Category Archives: Fish (general)

Can rice fields help save endangered salmon?

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A recent article in the LA Times asked: can rice fields help endangered salmon in the Central Valley? Because that article really did not answer the question, I thought I would try in this post. The answer is: absolutely.

A significant portion of the endangered winter-run and spring-run salmon populations are now made up of hatchery fish. Hatchery fish are important in keeping the populations from falling further toward extinction and in helping toward recovery. To make the hatchery tool in the tool-box of recovery more effective, it is essential that a greater percentage of hatchery eggs become smolts that reach the ocean. Studies show that hatchery smolts released at or near hatcheries have a very poor survival rate to the Golden Gate. Trucking the hatchery smolts to the Bay increases survival, but results in significant straying to other Valley rivers.

Rice-field-reared salmon. Source: UC Davis photo

One way to increase smolt production and survival is to rear a portion of the newly hatched fry in Valley floodplain rice fields closer to the Bay. There have been plenty of experiments that show fall-run hatchery fry do well in terms of growth and survival in rice fields. The next step is putting that knowledge into management action. At a minimum, rearing a portion of newly hatched fry from hatcheries in natural floodplains is more “natural” than rearing them in hatchery raceways.

Winter-Run Salmon: Winter-run fry from the Livingston Stone federal hatchery could rear in the rice fields of the upper Yolo Bypass during late fall and early winter. Conditions would be ideal for growth and survival. Even in drought years, water would be available from the Colusa Basin Drain, whose water source is primarily the upper Sacramento River. As proven last year, managers could explicitly divert water for this purpose from near Red Bluff on the Sacramento River, through the Colusa Basin to the upper Yolo Bypass rice fields, and finally to the Tule Canal. This would facilitate emigration of the smolts produced to the Bay. The planned Fremont Weir “fix” will provide Sacramento River water directly to the Yolo Bypass within several years. The alteration of Fremont Weir will also provide passage back to the Sacramento River for any adult winter-run that are attracted to Yolo Bypass flows.

Spring-Run Salmon: Spring-run fry from the Feather River state hatchery could rear in rice fields in the lower Sutter Bypass adjacent to the lower Feather River. Rearing would occur in winter, when conditions would be ideal. A late winter flow pulse could facilitate the emigration of these fish (as well as wild fish) out of the Feather River to and through the Delta, and to the Bay and ocean.

What ifs:

  • What about predators? Rice-field-reared winter-run smolts will have 100 miles less migration through the upper Sacramento River gauntlet of predators. Feather River rice-field smolts will be able to pass almost directly into the lower Sacramento River, thereby avoiding many miles of predator habitat in the lower Feather River. Yolo Bypass winter-run smolts would pass through 40 miles of the Tule Canal to reach Cache Slough in the Delta. Added flow and colder mid-winter water temperatures should minimize this real risk. Remember also that rice field habitat is seasonal. Bass and other species that dine on juvenile salmon don’t establish themselves in rice fields like they do in waters that are inundated year-round.
  • How will the progress of these fish be measured? Like all other hatchery fish, these fish should all be coded-wire tagged, and a small portion should be radio-tagged, prior to release.
  • What about straying? Rearing in the appropriate source water should help to minimize straying. Providing flow pulses during emigration will help in imprinting. Imprinting newly hatched fry at the hatcheries will also help.
  • What about contribution to the population, especially given potentially low Delta survival in dry years? If necessary, the rice-field-produced smolts could be readily transported by barge from nearby Verona on the Sacramento River. They could also be released directly to the nearby Sacramento River or trucked to the Bay. In any event, the rice-field-reared smolts should reach the ocean about a month earlier and at a larger size than their hatchery-reared counterparts, which should lead to a marked survival advantage.
  • What if such a program is too successful? This would be a great problem to have, for once. Too many hatchery fish could jeopardize the genetic viability of the population. If that becomes a problem, such a program (or the overall hatchery program) could be scaled back. But until we reach that day, floodplain rearing of hatchery fry is a more natural and more effective tool for the recovery toolbox than more conventional hatchery practices.
  • What about landowners? Many rice field land owners and managers are fully supportive and are committed to implementing such a program.
  • What about stakeholders and resource agencies? Such a program has yet to be implemented on a large scale to test if it can meet its objectives. There is a natural reluctance on the part of agencies to commit endangered salmon resources to something unproven like this. Pilot studies to date have proven the concept is viable. An appropriate next step is a large-scale contribution study involving several hundred thousand or more fry, in sufficient number to assess potential contribution to the population.

