Category Archives: Fish (general)

2017 Klamath Chinook Run – “Disaster or Catastrophe?”

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The Klamath River Chinook salmon fall run is expected to be a record low in 2017.1 Predictions are near or below the record low run in 1992. These record low runs followed extended droughts from 2013 to 2015 and 1990 to 1992, respectively.

A very low run in 2016 prompted the Yurok Tribal Council to cancel its commercial fishing season to protect future fish populations. The 2016 salmon allocation was the second lowest on record, and failed to provide each tribal member a salmon. The Tribe did not serve fish at the annual Klamath Salmon Festival for the first time in the event’s 54-year history. In January 2017, the federal government issued a disaster declaration for the 2016 Yurok Tribe fishery.2

An April 6, 2017 article in the Eureka Times Standard stated:

  • Tribal fishery scientists such as Michael Belchik of the Yurok Tribe stated the low return of spawners is the result of several severe years of drought conditions and river management practices, which caused the waters to warm and become hot beds for toxic algae and deadly parasites. In 2014 and 2015, up to 90 percent of juvenile Chinook salmon on the Klamath River are estimated to have died from an intestinal parasite, believed to be a major cause for this year’s low run, as were poor ocean conditions…. “All these things together conspire to create a real catastrophe for fisheries,” Karuk Tribe Natural Resources Policy Advisor Craig Tucker said.
  • Organizations see dam removal and changes to the federal government’s management of the river as being key solutions to the underlying causes of this year’s low salmon return.” “The solution for this problem is to remove the Klamath dams now,” Pacific Coast Federation of Fishermen’s Association Executive Director Noah Oppenheim said.

A Yubanet article described the expected ancillary effect on the whole California coastal fishery:

The disaster stems from a crash of Klamath salmon stocks, but in order to protect the few Klamath fish that are in the ocean, fisheries regulators have little choice but to close or nearly close the economically valuable commercial and sport fishing seasons along the length of the Northern California and Oregon coastlines. This will impact tribal and non-tribal families alike.

CDFW stated: “Chinook that will be harvested in ocean fisheries in 2017 hatched two to four years ago, and were deeply affected by poor river conditions driven by California’s recent drought.”

A UC Davis study placed some of the blame on hatcheries. “My results suggest that hatcheries’ harm to wild salmonids spans the entire Klamath River basin. For fall Chinook salmon, the decline is concurrent with increases in hatchery returns – a trend that could lead to a homogenous population of hatchery-reared Chinook”.

Having been involved in the Klamath River for 40 years, I provide some of my own insights in this post. In follow-up posts, I will take a closer look at the Scott and Shasta rivers, the two main salmon tributaries of the upper Klamath that contribute substantially to the overall upper Klamath salmon run.

A summary of the overall Klamath salmon run escapement numbers or spawner estimates for the past 40 years is shown in Figure 1. The spawning numbers in 2016 were low, yet this drop came only two and four years after near record runs. Contributions for all six upper Klamath subcomponents in 2016 were down substantially from 2014. Predictions of a poor run in 2017 come from the low number of two-year-old “jack” salmon in the 2016 spawning run.

The question is: why did the strong run in 2014 produce the expected record low run in 2017? And why did the strong run in 2012 produce the weak run in 2015? And on the flip-side, why were the runs in 2012 and 2014 so strong, especially given they occurred during the recent multiyear drought?

A close look at the spawner-recruit relationship (Figure 2), how recruits are related to the number of spawners three years earlier, provides further insight into factors controlling long-term recruitment.

