require more support by state agencies. Ongoing attention to increasing participation in California water resource management is also crucial to narrowing this gap. In the meantime, given the limited discussion of drinking water in many submitted plans, there is a need for more thorough assessments of the potential drinking water impacts per AB 685.

For more, see the full report available here (also available in español).

Kristin Dobbin is a PhD candidate in the Graduate Group in Ecology at the University of California – Davis.  Darcy Bostic recently received her Masters in Hydrologic Sciences from UC Davis.  Jessica Mendoza and Michael Kuo are undergraduate research assistants in the Center for Environmental Policy and Behavior at UC Davis.

Further Readings

Bernacchi, L. A., Fernandez-Bou, A., Viers, J. H., Valero, J., & Medellín-Azuara, J. (2020). A glass half empty: Limited voices, limited groundwater security for California. Science of The Total Environment, 139529.

Community Water Center. (2019). Guide to Protecting Drinking Water Quality Under the Sustainable Groundwater Management Act.

Dobbin, K. B. (2020). “Good Luck Fixing the Problem”: Small Low-Income Community Participation in Collaborative Groundwater Governance and Implications for Drinking Water Source Protection. Society & Natural Resources, 1-18.

Moran, T. & Belin, A. (2019). A Guide to Water Quality Requirements Under the Sustainable Groundwater Management Act.

Self-help Enterprises, Leadership Counsel for Justice and Accountability, and the Community Water Center (2020). Framework for a Drinking Water Well Impact Mitigation Program.

Water Foundation. (2020). Groundwater Management and Safe Drinking Water in the San Joaquin Valley.



Posted in Uncategorized | Leave a comment