Spring-Run Chinook Salmon in the Western United States : Status, Trends, Conservation and Reintroduction Efforts (hosted by AFS)

ROOM: Atlantis, Grand Ballroom 2
Spring-run Chinook salmon once persisted across the Pacific coast in great numbers. However, mining activities and the construction of large dams without fish passage have eliminated access to almost all their historical spawning habitat. Additionally, climate change, over- or illegal harvest, habitat degradation (e.g. barriers construction, watershed logging, water diversions, and water pollution), hatchery management, and introduction of non-native predators and disease have negatively affected these fish. As an example, California Central Valley (CCV) is home to spring-run Chinook salmon populations that were once a major component of the anadromous fish runs and occupied the headwaters of all major CCV river systems where natural barriers were absent. As a consequence of habitat degradation, only 4 self-sustaining natural populations remain of the 19 historical populations of CCV spring-run Chinook salmon (i.e. Butte, Mill, Deer and Battle Creeks). Similar situations in spring-run Chinook Salmon populations are common across the Pacific coast (e.g. Klamath River Basin and Columbia River Basin) and the decline of numerous Evolutionarily Significant Units have been documented in multiple systems, each with a unique situation. The goal of this session is to discuss trends, status, conservation, habitat restoration and re-introduction efforts of spring-run Chinook Salmon populations in Western US rivers. The session will start with an overview of the current status of spring-run Chinook Salmon that will set the stage for detailed presentations on the ecology, conservation biology, and adaptive management of spring-run Chinook Salmon populations used to inform and to guide their recovery.

8:00AM Spring Chinook Response to 21st Century Fish Passage Infrastructure
  Garth Wyatt, Nick Ackerman, Margaret David, Dan Cramer, Tim Shibahara
Spring Chinook Response to 21st Century Fish Passage Infrastructure in the Upper Clackamas River Basin Garth Wyatt, Nick Ackerman, Margaret David, Dan Cramer, Tim Shibahara Portland General Electric, Westside Hydro, Estacada, OR 97023 Portland General Electric (PGE) operates a 3 dam 123-MW hydro-complex (Project) on the Clackamas River with dams ranging in physical height from 14-63 meters (FERC 2195). Associated facilities either built and/or improved within the Project area relevant to this analysis are 1) new River Mill adult fish ladder, 2) 14 m3/s River Mill surface collector, 3) 28 m3/s North Fork floating surface collector, 4) 11.4 km juvenile fish bypass pipeline, 5) juvenile sampling facility, 6) adult fish sorting facility 7) spillway exclusion net, 8) and a suite of habitat improvement/minimum flow increases. Topics of interest included in this presentation are: 1. Adult run timing advancements and effect on spawning distribution. 2. Expansion of juvenile life history strategies collected and emigration timing following infrastructure improvement. 3. Apparent juvenile collection efficiency increase effect on recruits per spawner analysis. 4. Adult return trends of Clackamas spring Chinook relative to regional conspecifics after infrastructure improvement. 5. Observed reductions in spring Chinook pre-spawn mortality following migratory corridor improvements.
8:20AM Demographics of a Rebounding Wild Chinook Salmon Population in the East Fork Salmon River, Idaho.
  Eric Stark, Brian Ayers
Wild Chinook Salmon (Oncorhynchus tshawytscha) adult productivity measures were collected in the East Fork Salmon River (EFSR, Idaho) during 2014-2014. Fish were captured at an adult trap, fin tissue was collected for parentage genetic analyses, and temporally intensive and spatially extensive spawner and carcass surveys were conducted. Adult returns to the trap have varied from 0-548 fish per year, with an extended period of low returns during 1994-2003. However, during 2004-2014 adult returns increased dramatically, averaging 190 adults annually, with more than 200 adults trapped six of the last seven years. Adults were comprised primarily of age-4 fish (68.1%), and were highly female biased (31.3%). Parentage-based estimates of reproductive success (RS) found brood years 2006-2008 produced an average of 3.2 adult returns per spawning female parent. Estimates of total spawner abundance in the Upper Salmon River Major Population Group (MPG) also show an increase in productivity of the EFSR population relative to other populations. The number of recruits/female was highly correlated with SARs of wild Upper Salmon River Chinook. The EFSR remains a highly productive tributary for wild Chinook salmon in the Upper Salmon River MPG, but specific attributes influencing this productivity remain unknown.
