Category Archives: Chinook Salmon

Washington State increasing hatchery salmon production Major realignment toward wild population recovery

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Washington State is increasing salmon production to help in recovery of near extinct salmon populations and orca (killer whales). A Washington state Department of Fish and Wildlife webpage describes the role of hatcheries in restoring wild salmon stocks:

In recent years, state hatcheries also have taken on an equally important role in helping to recover and conserve the state’s naturally-spawning salmon populations. Nearly all the hatcheries in the Columbia River and a number of hatcheries in Puget Sound play a role in wild fish rebuilding programs, whether by rearing juveniles prior to release or holding fish through their lifespan to ensure the survival of depressed stocks. This renewed focus on wild stock recovery represents a major realignment in hatchery operations, as WDFW, the tribes, federal government and independent scientists worked to develop a comprehensive operations strategy for hatcheries in Washington. 1

The main reform actions being taken in Washington’s program are:

  1. Marking all hatchery salmon smolts allows identifying hatchery fish by hatchery and lot group. It also allows mark-selective fisheries that require release of wild salmon.
  2. Developing salmon population-specific recommendations intended to provide scientific guidance for managing each hatchery more effectively in the future.
  3. Keeping hatchery program budgets in pace with increasing operating costs (especially utilities, fish feed and labor costs), and not forcing cutbacks in some programs.
  4. Updating aging hatchery infrastructure.
  5. Supplementing wild stocks: to maximize egg fertilization and fry survival (of wild) and thereby increase the number of “wild-type” smolts heading out to the ocean.
  6. Maintaining captive broodstocks of endangered stocks with dangerously low population levels: juveniles are maintained in a hatchery for their entire life to ensure the stock’s survival.
  7. Minimizing interaction between naturally-produced and hatchery-produced outmigrating juveniles and adult fish returning to streams to spawn where necessary.
  8. Donating surplus adult salmon from hatcheries to non-profit hunger-relief programs.
  9. Introducing hatchery carcasses or analogs back to streams to increase natural productivity to low productivity streams.

While California is slowly moving toward some of these reforms, there is resistance to others. For more information and links on California hatchery programs see http://calsport.org/fisheriesblog/?cat=5 , https://www.wildlife.ca.gov/fishing/hatcheries , http://cahatcheryreview.com , https://www.fws.gov/sfbaydelta/Fisheries/hatcheries/NoCAHatcheriesUSFWS.htm .

 

Late-Fall-Run Salmon Update Record low runs in fall 2015 and 2016

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In an April 2017 post, I related factors likely important to late-fall-run Chinook salmon in the reach of the Sacramento River downstream of Shasta Reservoir. In this post, I update that assessment with 2015 and 2016 escapement estimates and coded-wire-tag return data from Coleman Hatchery smolt releases from brood years 2008-2013.

Late-fall-run Chinook salmon escapement reached new lows in 2015 and 2016 (Figure 1). The adult returns in these two years were the product of spawning in brood years 2012 and 2013 and of early rearing conditions in winter of 2013 and 2014 (critical drought years).

Figure 1. Late-fall-run escapement 2000-2016. Escapement refers to adult run counts beginning in late fall of spawning year. For example, 2016 represents late-fall-run for water year 2017 (Oct16-Sep17). Source: CDFW Grandtab.

The low escapement in 2015 and 2016 is also reflected in the spawner-recruit relationship (Figure 2).  There is a continuing significant positive spawner-to-recruit relationship and even stronger effect of water-year type, with poorer recruitment from dry-year winter rearing conditions.

The low 2016 escapement is likely in part a consequence of a very poor return from brood year 2013 hatchery smolts (Figure 3).  Of the approximately one million smolts tagged and released in 2014 at the Coleman hatchery near Redding, less than a tenth of a percent survived to be counted in fisheries and escapement surveys.  A good survival rate would be 1 to 3 percent, as occurred for brood year 2010 (2013 run).

Hatchery and wild smolts from brood year 2013 had poor flow conditions in early winter of 2014 (Figure 4), while brood year 2010 had the best flow conditions.  There were no flow pulses to help the smolts move the 200 miles down to the Bay-Delta in January 2014.

The fact that few late-fall smolts showed up in south Delta salvage in 2014 (Figure 5), compared to higher salvage in 2013 (Figure 6), is compelling evidence that smolt survival to the Delta was very poor in 2014.

Conclusion:  To sustain the late–fall-run salmon population, higher winter flows and flow pulses are warranted in the lower Sacramento River in drier years.

Figure 2. Spawner-recruit relationship for late-fall–run salmon. Number is log10-1.5 transformed escapement (recruits) for the fall of that year. For example, year “16” represents escapement for late fall 2016, which includes spawners from early winter 2017. Spawners represent escapement from three years earlier (brood year). In the example, spawners for year 16 were the progeny of escapement in 2013. Colors represent winter rearing condition two years earlier. In the example, red “16” represents dry winter 2014. Green represents normal years two years earlier. Blue represents wet years two years earlier.