  1. The spawner-recruit relationship is weak at best, reflecting the fact that estimates might be poor and/or that other factors are more important than just the number of spawners. The 1995 recovery after the record low 1992 run provides compelling evidence that survival and recovery can be strong even from the weakest of runs (with strong hatchery support – see hatchery component for 1995 in Figure 1). Unfortunately, 2017 appears to suggest that strong runs can produce very weak returns three years later if other factors such as drought are dominant.
  2. The population crashes (2016, 2004, 1992) occurred after multi-year droughts (Figure 3). Multiyear effects compound changes to sediment, pathogens, and water quality, the suggested causes of these crashes.
  3. Population expansions (2012-2014, 2007-2009, 2000-2003, 1995-1997, 1985-1988) occur after a series of wetter years.
  4. There may be some underlying effect of floods, as indicated by the poor run in 1999, a consequence of the New Year 1997 flood that washed out the fall 1996 spawn.
  5. The poor run in 2016 and the expected record low run in 2017, in addition to the effects of the 2013-2015 drought, may have been affected by poor ocean conditions, as was believed to be the case in the poorer than expected 2004-2006 runs.
  6. Several factors potentially affect production or survival per spawner: conditions during the spawning run (flows, water temperature, disease, upstream passage hinderances, etc), first year rearing and emigration conditions (flows, water temperature, predators, prey, disease, toxins, etc), and ocean conditions. It is likely that flows throughout the water year (Figure 4) have some effect on survival of the affected or subsequent brood years.
  7. The contribution of the Shasta River appears to have increased in recent years, likely as a result of the Nature Conservancy’s efforts at Big Springs (more on this in an upcoming post).

Overall, the droughts of 1990-1992 and 2013-2015 (Figure 3) were likely the single most important factors in the upper Klamath Chinook salmon population dynamics. The role of the Irongate Hatchery contributions seems relatively stable and a likely important contributor to recoveries after drought. I was unable to determine the contribution of hatchery salmon to the other components of the run, but it is likely a large factor in the Bogus Creek and upper Klamath elements. It is possibly a lesser factor in the Salmon, Scott, and Shasta river elements, which speaks to the importance of these potentially “wild” runs.

In closing, some thoughts on potential solutions:

  1. Knowing a good run was occurring in drought year 2014, managers could have done more to protect the spawners, eggs-embryos, and subsequent rearing-emigrating juveniles with better flows and water quality. Perhaps the recent federal court decision may help ensure future protections. In poor water supply years like 1990-1992 and 2013-2015 (Figures 3 and 4), water managers simply must provide protections for salmon.
  2. Future removal of the four dams may help reduce the adverse multiyear effect of droughts on disease and water quality and may provide additional spawning and rearing habitat.
  3. Much more could be done to increase run components from the Scott and Shasta rivers (more on this in upcoming posts).
  4. The hatchery program is long overdue for reform and upgrade. The program should shift from production to conservation of fall-run and spring-run Chinook, Coho and steelhead.
  5. These and other suggestions are discussed in a prior post.

Figure 1. Chinook salmon escapement estimates to the upper Klamath River including Irongate Hatchery, Bogus Creek, Scott River, Salmon River, Shasta River, and Klamath River mainstem below Irongate Dam. The preliminary prognosis for fall 2017 total escapement is 11,000. Source: http://www.pcouncil.org/salmon/background/ document-library/#EnvironmentalAssessmentsalLib

Figure 2. Spawner-Recruit relationship for upper Klamath River fall-run Chinook salmon population. The number is the transformed (log10X – 3.5) escapement estimate for the fall of that year as shown in Figure 1. The color represents winter-spring hydrology conditions in the Klamath River two years earlier when this brood year was rearing in river habitats. Red is dry, green is intermediate, and blue is wet (from Figure 3). Circle color represents late summer water year conditions in numbered year. For example: year 92 represents the recruits in fall 1992 from brood-year 1989 spawn that reared in 1990 winter-spring (red dry year); the red circle represents dry conditions in late summer of that water year (1992). Note that the spawning run for 2002, the year the large die-off of adult salmon occurred in the lower river due to low flow and high water temperatures, likely contributed to the poor returns (recruits) in 2004 and 2005.

Figure 3. Average annual discharge by water year (10/1-9/30) of Klamath River as measured at Link River near Klamath Falls, Oregon. Data source: https://waterdata.usgs.gov/nwis/ annual?site_no=11507500&agency_cd=USGS&por_11507500_113138= 545477,00060,113138,1962,2017&year_type= W&referred_module=sw&format=rdb

Figure 4. Monthly average flow (cfs) in Klamath River below Irongate Dam in selected years. Year 2011 was a wetter year. Year 1992 was a critically dry year. Years 2002, 2005, and 2013 were dry years. Year 2016 was an intermediate water year. Source: www.waterdata.usgs.gov.

