ArticlePublisher preview available

The effects of early sandbar formation on the abundance and ecology of coho salmon (Oncorhynchus kisutch) and steelhead trout (Oncorhynchus mykiss) in a central California coastal lagoon

Canadian Journal of Fisheries and Aquatic Sciences

February 2018
75(12):2184-2197

DOI:10.1139/cjfas-2017-0455

Authors:

Cynthia H Kern

University of California, Santa Cruz

Emerson Kanawi

Humboldt State University

Show all 5 authorsHide

We investigated how extreme drought conditions influenced the abundance, growth, movement, and seawater readiness of juvenile coho salmon (Oncorhynchus kisutch) and steelhead trout (Oncorhynchus mykiss) in a small central California coastal lagoon. In 2015, the seasonal sandbar at the mouth of Scott Creek formed over 2 months earlier than average, effectively trapping fish in the lagoon for 7 additional months (mid-May through December) before outmigration opportunities eventually resumed. Monthly mark–recapture sampling demonstrated that juvenile coho salmon and steelhead were able to persist in the lagoon during extended periods of high water temperature and low dissolved oxygen concentration. Both salmonid species exhibited similar temporal trends in abundance, growth, and Na⁺-K⁺-ATPase activity levels during lagoon residence; however, abundance and growth rates were consistently higher for steelhead. Stationary passive integrated transponder tag antenna detections revealed recurrent movement of individuals between the warm lagoon and cooler lower mainstem creek, suggesting individuals regulated key physiological processes by moving between the adjacent habitats. Our study provides new insight concerning the consequences of drought for imperiled salmonid populations and underscores the importance of life-history diversity during extreme climatic events.

Location map of the Scott Creek watershed and a detailed view of the lagoon study area (Santa Cruz County, California, USA)

…

Hydrology, sandbar dynamics, and historical migration timing of salmonids in Scott Creek, California (USA). Panel A contrasts the annual hydrograph of a wet water year (WY2011) with the drought conditions that occurred during the year of our study (WY2015). Panel B shows the historical distribution of migration timing for coho salmon (CO) and steelhead (SH) smolts and adults, averaged from 2002 to 2014. In both panels, the unshaded and light gray shaded regions together identify the period the creek mouth is typically open (241 days; 29 November – 27 July based on WY2002–WY2014), whereas dark gray shading denotes the period the sandbar is typically present and the lagoon is closed. The unshaded region, exclusively, represents the truncated period the creek mouth was open in WY2015 (165 days; 3 December – 16 May) immediately preceding this study

…

Abiotic conditions in the Scott Creek lagoon during three different environmental phases (bars atop panel A). All parameters were measured near the midpoint of the study area (∼rkm 0.4) at a depth of 0.3 m from the bottom of the lagoon, except for the surface temperature in panel A (dotted line), which was measured 0.3 m below the lagoon surface. Temperature and dissolved oxygen (DO) are depicted as lines and reflect mean daily temperature (MDT) and mean daily dissolved oxygen concentration (MDDO); shading around means reflects daily maximum and minimum values (A and B). Lagoon depth (C) and salinity (D) are from data recorded at 15 min intervals. Short breaks in the time series occurred during equipment maintenance

…

Monthly abundance estimates from the best-approximating POPAN model {(g)p(t)b(t)N*(g)} (A) and mean specific growth rates (B) for juvenile coho salmon and steelhead in the Scott Creek lagoon. Population estimates are only presented for 13 of the 14 sampling occasions because abundance cannot be estimated for the first sampling occasion when the probability of capture is time-dependent. Specific growth rates were plotted at the midpoint between sampling occasions to indicate average growth within that time interval. All point estimates are presented with 95% confidence intervals

…

The number of upstream (positive values; black bars) and downstream (negative values; gray bars) movement events exhibited by PIT-tagged coho salmon (A) and steelhead (B) at the lagoon PIT tag antenna array (∼rkm 0.6) during lagoon closure in 2015. Asterisks (*) denote the dates of lagoon sampling occasions

…

Figures - available from: Canadian Journal of Fisheries and Aquatic Sciences

This content is subject to copyright. Terms and conditions apply.

A preview of this full-text is provided by Canadian Science Publishing.

Content available from Canadian Journal of Fisheries and Aquatic Sciences

This content is subject to copyright. Terms and conditions apply.