Juvenile Salmon Survival in the Delta

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At its November 2016 Bay-Delta Science Conference, the Delta Science Program addressed salmon survival in the Delta..

The focus of this post is:

PART 1: EFFECTS OF WATER PROJECT OPERATIONS ON JUVENILE SALMON SURVIVAL IN THE DELTA: LITERATURE AND DATA REVIEW. Presenter: Dr. Rebecca Buchanan, Research Scientist with the University of Washington.

The presentation was summarized in Mavens Notebook. Some of the findings are provided with comment below.

“While water export operations contribute to salmonid mortality by way of direct mortality at facilities, this does not account for the majority of the mortality of salmon in the Delta; and the contribution of various stressors to the high mortality is unknown.”

Comment: the contribution of low flows and associated predation and high water temperatures are known, as are effects of hindering migrations of salmon both upstream and downstream. The finding does not take into account salvage inefficiency, especially from Clifton Court Forebay pre-salvage loss, and loss in the south Delta from diverting these fish from their migration routes.

“There’s been some moderate evidence of a positive association between exports and survival through the Delta, based on Delta and ocean recoveries of wire tag data.”

Comment: There is no such evidence. The association is simply between high natural production and/or high hatchery releases on the one hand, and high salvage rates on the other.

“The E:I ratio is found to be useful in a stage-structured life cycle model by Cunningham; they did not find it to be useful for other runs of fish, however,” she said. “Newman and Rice found a small effect, but it was not statistically significant for fall run using code wire tag data.”

Comment: the E:I ratio does not reflect the role of the individual factors in the presence of the other. For example, the low-export/low-inflow scenario is a far different than a high-export/higher-inflow scenario with the same E:I ratio.

“Our primary finding was that salmon survival in the South Delta is low, which is not a big surprise; we knew it was low, but what was somewhat surprising is just how low it is and how consistently low it has been, especially for the San Joaquin fall run chinook”.

Comment: The low survival through the Delta has long been known from tag studies and low run size resulting from dry years, especially in the San Joaquin watershed. Low flows have long been associated with poor habitat conditions and high salvage losses in the Delta.

“Insufficient data on survival in Delta for steelhead, Sacramento River Chinook (all runs).”

Comment: There is a tremendous amount of data on the role of the Delta in the overall production of salmon in the Central Valley. Much of the analyzed effects points to droughts, low reservoir releases, low river flows, low Delta inflows and outflows, and direct and indirect effects of Delta exports. There is sufficient information to support and warrant OMR (exports restrictions) from fall through spring in NMFS’s biological opinion. There is also sufficient information to show that the restrictions do work, an analysis that was not conducted in the study.

“The tag studies that we have available to us represent only part of the life histories in populations that use the Delta, smelt-sized hatchery fish, so we’re missing the smaller fish and we’re missing the wild fish”.

Comment: This is true. Tagging/release of springtime fall run smolts represents a limited fall run life history group forced to navigate the Delta later than they would in the wild. At minimum, a majority of emigrants would naturally leave earlier.

“I haven’t been talking about mechanisms that might explain indirect effects of water project operations on mortality in the Delta, but we did identify some possible mechanisms, and we didn’t find much research on that, so there’s a need for some work there.”

Comment: Indirect effects include water temperature effects, flow effects, habitat effects (e.g., location of X2), predators, etc. There has been much research on these effects, including substantial research on salmon.