Reclamation Requests Higher Smelt Take Limits

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The State and Federal water projects requested on March 16, 2017 a higher take limit for Delta smelt under their endangered species permits for the south Delta pumping plants. Under the present pattern, it appears that the take limit set in the 2008 Delta Smelt Biological Opinion may soon be exceeded. The request states:

“Although mechanisms underlying recent salvage events are unknown, some possibilities include relatively high turbidity throughout the Delta over an extended period of time leading to increased movement; broad distribution and/or high survivorship in the South Delta and connecting areas; and further migration movements due to natural seasonal influences and prevailing flow and environmental conditions. … Reclamation is not currently proposing any export restrictions, as we believe this would have little functional effect given high Delta outflow and optimal Delta smelt habitat conditions.”

In response, the US Fish and Wildlife Service stated it would review the situation and respond as soon as possible.

Acting in its role of advising the US Fish and Wildlife Service, the Smelt Working Group concluded on March 14:

“As the SWG is directed by the Biological Opinion to make OMR flow recommendations as indicated in these RPA’s, the SWG has no scope, within the adaptive range of the BiOp, to make recommendations to conserve the species. Should the Service like to suggest additional conservation tools for the SWG to evaluate (that are not indicated in the Biological Opinion), the group will meet to evaluate and make a recommendation.”

Comments:

  1. The presence of spawning adult Delta smelt, their concentration in the south Delta, and their presence in salvage collections are not at all surprising.1
  2. A broad distribution of adult smelt in the Delta is also normal.
  3. There is no evidence of “high survivorship.” The catch in the Kodiak Trawl Survey (Figure 1) and other surveys remains near record lows.
  4. High Delta outflow and Old-Middle River daily average flows do not necessarily equate to low risk. Figure 2 shows that conditions in late March carry a risk of adult smelt migrating into the south Delta on flood tides.

Recommendation. Since the Smelt Working Group did not provide a recommendation, I offer the following advice:

Wet year winter losses of adult spawning smelt have always been a concern. This is the reason for the take limits. Relaxing these limits this year is unwise and unnecessary. The adult Delta smelt are now in the peak of their annual spawning run. The state and federal projects have already exported an abundant water supply this winter, and the projects should limit exports at the peak of the Delta smelt spawning season. With the State Water Project pumps shut down for repairs, a reduction of Central Valley Project exports from the present 3800 cfs to 1200 cfs could provide a real benefit. There is all the more reason to do this considering the severely depressed state of the smelt population and the possibility of some recovery in this wet year.

Figure 1. Adult Delta Smelt Catch in the Kodiak Trawl Survey in winter months of 2002-2017.

Figure 2. Late March peak flood tide flows (cfs) in the Delta. Positive downstream flood-tide flows continue in the Sacramento River and San Joaquin River channels. The Delta Cross Channel remains closed, and very strong flood-tide upstream flows thus continue into the central and south Delta. Exports have been only 3800 cfs because the State Project pumps at Clifton Court were shut down for repairs to the forebay intake. A rise in take limits would allow exports to reach 10,000 cfs or higher once forebay repairs are completed. Data source: USGS.

Yuba River Chinook Salmon – Status

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A March 16, 2017 Yubanet article by South Yuba Citizens League (SYRCL) noted that the 2016 fall run of salmon for the Yuba River has dropped to the low level observed since 2007 and 2008 (Figure 1):

“The low salmon run size for the Yuba River appears to be part of another regional salmon collapse.”

Comment: the 2007-2008 Central Valley salmon collapse was attributed to several potential causes: poor ocean conditions for spawn/brood years 2004 and 2005, poor 2004-2005 Bay–Delta conditions, and lack of hatchery pen acclimation in the Bay.1 Most likely that collapse was related to drier river conditions from years 2001-2005 and critically dry years in 2007-2008, after wet conditions in years 1995-2000 resulted in high population levels. The new 2016 low is likely a consequence of the drought years 2012-2015, and specifically of poor conditions in the Yuba River.

The article also noted a high proportion of hatchery fish in the Yuba salmon run, and cited a Fishbio blog post for the following:

“It is time to decide whether we want to base our salmon production goals on sheer numbers of genetically similar hatchery fish, or on diverse, wild fish naturally supported by our local rivers.”