8:40AM The Application of Parentage-Based Tagging Improves Abundance Estimates for ESA-Listed Wild Adult Chinook Salmon and Steelhead in the Snake River Basin
  John Hargrove, Carlos Camacho, William C. Schrader, John Powell, Thomas Delomas, Jon E. Hess, Shawn R. Narum, Matthew Campbell
Parentage-based tagging (PBT) is a non-lethal tagging method that uses the genetic profiles of a set of parents to genetically tag all resulting offspring. In hatchery supplemented fish populations PBT affords the opportunity to identify the age and stock of origin for hatchery fish sampled at large by assigning them back to parental baselines. Chinook Salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) in the Snake River basin are classified as threatened under the Endangered Species Act and are subject to extensive supplementation efforts. To date, PBT technology has been used to monitor harvest and manage associated hatchery broodstock. We show that results from PBT can also improve the accuracy of abundance estimates of wild-origin adult Chinook Salmon and steelhead in the Snake River Basin. Whereas historical abundance estimates have relied upon the use of physical to quantify returns of hatchery and wild origin individuals, PBT techniques identified that between 2013 – 2017, an average of 20.4% of Chinook Salmon and 9.4% steelhead identified as wild based on phenotype were actually of hatchery origin. Therefore, PBT is a valuable tool to improve abundance estimates and to reduce potential bias in run-reconstruction and viability assessment efforts.
9:00AM Downstream Rearing Chinook Salmon in the Upper John Day River
  Michael Scheu, Guillermo R. Giannico, Ian Tattam
Juvenile spring Chinook salmon typically remain in headwater reaches until their second spring, a life history known as natal reach rearing (NRR). However, timing of juvenile movement from natal reach to estuary varies. In the John Day River, some juvenile Chinook salmon move downstream during their first spring, yet do not reach the Columbia River until their second spring, a life history known as downstream rearing (DSR). Spring conditions are favorable for salmon but summer water temperatures are inhospitable, and some fish seek thermal refuge in tributaries. We investigated summer tributary distribution in 2016 and compared summer growth rates of DSR and NRR fish in 2017. Results indicate that a minority of DSR fish move into lower reaches of small tributaries or long distances up larger tributaries in the summer. We found that spring size is greater in DSR than NRR fish, but mean summer growth rate is near zero for DSR fish holding in tributaries and much higher for NRR fish through the summer. DSR Chinook salmon have the potential to make significant contributions to abundances of out-migrating smolts and returning adults, however their negligible summer growth reduces their initial size advantage and summer conditions may impair their survival.
9:20AM Examining the Differences in Juvenile Rearing Strategies and Survival Rates between the Last Remaining Populations of Wild Spring-Run Chinook Salmon in California’s Central Valley
  Jeremy J. Notch, Flora Cordoleani, Matt Johnson
Spring-run Chinook salmon were once a major component of California’s Central Valley salmon stocks, with over two million adults returning annually to spawn. Today, wild populations are severely depressed and persist in only three tributaries to the Sacramento River: Mill, Deer and Butte Creek. Butte Creek consistently supports the largest return of spring-run Chinook salmon by an order of magnitude. Research suggests that the success of these fish may be attributed to the productive rearing habitat available in the Butte Sink and Sutter Bypass. Conversely, juvenile spring-run from Mill and Deer Creek have access to less productive rearing habitat within each tributary and the mainstem Sacramento River, which may negatively influence juvenile survival rates. In order to compare differences in growth rates, residence time, and outmigration survival between these populations, we gathered data through a variety of methods. We utilized acoustic telemetry to examine smolt outmigration survival rates, mark-recapture to measure juvenile growth rates and residence time, and adult otolith microchemistry to infer the life-history strategies exhibited by juveniles during their outmigration to the ocean. Together, this data has significant implications for management and conservation efforts of threatened populations of spring-run Chinook salmon in California’s Central Valley.