ARTICLE

The effects of early sandbar formation on the abundance and

ecology of coho salmon (Oncorhynchus kisutch) and steelhead

trout (Oncorhynchus mykiss) in a central California coastal lagoon

Ann-Marie K. Osterback, Cynthia H. Kern, Emerson A. Kanawi, Jeffrey M. Perez, and Joseph D. Kiernan

Abstract: We investigated how extreme drought conditions inﬂuenced the abundance, growth, movement, and seawater

readiness of juvenile coho salmon (Oncorhynchus kisutch) and steelhead trout (Oncorhynchus mykiss) in a small central California

coastal lagoon. In 2015, the seasonal sandbar at the mouth of Scott Creek formed over 2 months earlier than average, effectively

trapping ﬁsh in the lagoon for 7 additional months (mid-May through December) before outmigration opportunities eventually

resumed. Monthly mark–recapture sampling demonstrated that juvenile coho salmon and steelhead were able to persist in the

lagoon during extended periods of high water temperature and low dissolved oxygen concentration. Both salmonid species

exhibited similar temporal trends in abundance, growth, and Na

-K

-ATPase activity levels during lagoon residence; however,

abundance and growth rates were consistently higher for steelhead. Stationary passive integrated transponder tag antenna

detections revealed recurrent movement of individuals between the warm lagoon and cooler lower mainstem creek, suggesting

individuals regulated key physiological processes by moving between the adjacent habitats. Our study provides new insight

concerning the consequences of drought for imperiled salmonid populations and underscores the importance of life-history

diversity during extreme climatic events.

Résumé : Nous avons étudié l’inﬂuence de conditions de sécheresse extrême sur l’abondance, la croissance, les déplacements et

la préparation à l’entrée en mer de saumons cohos (Oncorhynchus kisutch) et de truites arc-en-ciel (Oncorhynchus mykiss) juvéniles

dans une petite lagune côtière du centre de la Californie. En 2015, la barre de sable saisonnière à l’embouchure du ruisseau Scott

s’est formée plus de 2 mois plus tôt qu’à l’habitude, piégeant ainsi les poissons dans la lagune pour 7 mois supplémentaires (de

la mi-mai à la mi-décembre) avant que ne se représentent des occasions de migration vers l’extérieur. L'échantillonnage mensuel

de poissons marqués démontre que les saumons cohos et truites arc-en-ciel juvéniles étaient capables de persister dans la lagune

durant des périodes prolongées de haute température de l’eau et de faibles concentrations d’oxygène dissous. Les deux espèces

de salmonidés présentaient des tendances temporelles semblables de l’abondance, de la croissance et de l’activité de la Na

-K

ATPase durant la résidence dans la lagune, l’abondance et les taux de croissance étant toutefois uniformément plus élevés pour

les truites arc-en-ciel. Les détections avec des antennes stationnaires d’étiquettes à transpondeur intégré passif révèlent des

déplacements récurrents d’individus entre la lagune chaude et le bras principal du ruisseau plus frais, donnant à penser que les

individus régulaient des processus physiologiques clés en se déplaçant entre les habitats attenants. L'étude fournit de nouveaux

renseignements sur les conséquences de la sécheresse pour des populations de salmonidés en péril et souligne l’importance de

la diversité des cycles biologiques durant des épisodes climatiques extrêmes. [Traduit par la Rédaction]

Introduction

The impacts of hydrological drought and reduced surface ﬂows

can be especially severe for diadromous ﬁshes that require con-

nectivity among freshwater, estuarine, and marine habitats at

multiple life stages (Lake 2011;Woelﬂe-Erskine et al. 2017). In

many coastal areas worldwide, drought conditions can extend the

closure of seasonal sandbar-built estuaries (Rustomji 2007), thus

affecting the migration of ﬁsh populations to and from the ma-

rine environment (Gillanders et al. 2011) and disrupting char-

acteristic life-history patterns. In California (USA), many at-risk

populations of anadromous Paciﬁc salmon (Oncorhynchus spp.) and

steelhead trout (anadromous Oncorhynchus mykiss) must contend

with seasonal sandbars at their river mouths (Kraus et al. 2002;

Heady et al. 2014), which constrain migration opportunities for

both outmigrating juveniles and returning adults (Shapovalov

and Taft 1954). During very low water years, barrier sandbars can

form during the typical spring juvenile (smolt) outmigration pe-

riod and effectively trap substantial numbers of salmon in the

estuary or in freshwater habitat where they must persist for many

months until the onset of winter rain reconnects the creek to the

ocean (Smith 1990;Hayes et al. 2008).

While oversummer use of small sandbar-built estuaries and

seasonal lagoons has been well-documented for juvenile steel-

Received 15 October 2017. Accepted 12 February 2018.