Comment: Since the Yuba River is the largest tributary of the lower Feather River, one would expect it to receive a portion of the wild and hatchery salmon production of the lower Feather. To define this as “straying,” given that the genetic stocks are identical, is debatable. What is unusual is that the Yuba run is made up of predominantly Feather River hatchery fish, thus indicating poor natural production from the Yuba itself, particularly in drier years. There is something about the Yuba that leads to poor natural salmon production at least during or after drought periods.

Having worked and fished on the Yuba over the past two decades, I thought I would share my insights in this post. Starting with the stock-recruitment (S-R) (recruits per spawner) relationship, I have found that, like other Central Valley salmon rivers, the Yuba has a telling and highly statistically significant S-R relationship (Figure 2) that supports the following findings:

  1. There is a basic underlying positive S-R relationship – lower spawner levels produce less recruits and visa-versa.
  2. There is a strong effect of water year conditions – wet years enhance production and dry years have generally poor production.
  3. Poor runs often come in dry years with low summer flows and high water temperatures (1988-1989, 1992, 2007-2009, 2015-2016), which may affect adult survival or the number of adults that seek the Yuba from the Feather River. Good runs occur in wet years that have higher summer flows and lower water temperatures (1982, 1996-1998). (See Figures 3 and 4.)
  4. Poor runs are also related to poor winter-spring rearing and emigrating conditions two years earlier in the Yuba and/or Bay-Delta (1989, 1992, 2009, 2015-2016). Stronger runs occurred when early rearing and emigrating conditions were good (e.g., 1986, 1995-2000).
  5. Poor runs in some years may be related to poor Feather hatchery smolt survival or poor early conditions for ocean rearing.
  6. Poor early ocean rearing conditions and lack of hatchery smolt pen acclimation in the Bay may have contributed to poor runs (e.g., 2006-2008).

In summary, there are a lot of factors that potentially affect the salmon run in the Yuba River. It is difficult to evaluate the importance of the various factors, but my bet is on two factors that stand out:

  • Higher winter-spring flows help carry young to and through the Delta, provide habitat and protection from predators, and initiate and speed migration.
  • Higher August through October flows (Figure 3): (a) attract adult salmon, (b) improve passage habitat, and (c) keep water temperatures down (Figure 4).

Figure 1. Fall-run Chinook salmon escapement estimates for Yuba River 1975-2016. Source: CDFW GrandTab.

Figure 2. Spawner – Recruit relationship for Yuba River fall run salmon. Year is recruit year escapement; for example, “16” is escapement in fall 2016 from 2013 spawn. Bold red years are critical water years. Non-bold red years are dry water years. Bold green years are above normal water years. Non-bold green years are below normal water years. Blue years are wet years. Circles represent winter-spring water year two-years earlier; for example, 08 blue circle represents winter-spring water year classification of “wet” in 2006 when the 08 spawners were rearing and emigrating from Yuba River. Yellow rectangle denotes years in which ocean conditions may have reduced escapement from poor ocean-rearing survival in prior years.

Figure 3. Lower Yuba River flow at Marysville in August-September period in years 2000-2016. Source: CDEC. Of note: lowest flows were in 2014-2016, and surprisingly in 2006.

Figure 4. Water temperature in the lower Yuba River at Marysville in 2015 and 2016. Red line is water temperature detrimental to adult salmon survival, passage, and egg viability. Yellow line denotes high stress level above 65°F. Green line is safe level below which adult survival and egg viability are good. Note: August 2015 water temperatures reached above 70°F; September-October 2015 water temperatures reached 65-70°F range. Source: Yuba River Accord M&E Field Update.

Efforts to Understand Delta Smelt Salvage

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This post addresses more from the November 2016 Bay-Delta Science Conference. In this latest review I focus on:

“Part 2: Collaborative Adaptive Management Team (CAMT) Investigations: Using New Modeling Approaches to Understand Delta Smelt State Salvage Patterns at the State Water Project and Central Valley Project”.1

First, some context:

“The Collaborative Adaptive Management Team, comprised of high level managers and senior scientists, is the group that works underneath the CSAMP2 policy group. The CAMT was established [in 2013] to work with a sense of urgency to develop a robust science and adaptive management program to inform both the implementation of the current BiOps and the development of revised BiOps.”