09:40AM Break
1:10PM A Multistage Gompertz Life Cycle Model Applied to Threatened Salmon
  Richard A. Hinrichsen, Charles Paulsen
Because the Gompertz model, like the Ricker model, may be fit using linear least squares, we analyzed its properties as a multistage stock-recruitment model. We found that if a life cycle model is a sequence of Gompertz stock and recruitment curves at each life stage, then the entire life cycle is also a Gompertz stock-recruitment model. This is similar to the well-known result for the Beverton-Holt stock-recruitment model. The Gompertz model is guaranteed to yield least squares estimates and therefore, can offer a distinct advantage over the Beverton-Holt model, which cannot be fit using linear regression and may not yield valid maximum likelihood estimates. We illustrate the use of this modeling framework by applying it to Snake River Spring/Summer Chinook Salmon. Past work by others on these populations has usually assumed that parr-to-adult survival is density-independent. However, we found that this assumption is incorrect: when we applied a two-stage Gompertz model to these populations, we found that density dependence also occurs at the parr-to-adult stage. This suggests that previous life cycle modeling has been overly optimistic about the benefits of survival rate increases in the hydrosystem and elsewhere to improve the viability of salmon populations threatened with high extinction risk.
1:30PM Habitat and Climate Factors Affecting Juvenile Spring Chinook Salmon Recruitment and Life-History Expression in an Endangered Population
  Mark H Sorel, Andrew R Murdoch, Eric R. Buhle, Richard W. Zabel, Sarah Converse
Juvenile Chinook salmon from the endangered spring run in the interior Columbia River rear in freshwater for an entire year, and their survival during this time is thought to limit population growth and recovery. To inform management of juvenile rearing habitat, we developed models of the abundance of juvenile migrants from natal streams, grouped by life-history strategy, in the Wenatchee River Basin. Data were drawn from juvenile captures at three migrant traps operated in 1997–2018. To estimate the number of daily juvenile migrants, we developed a time-series model that accounted for imperfect detection of fish and temporal autocorrelation in fish movements. The total number of migrants in a year from each stream was taken as the sum of all daily migrants, and life-history strategies were differentiated based on migration date and size at migration. The stock-recruit model accounts for density-dependent survival of juveniles as a function of adult abundance estimated from redd surveys, habitat characteristics (e.g., geomorphic indices of habitat quantity), and climate conditions (e.g., discharge) that differ among streams and years. Models of juvenile-recruit abundance can be used to project recruitment under scenarios of habitat restoration, hatchery supplementation, climate change, and in natal reaches without observation effort.
1:50PM Population Viability of Snake River Spring/Summer Chinook Salmon Under Climate Change Scenarios Based on Life Cycle Modelling
  Lisa Crozier, Richard W. Zabel, Brian J. Burke, Brandon Chasco
The spring Chinook salmon life history is strongly linked to physical conditions in their freshwater and ocean environments. Spring Chinook salmon, especially “stream-type” populations, spend a relatively long time in freshwater compared with other Pacific salmon, so they are highly exposed to climate change in these habitats. Climate impacts accumulate over the entire life cycle, and therefore life cycle models are needed to fully account for individual life stage effects. We developed a life cycle model for 9 populations of Snake River spring/summer Chinook salmon that tests population viability under climate change scenarios, where climate affects every stage of the life cycle. We compared population viability under a stationary climate, continuation of historical trends in climate, as well as scenarios from numerous Global Climate Models forced with low to high CO2 emissions. We also explored uncertainty across 4 hydrological models. We found that all populations showed steep declines in response to climate change. Variation across populations stemmed from population-specific sensitivities to changes in freshwater temperature and flow, and local carrying capacities. Our results indicate that improvements to freshwater conditions will be essential to mitigate for a rapidly changing ocean to maintain this iconic, keystone species in the western U.S.
2:10PM Thermal Exposure of Chinook Salmon throughout Their Freshwater Life History
  Alyssa FitzGerald, Sara John, Travis Apgar, Benjamin Martin
Temperature is the primary abiotic factor that influences the spatial distribution, daily and long-term survival, and evolutionary trajectory of ectotherms. We examined freshwater temperature exposure for 25 populations of Chinook salmon, a species that is economically important but declining. We first expanded a pre-existing spatial stream network model to predict mean monthly temperature for >380,000 river kilometers in the western U.S. Stream temperature modelling showed high predictive capabilities (r2 = 0.925; prediction error ~1°C). Stream temperatures were then joined to 52,261 empirical observations to examine temperature exposure of every population throughout their freshwater life history. Spring-runs were generally more thermally stressed than fall-runs due to warmer temperatures experienced during holding and incubation. We next examined the thermal suitability of ~56,000 km that were historically accessible for spring-run but are currently blocked by dams. Spring-run populations above dams would experience cooler temperatures in the summer and fall, reducing thermal stress. If thermally stressed spring-run populations are pushed further above their thermal tolerances, they will likely continue to decline unless 1) habitat is opened up above dams, 2) more cold water is released below dams during holding, or 3) spring-run adapt a later migration timing and shorten their holding period.
