Science, the Delta, and the future of San Joaquin salmon

by Peter B. Moyle

The Sacramento-San Joaquin Delta. Image credit: Carson Jeffres

I feel fortunate to be a biologist in an era and place, California, where science matters.  Routine scientific studies rarely make headlines but they are relied on by decision makers because they reduce uncertainty, bit by bit.   This seems to be true nationwide as well, except in the highest levels of the federal government.  There, scientific findings on such subjects as climate change, evolution of disease organisms, and the importance of ecosystems to human health can be discarded because they contradict traditional ignorance (“gut feelings”) or because they are somehow part of some mystical conspiracy (“deep state”).   I therefore think it is worthwhile to give an example of how typical scientific studies, even studies from outside the state, provide important information that can benefit all of us in California.

The example comes from reading the latest issue of the North American Journal of Fisheries Management (NAJFM).  This is a journal that publishes scientific studies related to managing fisheries, mainly in North America. The articles are by scientists from academia, government agencies, and the private sector, and are published only if they have survived critiques by other scientists, via the peer-review process.  The journal is published by the American Fisheries Society, one of the oldest scientific societies in the USA.  This is not a high-prestige journal for scientists, based on the citation rates of its articles in papers in other scientific journals.  Nevertheless, this respected journal publishes strong studies relevant to resource managers.  In other words, this is a journal for scientists who want to influence what goes on in the real world, rather than just impress colleagues.

Here I describe 5 (of 24) articles from the June 2018 issue of the journal, providing them with headlines as if their results attracted a lot of attention.  The full citations to the articles are provided at the end of this blog. I must admit I chose this issue because I thought the article by Buchanan et al. (2018, #1 below) was particularly important and because another article was on delta smelt.  But I was struck by the relevance of all five articles to our region.

  1. Flows do not improve San Joaquin salmon survival but salvage does.

This is an exhaustive study on factors influencing the survival of juvenile Chinook salmon in the San Joaquin River, its tributaries, and Delta, using acoustic tags.  The authors are very careful in their conclusions. The study nevertheless shows that juvenile Chinook from the San Joaquin region are not surviving passage through the south Delta and that increased flows are not likely to increase their survival.  Highest survival is for juveniles that are salvaged at the State Water Project pumping plant, because they avoid going through the Delta by being trucked past it. Large-scale improvement of habitat in the south and central Delta is likely the key to improved survival, as shown by higher survival rates of fish from the Sacramento River that pass through the north Delta.

  1. Hatchery delta smelt look different from wild delta smelt.

This study shows that individual delta smelt from the captive breeding program can be recognized by black dots (known as chromatophore patterns) on the chin. If introduced into the wild, they presumably can be distinguished from adult wild smelt when captured, without resorting to tags.  This study is part of the desperate effort to prevent the extinction of delta smelt, which will likely involve introducing hatchery smelt into the wild.  One of the concerns is that sampling programs trying to determine the status of wild smelt would not be able to distinguish wild from hatchery smelt.

  1. Game fish do not eat Atlantic salmon in a New Brunswick river

Native striped bass and non-native muskellunge are favorite game fishes in a New Brunswick river.  They have been accused of preying on Atlantic salmon juveniles and causing the decline of salmon runs in the river. Both species were found not to prey on salmon.  Similar accusations fly around about striped bass and other predators being the major cause of Chinook salmon decline in central California.

  1. Striped bass decline is caused by the fishery for large individuals.

Striped bass populations on the Atlantic Coast have generally recovered to historic abundances thanks to reductions in pollution and improved management. An exception has been the population in the Neuse River estuary in North Carolina.  This paper, using diverse models, examined possible causes of decline and concluded that the main cause was removal of most of the larger individuals by anglers. The largest and oldest fish are typically females, which produce the most and healthiest eggs. This suggests that problems with large females may be contributing to the decline of striped bass in the San Francisco Estuary.

  1. Effects of predator control on native fish is unproven but continues anyway.

This paper reports results of a program to remove large channel catfish from the San Juan River (southwestern USA), to enhance native fish populations. The program did not cause a collapse of the catfish population, as had been hoped, but did alter the size structure of the population, increasing the proportion of smaller individuals.  Effects on native fishes could not be determined, nor could any unintended consequences. “Non-native fish removal….has continued under the guise of beneficial effects to native fishes and in the absence of other available management actions for reducing threat to native fishes… (Pennock et al. 2018, p 576).”

