Newly published paper: Using Bayesian hierarchical models to estimate coho salmon escapement to a river with limited data

The first chapter of my doctoral dissertation was recently published in the Canadian Journal of Fisheries and Aquatic Sciences. The article entitled Coho salmon escapement and trends in migration timing to a data-poor river: estimates from a Bayesian hierarchical model has recently been uploaded to the CJFAS website in publication format.

As fisheries management agencies consider shifting towards more ecosystem based approaches to managing fisheries, they need to manage species which have historically garnered limited interest from fishers and researchers. As such, there is generally limited information on the basic ecology of these species in the systems which are being managed. In the Chignik salmon fishery on the Alaska Peninsula, fisheries management and harvest has historically focused on sockeye salmon. The system also supports a population of coho salmon, but they are not managed or directly targeted for harvest due to low economic value and logistic factors. However, previous research (Ruggerone and Rogers 1992) has estimated that juvenile coho salmon consume over half of the emerging sockeye salmon fry in the rearing lakes annually, presenting a potential predation bottleneck to the productivity of the sockeye salmon fishery. Therefore, there is increasing interest in managing the coho salmon population for increased harvest in order to reduce this predation pressure on sockeye salmon.

As there has been limited interest in coho salmon historically, there are limited data available to estimate the numbers of coho salmon returning to the system each year. Sockeye salmon are enumerated at a seasonal weir. However, due to a later spawning migration time, coho salmon are just starting to return to the system when the weir is removed for the season. Therefore, only the beginning of the coho salmon run is counted. In this paper, co-author Daniel Schindler (UW) and I used a Bayesian hierarchical modeling approach to estimate the number of adult coho salmon returning to the system in years for which limited data are available. The Bayesian hierarchical model structure assumes that there is a river-level mean escapement date, migration duration, and escapement size, and that the peak escapement date, migration duration, and escapement size in any given year are drawn from a distribution around these river-level means. This allows the model to use years with more escapement data to inform years with less data available. Our estimates of escapement were more precise in years for which more daily escapement counts were available, and less precise when fewer data were available, relying more heavily on the historical mean values than the few observations in those years. The Bayesian hierarchical model structure also provides estimates of uncertainty around the annual escapement estimates.

Additionally, we examined the trends in peak escapement timing over time and in relation to broad-scale environmental conditions. We found that coho salmon escapement is negatively correlated with PDO index, being earlier in positive PDO years, and that it is getting later over time. However, the significance of these trends depends on the assumptions made about the shape of the spawning migration arrival timing. If we assume normally distributed arrival timing, only the relationship with PDO was significant. If we assume a gamma distributed arrival timing with a long descending limb, only the relationship with time is significant.

Overall, our results have implications for the management of any future coho salmon fishery that may be implemented. The escapement estimates allow for the calculation of escapement goals, under either single-species or multi-species management frameworks. Further, knowing the productivity of the coho salmon populations allows us to simulate the fishery dynamics under different harvest scenarios, as well as under different environmental and economic conditions. Such simulations are important to provide stakeholders with knowledge about the viability of alternative harvest strategies for their fishery. The relationships of peak escapement timing with time and environmental conditions can aid managers and fishers with in-season decisions about when to allow fishing and when the run has likely peaked. Finally, the precision of our annual escapement estimates (or lack thereof in data poor years) highlights the importance of monitoring data if coho salmon populations are to be effectively managed.


Walsworth TE and Schindler DE (In press) Coho salmon escapement and trends in migration timing to a data-poor river: estimates from a Bayesian hierarchical model. Canadian Journal of Fisheries and Aquatic Sciences. Accepted July 25, 2015. DOI: 10.1139/cjfas-2014-0554.


Newly published paper: Ecological niche models to predict effects of restoration activities along a desert river corridor

Species conservation efforts are often limited by funding for restoration activities, and time in the face of decreasing populations. Therefore, it is critical that restoration activities be prioritized such that the greatest benefit to target species and communities can be achieved. In a paper recently published in Transactions of the American Fisheries Society, co-author Phaedra Budy (Utah State University) and I describe a modeling effort to predict where different restoration activities would have the greatest benefit for imperiled native species in the San Rafael River (Utah).