A.-M.K. Osterback. University of California, Santa Cruz, afﬁliated with Southwest Fisheries Science Center, National Marine Fisheries Service, National

Oceanic and Atmospheric Administration, 110 McAllister Way, Santa Cruz, CA 95060, USA; University of California, Santa Cruz, Institute of Marine

Sciences, 1156 High Street, Santa Cruz, CA 95064, USA.

C.H. Kern, E.A. Kanawi, and J.M. Perez. University of California, Santa Cruz, afﬁliated with Southwest Fisheries Science Center, National Marine

Fisheries Service, National Oceanic and Atmospheric Administration, 110 McAllister Way, Santa Cruz, CA 95060, USA.

J.D. Kiernan. Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric

Administration, 110 McAllister Way, Santa Cruz, CA 95060, USA; University of California, Santa Cruz, Institute of Marine Sciences, 1156 High Street,

Santa Cruz, CA 95064, USA.

Corresponding author: Joseph D. Kiernan (email: joseph.kiernan@noaa.gov).

Copyright remains with the author(s) or their institution(s). Permission for reuse (free in most cases) can be obtained from RightsLink.

2184

Can. J. Fish. Aquat. Sci. 75: 2184–2197 (2018) dx.doi.org/10.1139/cjfas-2017-0455 Published at www.nrcresearchpress.com/cjfas on 28 February 2018.

California steelhead populations were regionally buffered and individually resistant to a severe multi-year drought

Article

Full-text available

Jul 2024

Weather extremes, such as drought, are predicted to be a strong determinant of species persistence under climate change. Yet predictions often fail to consider that variation in streamflow responses, variation in population dynamics, or adaptations to drought could buffer species against extremes. In this study, we examined the responses of eight California (USA) steelhead populations to a severe drought from 2012 to 2016. We observed that streamflows were highly synchronous across the region in all seasons and did not appear to buffer drought impacts. Population dynamics were variable across the region and did appear to buffer the region from drought impacts. Some populations had very low productivity for 4 years associated with the drought, while others had slightly below-average productivity for only 2 years. Population synchrony was associated with spring-smolt flow, temperature, and drought over time, but was not associated with winter-spawner or summer-juvenile drought, suggesting populations may be adapted to drought conditions. Our results highlight how regional buffering and adaptation can be important mechanisms against climate extremes both now and into the future.

High‐frequency and long‐term observations of eDNA from imperiled salmonids in a coastal stream: Temporal dynamics, relationships with environmental factors, and comparisons with conventional observations

Article

Full-text available

Mar 2022

A greater understanding of eDNA behavior in the environment is needed before it can be employed for ecosystem monitoring applications. The objectives of this study were to use autonomous sampling to conduct long‐term, high‐frequency monitoring of the eDNA of native salmonid species in a Californian coastal stream, describe temporal variation of eDNA on multiple scales and identify environmental factors that drive this variation, and evaluate the ability of the eDNA datasets to detect rare species and represent organismal abundance. Using high‐throughput autonomous environmental sample processors (ESPs) and qPCR, we enumerated eDNA concentrations from 674 water samples collected at subdaily intervals over 360 days at a single site. We detected eDNA from two imperiled salmonids (coho salmon Oncorhynchus kisutch and steelhead/rainbow trout O. mykiss) in most samples; O. kisutch eDNA was generally in lower concentration and more variable than O. mykiss eDNA. High‐frequency (i.e., subdaily and daily) variability in salmonid eDNA concentrations showed occasional patchiness (i.e., large differences between consecutive samples), while seasonal differences were observed consistent with the ecology of the species at this site. Salmonid eDNA concentrations were significantly associated with creek discharge, photoperiod, and whether the creek mouth was open or closed by a seasonal sandbar. The release of hatchery‐origin O. kisutch parr into the stream was associated with a significant increase in eDNA concentration for the remainder of the study. We compared eDNA signals with fish abundance data collected from traps located at the site. Fish were detected more often by eDNA than from trapping. Significant positive associations between fish abundance and eDNA concentrations were observed for O. mykiss; however, no such associations were observed for O. kisutch. This study adds to our knowledge on the occurrence and behavior of fish eDNA in lotic systems and informs future biomonitoring efforts using automated sampling technology. The objective of our study was to conduct high‐frequency autonomous sampling of salmonid eDNA in a coastal stream, elucidate the temporal patterns and environmental correlates of the eDNA signal, and compare the signal with a measure of abundance obtained from a fish trap collocated at the study site. We sampled one to three times per day for approximately one year, collecting nearly 700 samples. The eDNA signals showed high variability on short time scales and were aligned with expected salmonid seasonal trends in this ecosystem. Salmonid eDNA was significantly associated with creek discharge, photoperiod, and whether the creek mouth was open or closed by a seasonal sandbar. Comparing eDNA with fish counts from traps, we found that eDNA detected fish more often than traps but that eDNA concentrations were weakly or not at all correlated with fish abundance.

