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New Winter Run Salmon Science

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.