Assessing portfolios of actions for winter-run salmon in the Sacramento Valley

by Francisco Bellido Leiva, Robert Lusardi and Jay Lund 

We may be entering a time when more mechanistic understanding can be used to estimate effects of habitats and flows on fish populations and health, and help design ecosystem restoration efforts.

An integrated portfolio approach to protecting and restoring winter-run salmon would begin with a model estimating the effectiveness of a set of restoration actions on juvenile salmon out-migrating populations. The recently-published Winter-Run Habitat-based Population model (WRHAP) does just this. 

A summary of this model is presented in this blog and the accompanying video. This work was   motivated by the absence or misrepresentation of important juvenile rearing habitats (Phillis et al. 2018) in existing modeling efforts.

Video summary of paper on modeling winter-run salmon life-cycle in the Sacramento Valley (9 minutes)

WRHAP’s conceptual structure allows analysis of the effects of rearing history and alternative habitat and flow availability on juvenile growth and out-migration success. Table 1 and Figure 1 illustrate outputs from this analysis, which identified intermittent off-channel and floodplain habitats as those providing enhanced rearing conditions, following reported parameter values (Sommer et al. 2001; Limm and Marchetti 2009). The model suggests that these off-mainstem habitats contributed substantially to total out-migration biomass (Figure 1), despite their limited spatiotemporal availability throughout the Central Valley (Table 1). Larger, healthier juveniles are also thought to improve initial ocean survival (Woodson et al. 2013).  This suggests off-channel habitats may also enhance early marine-stage survival of winter-run Chinook.

The model found that the greatest fry-to-smolt mortalities occurred during brood years with low flow conditions and sparse alternative habitats (e.g., brood years 2001, 2006 and 2014), suggesting that off-mainstem habitats are crucial to out-migration success. Actively managing such habitats during a drought or low flow periods may be critical to the long-term recovery efforts for winter-run Chinook salmon populations.

Out-migrants1,132,364100% (21.9%)45.1%33.9%17.5%
Biomass [kg]19,30341.3%19.9%9.9%28.9%
Avg. Rearing Time [days]16778.1%11.2%3.3%7.4%
Table 1: Proportion of simulated juveniles that used each available rearing habitat at any life stage and proportion of the total biomass generated within them. Parenthetic value is percentage of simulated juveniles rearing only in the mainstem (from Bellido-Leiva et al 2021).
Figure 1: Model-estimated out-migrating biomass and fraction of growth for each available rearing habitat. Note large and varying fractions from off-mainstem habitats, especially in successful years (from Bellido-Leiva et al 2021).

The WHRAP habitat-flow-population model is an initial step to understanding the relative value of managing new and existing habitats to sustain winter-run Chinook salmon. Information from analysis of model outputs illustrates the model’s potential to assist in decision-making for this endemic and federally endangered fish.

For water resource management, links between water operations and Sacramento Valley environmental conditions (i.e., flow and temperature regimes that define habitat availability and quality) can help define environmental flows that support specific salmonid life stages and estimate the effectiveness of proposed combinations of restoration policies or alternatives on federally listed populations.

The next focus of this work is to employ this population model to explore optimized portfolios of habitat restoration actions and their relative effects on winter-run Chinook (Figure 2). As such, additional modules are being developed to better simulate expected changes in winter-run abundance over several generations for each proposed restoration action and the combined effect of multiple restoration alternatives (denoted as WRHAP-Sea).  

Figure 2: Conceptual framework embedding WRHAP into an optimization algorithm to define optimized portfolios of habitat/water management actions to recover the winter-run Chinook salmon ESU.

The paper upon which this blog is based also is available as a 9-minute video at:

Francisco Bellido Leiva is a PhD Candidate in Environmental Engineering at the University of California – Davis.  Robert Lusardi is an Adjunct Assistant Professor in the Wildlife, Fish, and Conservation Biology at the University of California – Davis.  Jay Lund is a Professor of Civil and Environmental Engineering at the University of California – Davis. The authors thank CalTrout, especially Jacob Katz and Jacob Montgomery, for providing valuable input during model development and sharing helpful datasets.

Further reading

Bellido-Leiva, F., Lusardi, R.A., and Lund, J.R. (2021), “Modeling the effect of habitat availability and quality on endangered winter-run Chinook salmon (Oncorhynchus tshawystscha) production in the Sacramento Valley,” Ecological Modelling, Vol. 447, May 2021.  9-minute video version:

Limm, M. P. and Marchetti, M. P. (2009), ‘Juvenile Chinook salmon (Oncorhynchus tshawytscha) growth in off-channel and main-channel habitats on the Sacramento River, CA using otolith increment widths’, Environmental Biology of Fishes 85(2), 141–151.

Phillis, C. C., Sturrock, A. M., Johnson, R. C. and Weber, P. K. (2018), ‘Endangered winter-run Chinook salmon rely on diverse rearing habitats in a highly altered landscape’, Biological Conservation 217, 358–362.

Sommer, T. R., Nobriga, M. L., Harrell, W. C., Batham, W. and Kimmerer, W. J. (2001), ‘Floodplain rearing of juvenile Chinook salmon: Evidence of enhanced growth and survival’, Canadian Journal of Fisheries and Aquatic Sciences 58(2), 325–333.

Woodson, L. E., Wells, B. K., Weber, P. K., MacFarlane, R. B., Whitman, G. E., and Johnson, R. C. (2013), ‘Size, growth, and origin-dependent mortality of juvenile Chinook salmon Oncorhynchus tshawytscha during early ocean residence’, Marine Ecology Progress Series, 487, 163-175.

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