Flannelmouth sucker, bluehead sucker, and roundtail chub are three imperiled species native to the Colorado River Basin. Populations of each of these species have declined dramatically in the last century in the face of habitat and flow alteration, and invasive species establishment. The states of the upper Colorado River Basin have signed agreements to conserve these three species, but in the face of numerous widespread threats, management agencies need to know where they should focus management and restoration efforts.

In this paper, we fit random forest models biotic and abiotic variables measured at sampling locations to determine the factors most limiting to each of the native species. We then used data from a longitudinal habitat survey of the lower 64 km of river to predict the effect of habitat restoration and non-native species removals at different locations along the San Rafael River. Expanding areas of high quality habitat was predicted to result in greater benefits for the native species than improving isolated patches of habitat. Additionally, the greatest benefit to the native species occurred when non-native species were removed to below about 10% of their current abundance. Non-native species present sources of predation and competition to the native species, and as such can limit the number of native species a habitat unit could support. In fact, our models predicted that habitat restoration without non-native species removals could reduce native species abundances in certain reaches, likely due to increased non-native species following habitat restoration.

Overall, this study highlighted the importance of considering both biotic and abiotic drivers of abundance and persistence of threatened species. Only considering abiotic drivers can lead to unexpected and even negative restoration results, wasting limited time, money, and opportunity. Additionally, river-scale ecological niche models can describe systems at the scale at which endemic species interact with their environment, and can allow for managers to obtain spatially-explicit information at the scale at which restoration activities will occur. Further, we recognize and discuss the importance of restoring the processes that shape river ecosystems (e.g., natural flow regime) in order to ensure the long-term success of any restoration strategy.

Timothy E. Walsworth & Phaedra Budy (2015) Integrating Nonnative Species in Niche Models to Prioritize Native Fish Restoration Activity Locations along a Desert River Corridor, Transactions of the American Fisheries Society, 144:4, 667-681

Diverse juvenile life-history behaviors

Sockeye salmon demonstrate extraordinarily diverse life-history strategies, with individuals balancing trade-offs in growth and reproductive opportunity with risks of predation and competition throughout their life-cycle.  This diversity is widely appreciated at the scale of years, with different populations spending more or less time in freshwater and saltwater before spawning.  However,  life-history diversity within single populations has been less well studied.


Our paper examining the diversity of juvenile life-history behaviors within a single population of sockeye salmon has recently been published in Ecology of Freshwater Fish.  We examined the life-history behaviors of adult sockeye salmon that had survived to spawn in the Alec River.  Otoliths (ear bones) provide a chronological record of an individual’s age, growth, and the environmental conditions to which it was exposed.  We examined the microchemical signatures of the otolith to determine how much growth was accumulated in the different rearing lakes of the Chignik River watershed.

Black Lake, in the upper watershed, is a shallow, warm and highly productive lake that supports rapid growth for juvenile sockeye salmon.  All sockeye salmon juveniles that rear in Black Lake eventually migrate downstream to Chignik Lake, a deep, colder and less productive lake that also supports different populations of sockeye salmon from the lower watershed.  Previous research found that earlier migrants to Chignik Lake were smaller, and in poorer condition, suggesting that these individuals would be less likely to survive to reproduction.  However, our analyses determined that Black Lake contributed to only about half of the juvenile freshwater growth on average for this population, and that 47% of individuals accumulated at least half of their juvenile growth in Chignik Lake or Chignik Lagoon.  Additionally, we detected an unexpected life-history behavior in which juveniles from the upper watershed move downstream quickly to the estuarine Chignik Lagoon and rear in brackish to saltwater for the summer prior to migrating back upriver to freshwater to overwinter.

Overall, the analysis revealed the broad diversity of life-history behaviors that contribute to a single spawning population of sockeye salmon.  In certain environmental conditions, one of the strategies may be more successful than the others, but it may fare less well under alternative environmental conditions.  The presence of these diverse viable life-history behaviors may buffer the population against extreme poor conditions in any single rearing environment.

Walsworth TE, Schindler DE, Griffiths JR, Zimmerman C (2014) Diverse juvenile life-history behaviors contribute to the spawning stock of an anadromous fish population. Ecology of Freshwater Fish. DOI: 10.1111/eff.12135