Figure 3. Hatchery smolt survival for brood years 2008-2013 based on coded-wire-tag returns.

Figure 4. January river flow at Wilkins Slough in lower Sacramento River 2009-2014. Note very low flows and lack of flow pulses in January 2014.

Figure 5. Salvage of salmon at the Delta pumps in water year 2014. Note only one late-fall tagged smolt (yellow dot), collected in March after January release.

Figure 6. Salvage of salmon at Delta pumps in water year 2013. Note many late-fall tagged smolts salvaged (yellow dots) beginning in December, coincident with flow pulses after December and January releases of hatchery smolts.

 

Fall Pulsed Flow Protections for Winter Run Salmon Not in 2017 and 2018

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It is well known that juvenile winter-run salmon migrate downstream to the Delta from their upper Sacramento River rearing area near Redding/Red Bluff with the first fall-winter flow pulses.1 Protection of this critical migration of winter-run has been recommended in recent Delta proceedings. In the WaterFix petitions process at the State Water Resources Control Board, such protection is referred to as “pulse protection.” So based on the importance of protecting winter-run during this key life-history stage, one would think such protection would have been applied in the fall of our most recent wet year 2017 and below-normal 2018. A quick check of the facts indicates otherwise.

In 2017, the initial pulse of juvenile winter-run salmon passed Red Bluff (rivermile 240) during September and October, prior to any flow pulses (Figure 1). The first major pulses of flow occurred in the latter half of November 2017. A migration spike of winter-run-sized smolts at Knights Landing screw traps (rivermile 90) did occur during the flow pulse (Figures 1 and 2). Instead of protecting these winter run as they were entering the Delta, south Delta exports were increased to take advantage of the available inflow (Figure 3). The increase occurred with the Delta Cross Channel partially open (Figure 4), increasing the risks of migrating salmon to south Delta exports. Other than a four-day pulse, Delta outflow generally declined before and after the flow pulse (Figure 5). Salinity in the lower Sacramento and San Joaquin Delta channel generally increased with the higher exports and lower outflows (Figures 6 and 7).

In 2018, the initial pulse of juvenile winter-run passed Red Bluff in September and October prior to flow pulses (Figure 7). The first major pulse of flow occurred at the end of November. A migration spike of winter-run-sized smolts at Knights Landing screw traps occurred during this flow pulse (Figures 7 and 8). Instead of protecting these juvenile winter run as they were entering the Delta, south Delta exports were increased to take advantage of the available inflow, with nearly two-thirds of the Delta inflow being exported (Figure 9).

The lack of protection is likely a consequence of the young salmon not showing up in salvage (Figure 2). For me, the high risk factors are clear.

  1. The lack of salvage simply indicates that few of the migrating salmon survive upon entering the Delta under high exports. High late-November and early-December south Delta exports are a high risk to the juvenile winter-run survival. Traditional high December exports of up to 65% of Delta inflow allowed under D1641 water quality standards are a major risk factor for winter-run salmon that must be changed.
  2. Declining flows below Keswick Dam (rivermile 300) during the fall, combined with the lack of flow pulses, are also a real concern. Juvenile salmon that pass Red Bluff (river mile 240) in September and October are sustained in low flow conditions for nearly 200 miles of modified river channel until the first rains in late November or early December. And the spawning reach directly downstream of Keswick gets no added flow even when it rains, because inflows to Shasta Reservoir are all captured.

For additional information, see agency discussions and data presentations in: http://www.westcoast.fisheries.noaa.gov/publications/Central_Valley/Water%20Operations/Delta%20Operations%20for%20Salmonids%20and%20Sturgeon/DOSS%20WY%202018/winter-run_juvenile_production_estimate__jpe__for_brood_year_2017_-_january_29__2018__1_.pdf

Figure 1. Juvenile winter-run salmon estimated passage and stream flow at Red Bluff (rivermile 240) from late summer 2017 to June 2018.

Figure 2. Lower Sacramento River screw trap collections at Knights Landing (rm 90) since August 2017 along with flow, turbidity, and water temperature. Note late November catch event during flow pulse.

Figure 3. South Delta exports in fall 2017. Note peak exports mid-November through early December – total 10,000-11,000 cfs (22,000 acre-ft per day). Chinook salvage is shown as zero.

Figure 4. Flow through Delta Cross Channel August through December 2017. Note sporadic opening late September through November 2017, and closure at end of November.

Figure 5. Delta outflow August through December 2017.

Figure 6. Salinity (EC) near Rio Vista on lower Sacramento River channel in the Delta, August through December 2017.

Figure 7. Salinity (EC) near Jersey Pt on lower San Joaquin River channel in the Delta, August through December 2017.

Figure 8. Juvenile winter-run salmon estimated passage and stream flow at Red Bluff (rm 240) from late summer 2017 to June 2018.

Figure 9. Juvenile winter-run salmon estimated passage at Knights Landing (rivermile 90) and stream flow at Wilkins Slough (rivermile 125) from late summer to fall 2018. Note early December pulse of fish, flow, and turbidity.