“Formal analysis of relationships between inflow, exports, I:E and survival is incomplete for existing data, especially on the San Joaquin.”

Comment: Formal analyses have been conducted over the past half century. All these analyses have led to the same conclusion: salmon survival is low when through-Delta flows are low, when exports are high, and when salmon salvage is high.

“Even when we have those analyses done, there will still be some constraints on our understanding. One, all of the observations that we have are in the presence of the management operations, which is understandable, but it does make it difficult to assess their effectiveness because we’re lacking control and we’re lacking variability in the conditions; without that variability, it’s very difficult to identify a relationship. We also don’t have very many observations at higher levels of exports or inflow. The low overall survival makes it difficult to detect changes in survival because of low effect of sample sizes and the high uncertainty in the results.”

Comment: Again, the available information and analyses are extensive. The range of observed conditions is wide. The range of survival and recruitment into the populations is also wide. These statements are little more than excuses offered to sustain additional decades of the present review process that is reluctant to state conclusions and even more reluctant to take appropriate management action. There has been minimal analysis that highlights the beneficial effects of actions required in the 2009/11 Biological Opinion. The requirements of the Biological Opinion led to significant reductions in winter exports. These reductions have had a marked positive effect on the survival of salmon through the Delta.

New Winter Run Salmon Science

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The November 2016 Science Conference had a series of presentations on the latest Sacramento River winter run Chinook (SRWRC) salmon science. Some conclusions from the presentations with my comments follow:

  1. “Recent modeling advances reviewed here give deeper insight into the interacting causes of SRWRC’s vulnerability to extinction and add further support to the need for the high-priority actions identified in the SRWRC recovery plan.” Models show the continuing risk posed by the existence of just one spawning run, downstream of Shasta. The NMFS Recovery Plan prescribes a Battle Creek population and an above-Shasta population. Progress toward both has been slow.
  2. “Winter run chinook salmon have gone through several major droughts in 1977-76, 1988-92, and 2013-2016 where environmental conditions were extremely poor. With each new drought, new insights are realized and additional levels of management actions are taken, or proposed using an ever-increasing science based knowledge base.” Over the years, there have been major actions to improve the condition of winter run salmon downstream of Shasta: (1) a temperature control tower at Shasta Dam, (2) removal of the Red Bluff Diversion Dam, (3) screening of major Sacramento River water diversions, (4) the addition of a winter run hatchery, and (5) restrictions on winter exports from the Delta. All of these actions have certainly helped. However, the continuing drawdown of Shasta Reservoir during dry years leads to loss of the cold-water pool and to low water releases. These conditions undermine spawning, egg incubation, rearing, emigration survival, and thus limit subsequent adult spawner returns. Better water management below Shasta is essential for winter run salmon recovery.
  3. “Lessons from the ongoing drought have highlighted the potential benefits of improved forecasting capabilities of temperature dynamics above, within, and below Shasta Reservoir for better management of cold-water resources.” The lesson learned is that agencies cannot stretch water deliveries to the limit without jeopardizing short- and long-term water supplies and salmon habitat conditions. Poor forecasting tools have not helped. Improved monitoring has helped. But in the end, it has been risk-taking that has undermined the winter run salmon population. Chief among the risks have been flow and temperature regimes at or worse than the known tolerance of the salmon.
  4. “We conclude that descriptive models of thermal tolerance can drastically underestimate species responses to climate change and that simple mechanistic models can explain substantial variation in the thermal tolerance of species.” In other words, reliance on the tolerances of eggs and embryo salmon as observed in the laboratory fails to take into account nuances in the river habitats of salmon. Such reliance underestimates the effects of management actions. “New science” will lead to more conservative prescriptions for protecting salmon in the future, with corresponding impacts to water supply.
  5. “Infection by the myxozoan parasites, Ceratonova (previously Ceratomyxa) shasta and Parvicapsula minibicornis, has been observed in all Sacramento River adult runs, and juvenile fall and winter-run Chinook. In 2014, infections were lethal for over half of the spring out-migrants sampled from the lower river. In fall of 2015, sentinel juvenile salmon, held above Red Bluff diversion dam, incurred a high prevalence of severe infection.” Another consequence of very low river flows in fall and winter of drought years is the prevalence of disease, which reduces survival of rearing and out-migrating salmon. This may be the most significant new science, because it could lead to more protective water quality standards in the Sacramento River downstream of Shasta.
  6. “For salmon in a natural system increased river flow from rainstorms is the environmental cue that causes synchronous mass out-migration of juveniles.” When there are natural flow pulses in the Sacramento River system, there is the obvious need to mimic those pulses with corresponding flow releases from Shasta and Keswick dams. Otherwise, the 10-mile tailwater immediately downstream of Keswick will not have a stimulus flow to match that of un-dammed tributaries further downstream (e.g., Battle Creek).1
  7. “Non-natal habitats that could be identified were the Mt. Lassen tributaries (used by 56%, 19%, and 15% of all non-natal rearing fish from escapement years 2007-2009), the American River (22%, 40%, and 38%), and the Delta (11%, 36%, and 32%). The time period spent within the non-natal habitats ranged from approximately 2 to 16 weeks. These results suggest the extent of WRCS juvenile rearing habitat is likely under sampled and that non-natal habitats are potentially contributing significantly to the WRCS spawning population. Thus, we believe protecting and restoring,non-natal rearing habitats can play an important role in recovering the winter-run Chinook salmon population.” It has been long known that Chinook salmon use non-natal tributaries in the Central Valley for rearing. What is new is the understanding of the extent of this life history pattern. Winter run are known to start their emigration in the fall and spend much of the winter in the lower River and upper estuary before migrating to the Bay and ocean in late winter. The 2 to 16 weeks spent in lower tributaries and other floodplain habitats can double the weight of smolts and greatly increase their survival potential upon reaching the ocean. This research is likely to result in more emphasis on habitat restoration in the lower tributaries.
  8. “Ultimately, the productivity of the shelf ecosystem is tied to the survival and growth of the out-migrating salmon…. Larger out-migrating individuals, when faced with an unproductive ecosystem, have a greater likelihood of survival.” Survival of young salmon is tied to freshwater conditions that promote growth: habitat. food availability, water temperature, and flows.