2:30PM Dam Removal, Increased Stream Flow, and Habitat Restoration for Spring Chinook in Clear Creek and Battle Creek
  Matthew R. Brown
Active restoration of spring-run Chinook Salmon in Clear Creek and Battle Creek in the Northern Central Valley of California started in the 1990s. Adult population estimates increased until 2013 and then decreased. Actions such as increased stream flow, habitat improvement, and dam removal have improved habitat conditions, potentially leading to the apparent increase in populations. Subsequent declines may be attributed to fire, drought, warm water temperatures, and operations of the Central Valley Project and other hydropower facilities. Recent catastrophic fires have degraded habitat in these and other spring Chinook streams by filling in holding and spawning habitat with fine sediment, smothering redds with ash, and eliminating streamside vegetation due to increased flooding and erosion. Juveniles produced per redd decreased after these fire impacts. Adaptive management and monitoring have been effective in improving dam operations and habitat restoration. To estimate populations and evaluate restoration effectiveness, we use adult counting and segregation weirs, video and sonar imaging, snorkel- and kayak-based stream surveys, rotary screw traps, direct observation of juvenile habitat use, habitat mapping, IFIM, sediment monitoring, and geomorphic studies. Restoration success is also highly dependent on watershed conditions downstream in the Sacramento River, California Bay-Delta, and ocean.
2:50PM Refreshment Break
3:20PM Mismatching Phenotype and Genotype; Resolving the Source of Recolonization By Threatened Chinook Salmon from the California Central Valley
  Neil Thompson, Christian Smith, Kieslana Wing, Matt Brown, John Carlos Garza
Spring-run Chinook Salmon have experienced large declines in abundance due to dams and other factors. Restoration efforts include habitat improvement and using captively reared fish for supplementation. Fish exhibiting spring-run timing have colonized newly available habitat in Clear Creek, but genetic stock identification (GSI) analysis indicated that many of them were fall-run (not ESA listed), or hybrid fish. We used sequences of a genome region (RoSA) that strongly influences ecotypic variation in Chinook Salmon to resolve the mismatching phenotype and genetic stock id results. We also identified the population of origin for colonizing individuals and assessed whether assortative mating among populations had occurred. No single population was identified in colonizers of Clear Creek and no evidence for assortative mating was present. RoSA genotype results showed that individuals exhibiting spring-run timing uniformly harbored the early-run haplotypes although they assigned to fall-run with GSI. These contrasting genetic signals indicate that some colonists to Clear Creek were from the admixed Feather River stock. We conclude that the use of functional genetic variants can improve our ability to inform management of salmon species, and that one of the major habitat improvement projects targeting the threatened California Central Valley spring-run appears to have been successful.
3:40PM The Genetic Basis of Adult Migration Type in Chinook and Applications for Conservation
  Tasha Thompson
Recent research revealed that variation at a single genetic locus is strongly associated with adult migration type (spring-run and fall-run) in Chinook salmon. Here, we consider how this finding can be used to inform conservation and restoration actions. First, we review the discovery of this locus and the development of diagnostic markers for migration type. Next, using theoretical models from the Rogue River as well as empirical evidence from the Klamath River, we explore whether fall-run populations act as reservoirs of spring-run alleles in the event that spring Chinook are extirpated. Finally, we discuss how the genetic and evolutionary basis of spring migration can be directly applied to inform conservation and restoration tactics.
4:00PM The Status of Central Valley Spring-Run Chinook Salmon in the San Joaquin River
  Hilary Glenn
Historically, Central Valley (CV) spring-run Chinook salmon (Oncorhynchus tshawytscha) occurred in the headwaters of all major river systems in the CV where natural barriers to migration were absent. Large dams have eliminated access to almost all historical CV spring-run Chinook salmon spawning and holding habitat. Before construction of Friant Dam, nearly 50,000 adults were counted annually in the San Joaquin River (Fry 1961); likely making the San Joaquin River population the largest spring-run Chinook salmon population in the state. By the 1940’s, however, the San Joaquin River population was effectively extirpated, with only small remnants of the run persisting through the 1950s in the Merced River (Yoshiyama et al. 1998). Current causes for concern for the long-term viability of the CV spring-run Chinook salmon ESU include: high pre-spawn and egg mortality during the 2012 to 2015 drought, poor juvenile survival, poor ocean conditions, a high level of straying of Feather River Fish Hatchery spring-run, and the recent declines of the self-sustaining populations. The San Joaquin River Restoration Program is currently reintroducing CV spring-run Chinook salmon back into the San Joaquin River. This presentation will provided an overview of that effort and associated juvenile monitoring.