What does this admittedly biased and limited sample of studies tell us?  First, the problems of saving native species, including harvested species, are found throughout North America and are a major concern of fisheries managers. Each region, of course, has its own distinctive problems and solutions. California is not alone in our efforts to save native fishes; we just have especially big battles to fight. But we can benefit from what has been learned elsewhere (e.g. causes of striped bass decline as in #4 above).

Second, causes of decline are diverse and vary from region to region. Predation by non-native species comes up repeatedly as a possible cause, but it often winds up being discounted after intensive study.  As is true in California, predation is most likely to be a problem in highly altered habitats that make native fishes (such as Chinook salmon) especially vulnerable to predation.

Third, scientific papers and their conclusions are tied to a long history of other studies, which usually (but not always) support the study that cites them.  This is not surprising considering that each paper cites an average of 37 other papers in a chain that goes back to Charles Darwin and beyond.  Each of the five papers cited here was based on studies that first had to be approved for funding, often by a committee of peers, as valid and useful. After the data collection and analysis is done, drafts of the paper are typically discussed and modified by the coauthors. The five papers cited here average 5 coauthors, with a range of 3-10.  The approved draft is then sent to a journal for review. If the journal editor agrees it is suitable, it is sent out for peer review by 2-3 scientists familiar with the field. If the reviews are positive (including “major revision required”) and the editor agrees with the reviews, the paper is revised, resubmitted, and eventually published.  I describe this process to emphasize peer-reviewed scientific papers are generally reliable sources of information. There are always exceptions, of course, but they are rare and problem papers are often ‘caught’ once they are read by the scientific community.

Despite the rigorous process just described, scientists are remarkably cautious about drawing conclusions from their data, except, of course, “more research is needed.”  Yet their conclusions are often the most important part of the paper because they represent the opinions of scientists who have been deeply involved in the research and have a good idea of what it all means, or should mean.  A good example can be seen in the San Joaquin Delta (SJD) study by Buchanan et al. (#1, above).

The SJD study was important because (1) fall-run Chinook salmon are the major support of sport and commercial fisheries for salmon; (2) the San Joaquin River and its tributaries are the focus of restoration efforts to increase Chinook salmon numbers; (3) the State Water Resources Control Board is currently examining the potential of increasing flow releases down the San Joaquin, Tuolumne, Merced, and Stanislaus rivers to benefit salmon; and (4) the results are applicable to spring-run and winter-run Chinook, both listed under state and federal endangered species acts.  The basic questions being asked are: How well do juvenile salmon from the San Joaquin watershed survive passage through Delta? What are the implications of the findings for salmon and water management?

The SJD study was a huge undertaking, involving surgically implanting over 9,000 acoustic telemetry tags in juvenile fall run Chinook salmon over a six-year period (2010-2015).  The fish, all of hatchery origin, were released into the San Joaquin River above the Delta and their movements were tracked by their passage past 12 stations with receivers to detect signals emanating from the tagged fish.  The movement of the few surviving fish through the Delta took 1-11 days for the 92 km-long principal route.  Alternate routes were also available, including via the pumping plant of the State Water Project, where fish are trapped, trucked, and released below the Delta.

The basic results showed such low survival of salmon passing through the Delta that returning adults would be too few to sustain the salmon populations in the San Joaquin basin.  The study indicates that the lack of decent habitat for juvenile salmon in the Delta means that most are picked off by predators (as shown in part by tagged fish moving in the wrong direction because the tags are in the stomachs of predators).   Essentially, fall-run Chinook populations in the San Joaquin basin are being sustained by straying hatchery fish from the Sacramento River system.

I suspect the cautious wording of the scientists will annoy non-scientists trying to read the paper.  For example:  “Thus, the low survival estimates observed in the acoustic-telemetry studies may be considered to represent the Delta survival of the smolt-sized migrant component of the natural-spawned population, to the extent to which hatchery fish may represent natural fish (p. 675)”.   This statement says that despite the huge and well-considered nature of the study, we will never have complete certainty of its meaning.  Nevertheless, the findings strongly point to conclusions that survival of salmon in the south and central Delta is extremely low. This in turn implies that massive habitat restoration is required to improve survival.  Without improving habitat, just increasing flows through the region is unlikely to have much effect on salmon survival.

The moral of this story is that scientists can provide answers to complex questions, but the answers may not be what managers want to hear.  For the SJD study, perhaps the real question is: How badly do we want to restore self-sustaining salmon runs to the San Joaquin and its tributaries? This question has to be asked in the context of future scenarios of climate change with increasingly variable conditions and likely permanent flooding of Delta islands.  What the science provides is the basis for developing realistic management alternatives, as shown by close reading of studies such as those presented here.