San Joaquin Salmon Population Status – End of 2016

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Recently, I wrote about the fall Chinook salmon runs on the San Joaquin River and its three major tributaries over the past six years.  Salmon counts in San Joaquin tributaries showed an increase in returning adults in 2012-2015 compared to the devastating returns in 2007-2009.  This increase occurred despite the five-year (2012-2016) drought in the San Joaquin watershed.  The number of spawners in 2012-2015 was still well below the returns in the eighties and nineties that corresponded to wet water year sequences.  See Figure 1.

A close look at recruitment per spawner in the population over the past 40 years (Figure 2) provides clear evidence that recruitment suffers in years with dry winter-springs or dry falls.  That relationship overwhelms the background relationship between spawners and recruits three years later.

  1. Recruitment is significantly depressed in drier years compared to wetter years. The major contributing factor is likely poor survival in winter-spring of juveniles in their first year.
  2. Recruitment is severely depressed for year classes rearing in critical years and returning as adults two years later in critical years (e.g., 88, 89).
  3. Recruitment can be depressed for year classes with good winter-spring juvenile rearing conditions but poor conditions when adults return (e.g., 05, 06).
  4. Recruitment can be enhanced for year classes with poor winter-spring young rearing conditions but very good fall conditions for adults returning (e.g., 81).
  5. Recruitment was enhanced in recent years likely as a consequence of increased flow requirements since 2009 (e.g., 09-13).
  6. There is an underlying positive spawner/recruit relationship, but it is overwhelmed by the effect on recruitment of flow-related habitat conditions.
  7. Poor ocean conditions in 2005-2006 likely contributed to poor recruitment.

Figure 1. Chinook salmon runs in the San Joaquin River as comprised by its three spawning tributaries from 1975-2015. Data source: CDFW.