4:20PM Testing the Effects of Temperature and Feeding Regime on Precocious Maturation of Spring-Run Chinook Salmon
  Stephen Winsor
Salmonid populations of the San Joaquin River (SJR) have been in decline for decades, making essential hatchery practices that combine conservation strategies with targeted research to optimize reintroduction success. Conservation-style hatcheries promote practices that maximize long-term success of the reintroduced population while minimizing impacts to the health and longevity of existing wild populations. Hatchery populations generally exhibit a higher incidence of early maturation (or “precocity”) in produced males than in natural populations. This issue can potentially skew sex ratios for a particular year class having impacts on the wild population’s genetics, and resulting in a decrease of returning adults. However, optimal practices as they pertain to temperature and feeding regimes have yet to be established to lower the incidence of precocity in hatchery reared male spring-run Chinook Salmon (Oncorhynchus tschawytscha). To further assess this, we propose exposing fertilized salmon eggs to two temperature regimes as two subgroups of high and low feeding regimes upon post-exogenous feeding. Fertilized eggs from the same female will be used for each treatment level to control for genetic variation. Optimizing Chinook salmon rearing techniques is critical, not only to lessen the incidence of precocity and identify the causal parameters, but also to maximize successful reintroduction.
4:40PM Disentangling Patterns of Survival and Route Selection for Juvenile Spring-Run Chinook Salmon in the San Joaquin River
  Gabriel P. Singer, Colby Hause, Leah Mellinger, Matthew Pagel, Nann A. Fangue, Andrew Rypel
Spring-run Chinook Salmon are in a prolonged state of decline in California’s Central Valley, especially in the San Joaquin River where the ESU was extirpated. Ecosystem restoration and reintroductions are ongoing, but much information remains lacking. From 2017-2019, we implanted annually 700 juvenile Chinook Salmon with miniaturized acoustic transmitters and tracked survival and emigration from restored river reaches to the ocean. We developed a multinomial mark-recapture model to estimate reach-specific survival, routing through the Sacramento-San Joaquin Delta, and detection probabilities at acoustic receivers. Results suggest survivorship increases alongside overall river discharge. Additionally, the current strategy of constructing a rock barrier to prevent fish from entering the Old River route when discharge is low may not provide survival benefits, and ironically may force fish to transit a poor survivorship route. In 2019, we enhanced our telemetry surveys with high-speed environmental sampling through the riverine portion of the migratory route, and also added targeted physiological investigations. Our goal is to develop a more holistic understanding of spatiotemporal drivers of juvenile Chinook Salmon mortality in the San Joaquin River to facilitate conservation and management.
5:00PM Status Update on North Yuba River Reintroduction Efforts
  Jonathan Ambrose
Reintroduction of imperiled species into historical habitats is a frequently used conservation tool for many terrestrial and avian species, however it is less commonly used for at-risk fish species (including anadromous salmonids during their freshwater lifestage), particularly in California. NOAA Fisheries has determined that reintroduction of Central Valley spring-run Chinook salmon to historical habitats is a necessary action to conserve and recover these iconic species. In California’s Central Valley, most rivers feature high-head dams just above the valley floor. Every one of these dams lack fish passage facilities, thus preventing salmon and steelhead from accessing high quality spawning, holding and rearing habitats found at higher elevations. The consequence of this loss of access is that the overall viability of spring-run Chinook salmon has been compromised and these species are now listed under the Endangered Species Act. In the Pacific Northwest, unlike California, reintroduction above high-head dams is an ongoing fisheries management practice. California is finally in the beginning stages of trying to catch up to Oregon and Washington by initiating fish passage projects into currently inaccessible habitats including into the upper North Yuba River. I will describe the status of this project, some of the challenges, and potential engineering solutions.

Organizers: Flora Cordoleani
Supported by: AFS Fish Habitat Section

Location: Atlantis Hotel Date: September 30, 2019 Time: 8:00 am - 5:20 pm