Peter Moyle is Distinguished Professor Emeritus at the University of California, Davis and is Associate Director of the Center for Watershed Sciences.

Further reading

  1. Buchanan, R. A., Brandes, P. L. and Skalski, J. R. (2018), Survival of juvenile Fall‐Run Chinook Salmon through the San Joaquin River Delta, California, 2010–2015. North American Journal of Fisheries Management 38: 663-679. doi:10.1002/nafm.10063
  1. Castillo, G. C., Sandford, M. E., Hung, T. , Tigan, G. , Lindberg, J. C., Yang, W. and Van Nieuwenhuyse, E. E. (2018), Using natural marks to identify individual cultured adult Delta Smelt. North American Journal of Fisheries Management 38: 698-705. doi:10.1002/nafm.10066
  1. Andrews, S. N., Zelman, K. , Ellis, T. , Linnansaari, T. and Curry, R. A. (2018), Diet of Striped Bass and Muskellunge downstream of a large hydroelectric dam: a preliminary investigation into suspected Atlantic Salmon smolt predation. North American Journal of Fisheries Management 8: 734-746. doi:10.1002/nafm.10074
  1. Bradley, C. E., Rice, J. A. and Aday, D. D. (2018), Modeling the effects of vital rate manipulation and management scenarios to predict the population impact of restoration programs on an unrecovered coastal population of Striped Bass. North American Journal of Fisheries Management 38: 639-649. doi:10.1002/nafm.10062
  1. Pennock, C. A., Durst, S. L., Duran, B. R., Hines, B. A., Cathcart, C. N., Davis, J. E., Schleicher, B. J. and Franssen, N. R. (2018), Predicted and observed responses of a nonnative Channel Catfish population following managed removal to aid the recovery of endangered fishes. North American Journal of Fisheries Management 38: 565-578. doi:10.1002/nafm.10056
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6 Responses to Science, the Delta, and the future of San Joaquin salmon

  1. In the last few paragraphs of this blog, Dr. Moyle highlights a 2010-2015 study of salmon passage through the Delta in the San Joaquin River. The study found that most of the surviving salmon were those salvaged (collected and trucked downstream) at the south Delta pumps near Tracy and Byron. These six years included just two relatively wet years and four consecutive dry years. Dr. Moyle does not break down the salvage numbers by year; without having seen the study is it possible that most of the salvage occurred from 2012-2015, the four driest years of the period involved? Instead of breaking this out, Dr. Moyle takes the scientist-authors’ conclusions to mean that “survival of salmon in the south and central Delta is extremely low (from the San Joaquin side). “This in turn implies,” he says, “that massive habitat restoration is required to improve [salmon] survival. Without improving habitat, just increasing flows through the region is unlikely to have much effect on salmon survival.”

    Two things: One, no one on the environmental water side ever argues that flows should be increased AND that habitat restoration is unneeded. We do say that flow is itself habitat and a necessary component of restoration implementation.

    Second, Dr. Moyle fails to break out the salvage numbers from the various years to give readers a more fine-grained sense of how salmon in the San Joaquin actually did in those six years (most of which were low flow years).

    These were hard years for the Delta (2012-2015) and the rest of California. How certain can we be that Dr. Moyle has accurately presented the implications of the study when it is behind a paywall at the North American Journal for Fisheries Management to judge for ourselves?

  2. Chris Enright says:

    This is an insightful commentary from one of the great thinkers in our system. I hope it’s read widely. Peter describes the enormous effort required to bring credible and management-relevant analyses into the knowledge base. I’m struck that plain language summaries of recent work with clear reminders of the implications for management by science elders are probably as important as the work itself.

  3. Philip Bowles says:

    Think of the demonstrable benefits if the hundreds of millions thrown into the San Joauquin boondoggle were redirected to improve the Trinity and other North Coast rivers. Instead of a handful of doomed hatchery fish, we could have thriving wild fish in a living river system. Yes, a good part of the San Joaquin has been ruined. So have the wetlands that were downtown San Francisco, most of Sacramento, and the natural floodplains of the Sacramento River. It is a waste of time to try to turn back the clock, especially when there are excellent alternatives.

  4. Enlightening article absent the gratuitous political commentary.

  5. Pingback: The road to viable Central Valley Chinook salmon populations is paved with cost-effective management actions. Do spring export restrictions fit the bill? – True Fish Scientist

  6. Pingback: Acoustic tagging studies. What have they told us about export effects on juvenile salmon in the Delta? – True Fish Scientist

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