Delta Smelt Salvage

“CAMT examined historical (1993-2015) salvage data to determine what factors affected Delta Smelt salvage at the State Water Project (SWP) and Central Valley Project (CVP) fish facilities. The objective was to determine if new approaches could be applied to the data to yield new insights about the factors that explain Delta Smelt salvage patterns within and across years.”

Comment: First, it is surprising that CAMT would apply “new” approaches and “insights” given that so much has been studied and learned about Delta smelt salvage at the south Delta pumping plants. The salvage problem had been addressed by limiting exports in winter and spring with OMR limits3 and active management by the Smelt Working Group (SWG), an effort that is both highly sophisticated and effective. The working group’s measures have markedly reduced salvage losses but have failed to curb the population decline. The measures came far too late, and managers often did not take the SWG’s advice.

More study of salvage is not going to help in learning more about the population decline. Less than ten Delta smelt were salvaged so far this winter (compared to thousands per day historically). The study of the population decline should be focusing now on freshwater inflow, Delta outflow, and spring-to-fall habitat conditions (i.e., Low Salinity Zone and water temperatures), and on the indirect effects of Delta exports. It would be far more effective to showcase the SWG’s actions and other actions required by the biological opinion and by water quality standards, It would also be more consequential for the CAMT to evaluate the consequences of weakening these standards in drought years.

“Mr. Grimaldo said that one of the initial sparring matches within the CAMT team was over conceptual models.”

Comment: The CAMT analysis and conference focused on adult Delta smelt winter salvage and the modeling effort employed to understand it. Why? Because the CAMT water contractor members do not like cutting back on exports during the infrequent winter storms in dry years, when the smelt make their spawning runs. Much of a dry year’s water supply comes in infrequent winter storms. Under the conceptual model, higher exports at such times simply draw the smelt spawners into the south Delta4 to be salvaged (killed at fish screens or lost in forebay). When the spawn is in the south Delta, it also makes the annual production of larvae more vulnerable to unmonitored/unmeasured entrainment into the export pumps later in spring. The US Fish and Wildlife’s Delta Smelt Biological Opinion addresses these risks by limiting winter-spring exports. There is no doubt that until these risks are further reduced, there will be no recovery of the Delta smelt population (or other listed Delta fish). Furthermore, until protective actions are extended to Delta outflow, salinity, and water temperatures, there will be no recovery, and the conflict with water supply will remain unresolved and a perpetual problem.

“Grimaldo acknowledged that the Fall Midwater Trawl nowadays is pretty lousy for sampling Delta smelt. “We get very few,” he said. “So this problem is even worse as now we don’t even have a gear, so we don’t even have an idea what the size is coming into December.”

Comment: There is nothing wrong with the Fall Midwater Trawl Survey. It captures few smelt because there are few left. All the surveys support this conclusion (see chart below). We are doing just fine in data gathering with the Smelt Larval Survey, the 20-mm Survey, the Summer Townet Survey, the Fall Midwater Survey, and the Fish Salvage Survey.

The relationship (log-log) between the fall midwater trawl index and the subsequent summer townet survey index (year noted) is remarkably significant, especially when water-year type is taken into account. Red years are dry/critical. Green years are below/above normal. Blue years are wet.

“Grimaldo suggested that a Kodiak trawl should start in September. “We know that it catches fish better than the fall midwater trawl. I think folks just have to make the leap. I think folks are used to the Fall Midwater Trawl being this 40 year plus monitoring device, but maybe we need to switch things up, because we know from other work that Ken Newman and Randy Baxter are doing that this Kodiak is a better gear for sampling Delta smelt, so why not go for it. This could potentially allow for salvage losses to be evaluated in the context of a recruit responder model,” he said. “At least you could have an idea going into the salvage season what your salvage actually means.”

Comment: The context that matters is that the indices and salvage are near zero and have been for several years. Yes, the highly effective Kodiak trawl would be more effective at near zero population. Do we really want to manage the population down at zero, or do we want to smelt to recover?

Final point: It is sad that we have to resort to court-directed science in the form of CSAMP/CAMT to resolve the perpetual conflict between water management and the Delta ecosystem. All the effort will be focused on how the ten smelt salvaged this year could have been reduced to five.

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.