Figure 2. Recruits per spawners relationship ((log10X)-2) for San Joaquin River fall run Chinook salmon 1976-2015. The year shown is the year that the salmon were rearing as juveniles in the rivers in their first year of life. (For example: year 13 represents the progeny of the fall 2012 spawn; these juveniles in 2013 would have spawned as 3-year-old adults in 2015). Red years are critical and dry water years. Blue years are wet water years. Green years are normal water years. Red circles represent years when fall conditions during spawning would have reduced recruitment (for example: year 13 red circle indicates poor fall conditions during the fall of 2015). Blue circles represent years when fall conditions were good when recruits returned. (For example: year 81 has blue circle because 1983 fall conditions were good/wet year). Note that year 14 is as yet unavailable for inclusion in the dataset because run counts for fall 2016 are not yet available.

Annual Runs in the Back Yard

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Last week, the annual arrival of cedar waxwings hit my back yard near Sacramento. Each January, these magnificent birds fill my small back yard by the hundreds to feast for several days on the fermented fruit of three tall grape trees. The birds eat nearly every grape, likely a ton of fruit hanging from the branches. In several days the birds are gone, not to return for another year. I often wonder how important my little backyard piece of habitat is for this population of Cedar Waxwings, and how much of their winter energy comes from this small crop of fruit.

The birds remind me of another annual backyard run, the Cook Inlet Coho and Chinook salmon near Anchorage, Alaska, where I lived for three years in the mid-1980s. A large run of Coho showed up right on time each year at the end of summer in a creek that was literally in my back yard. Only kids were allowed to fish the city’s creeks for salmon, so I taught the neighborhood’s boys, including my 12-year-old son, how to catch and release the Coho. For a week or two, they could catch five or so bright ten-pounders in an hour or two a day. Me, I canoed down a tidal creek on the Kenai Peninsula side of the inlet and camp for a weekend to fish the fresh Coho run entering from the Inlet. I built a blind right on the creek within sight of the inlet. I could see the white backs of dozens of Beluga whales herding and feeding on the incoming salmon just a few dozen yards off the creek mouth. At night, the Coho approached the light of my Coleman lantern, even allowing a brief pet or two on my part, while maintaining steady and wary eye contact.

In the spring (late May), I often hitched a plane ride across the inlet (10 minutes and $40) to fish the spring Chinook run for a weekend of 24-hour daylight. At low tide, the small rivers were over 30-ft below the tule-lined channel. At high tide, the channel filled to the tules, along with seemingly bank-to-bank 30-lb spring-run salmon that obligingly hit any lure I put in front of them. This annual rush of spring Chinook lasted for a week or two before the fish moved upstream to await their late summer spawn.

Today, thirty years later, things are not so good. After 30 years of increasingly intense subsistence, personal use,1 sport, and commercial fishing pressure, and most importantly severe ecological drought, the salmon runs have sharply declined. No doubt global warming has hit Alaska worse than other parts of North America, with high temperatures and low precipitation.2

Many of the streams are now closed to fishing. Where open, the annual bag limit of Chinook is only one fish per year. The Cook Inlet Beluga that once numbered in the thousands are down to several hundred and were listed as endangered in 2008. This decline occurred despite the fact that much of the habitat remains virtually pristine and untouched by man, with little influence of hatcheries. Global warming, overfishing, natural cycles, or ocean conditions: no one knows the cause for sure. Regardless, Alaska’s fish agencies must now manage its fisheries very conservatively with intensive adaptive management science. If you asked these agencies, they would say they had already been doing that for decades. They would also admit they learned a hard lesson. For more on their situation see:
http://www.adfg.alaska.gov/index.cfm?adfg=wildlifenews.view_article&articles_id=516 .

  1. Each state resident family could use a gillnet in the Inlet to catch 50 salmon per year for “personal use”. ↩
  2. https://nccwsc.usgs.gov/content/ecological-drought-alaska ↩