Figure 10. Export rates from two south Delta pumping plants (Tracy TRP and Banks HRO) summer and fall 2018.

Figure 11. Lower Sacramento River flow at Freeport (FPT, rm 55) and Delta outflow (DTO) summer and fall 2018.

Mokelumne River Salmon Update – Fall 2018

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Dan Bacher’s report on 2018 salmon returns to the Mokelumne River Hatchery provides continuing good news for the Mokelumne River salmon run.

When I last reported on the fall run of Mokelumne River salmon, I described strong runs from 2010-2016. The 2017 run was exceptionally strong (Figures 1 and 2), despite being the product of the 2013-2015 drought. This success story is in large part due to the management of the Mokelumne River Hatchery, as reported in the Bacher article. Trucking hatchery smolts to the lower San Joaquin in the western Delta near Jersey Point greatly improves survival over releases of salmon in the lower Mokelumne River.

Best returns from the spring 2015 releases were from smolts barged and released near the Golden Gate. That group of 101,000 smolts (tag code #060593) had a good return of 1.35 percent compared to 0.06-0.80 % from smolts released in the west Delta and 0.01 % released in the lower Mokelumne River. In early May 2015, soon after river and Delta smolt releases, water temperatures reached 68oF in the west Delta and 72oF in the lower Mokelumne in the central Delta, levels stressful to smolt salmon. Delta outflow in early May 2015 was critically low at ~5000 cfs. Net flow in the lower San Joaquin River in the west Delta, with the Delta Cross Channel closed, was near zero.

The returns from tag group #060593 (shown in Figure 3), which represented only about 3% of the total smolts releases from the Mokelumne Hatchery in 2015, exemplifies the kind of return pattern that can be achieved by a progressive hatchery program. The majority of the adults returning from this tag group to the Central Valley were to the hatchery (192), although a significant number strayed to the neighboring American River (82) and San Joaquin River and its tributaries (40). In previous years, the California Department of Fish and Wildlife achieved similar success barging smolts from the Feather River Fish Hatchery.1

Figure 1. Mokelumne River in-river fall Chinook returns (escapement) 1975-2017.

Figure 2. Mokelumne River hatchery fall Chinook returns (escapement) 1975-2017

Figure 3. Mokelumne River fall Chinook tag returns through 2017 from 101,000 Mokelumne River Hatchery smolts, tag group #060593, barged to and released near the Golden Gate Bridge.

Sacramento River Salmon Science

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A recent paper in the prestigious Canadian Journal of Fisheries and Aquatic Science discusses Central Valley salmon. The paper concludes: “Wild stocks in several California rivers are now dominated by hatchery fish (Barnett-Johnson et al. 2007; Johnson et al. 2012; Quiñones and Moyle 2014), potentially eroding the long-term resiliency of wild, locally adapted populations by disrupting selection for heritable traits that improve lifetime reproductive success in variable environments.”

First, wild or naturally spawning stocks or runs of fall-run Chinook salmon in Valley rivers are all dominated by hatchery salmon. Without hatcheries and straying of hatchery salmon to non-hatchery rivers (e.g., Yuba, Cosumnes, etc.), there would be almost no salmon runs of significance.

Second, there are hardly any significant locally adapted (wild) traits left to erode. River flows, water temperatures, gravel spawning beds, large woody debris, predators, and channel morphologies have become so limiting or compromising that wild salmon survival is nearly nonexistent.

Third, the “lifetime reproductive success” potential of wild fish is primarily compromised by water and fisheries management. Flows are too low, and fisheries continue harvesting much of the wild salmon production.

Fourth, the recent salmon population crashes of 2009 and 2016 are blamed by many salmon scientists on poor ocean conditions, with little regard for poor river habitat or water management as contributing factors, let alone hatcheries. By contrast, the federal Battle Creek hatchery managers knew they had to truck some of their smolt production to the Bay during the drought because of poor river conditions if they hoped for some survival and contribution to future runs.

The authors of the paper imply that hatcheries are the problem. No doubt the hatchery programs could be improved to lessen their negative effects and improve their contribution to salmon recovery. But for sure the fault is not with the hatcheries. Lack of support for hatcheries by scientists and resource agencies will dry up hatchery funding by water-user entities and make the problem worse.

The paper’s authors conclude: “There is a growing concern that salmon populations in the C[entral] V[alley] of California are becoming dependent upon hatchery supplementation, a conservation status recently identified as “mitigated extinction” Baumsteiger and Moyle 2017).” California salmon have been dependent on hatcheries for many decades. This is not a new development. Dams and diversions wiped out the wild salmon and their critical habitats, while hatcheries kept the dream going. Now scientists want to take the dream away.

Give the authors some credit for ending by saying: “Hatcheries can play a key role in the recovery of wild stocks, supplementing the fishery, and the reestablishment of natural areas, but only with cautious and appropriate management.” Despite the ambiguity, I had similar recommendations for improving hatchery programs in a recent post. 1