Spatiotemporal Variability in Environmental Conditions Influences the Performance and Behavior of Juvenile Steelhead in a Coastal California Lagoon

Article

Full-text available

Nov 2021

In California (USA), seasonal lagoons provide important oversummer rearing habitat for juvenile steelhead trout (anadromous Oncorhynchus mykiss ). However, key water quality parameters such as temperature and dissolved oxygen concentration can periodically approach or exceed the physiological tolerances of steelhead during the protracted dry season. A field study employing distributed temperature sensing technology, water quality monitoring, habitat mapping, and mark-recapture sampling was conducted to examine how shifting environmental conditions affected the performance and behavior of juvenile steelhead in the Scott Creek estuary/lagoon (Santa Cruz County). Abiotic conditions were driven by episodic inputs of seawater to the typically freshwater lagoon. During midsummer, the water column was vertically stratified which reduced suitable lagoon rearing habitat by approximately 40%. Nevertheless, steelhead abundance, growth, and condition factor were high during the summer and decreased in autumn following lagoon destratification and cooling. Unlike previous work, this study identified limited emigration from the lagoon to riverine habitat during the summer. Instead, juvenile steelhead exhibited crepuscular movement patterns within the lagoon, with peaks in upstream (to upper lagoon habitat) and downstream (to lower lagoon habitat) movement occurring at dawn and dusk, respectively. This study underscores that habitat complexity and connectivity are critical for juvenile steelhead production and persistence and provides insight into steelhead habitat use and behavior in seasonal lagoons.

Reduced recruitment of Chinook salmon in a leveed bar-built estuary

Article

Full-text available

Feb 2021

Estuaries are commonly touted as nurseries for salmonids, providing numerous advantages for smolts prior to ocean entry. In bar-built estuaries, sandbars form at the mouth of rivers during periods of low stream flow, closing access to the ocean and preventing outmigration. We evaluated how summer residency in a leveed bar-built estuary affects the growth, survival, and recruitment of a Chinook salmon (Oncorhynchus tshawytscha) population. We performed a mark–recapture study on outmigrants to determine juvenile estuary abundance, growth, and survival. We used returning adult scales and otoliths to determine the relative proportion of summer estuary residents in spawning adults. Juveniles in the estuary grew less after mouth closure, and ultimately summer estuary residents had lower smolt-to-adult survival and contributed disproportionately less to the spawning population than juveniles that reared in the ocean their first summer. Mouth closure may lower food availability and deteriorate estuary conditions by reducing marine prey influx and estuary circulation. This research demonstrates the complexity of estuary dynamics and function as salmonid nurseries, particularly when considering the extensive modification of estuaries.

Predicting the effects of currents on the adaptive movement of juvenile salmonids

Article

Full-text available

Jan 2022
EVOL ECOL RES

Richard Hinrichsen

Background: Anadromous salmonids present a marvellous opportunity to study animal movement, with some juveniles in the Yukon and Amur rivers travelling more than 2000 km from their natal areas to the ocean. During their freshwater residence, juvenile salmonids, regardless of river of origin or migration distance, balance the pressures of feeding, predator avoidance, and migration to survive. Questions: What are the choices of current and swimming velocities that stream-dwelling juvenile salmonids use to optimize lifetime reproductive success? How are these influenced by maximum current velocity in the stream or river that they inhabit? Mathematical methods: I developed a dynamic optimality model that treats current and swimming velocities as decision variables. The state variables are downstream river location and fish size. I solve the optimality model using optimal control theory and apply it to juvenile ocean-type Chinook salmon in the Hanford Reach, Columbia River, Washington. Results: Five fundamental behaviours or movement phases result from the optimality model: rapid upstream migration, appetitive ('foraging') upstream movement, station holding, appetitive downstream movement, and rapid downstream migration. These fundamental behaviours were not specified a priori, but emerge when optimizing lifetime reproductive success over the full range of possible behaviours. The appetitive and station holding behaviours are broadly characterized as foraging/ predator avoidance. Rapid migration is favoured over foraging/predator avoidance whenever the magnitude of the marginal value of displacement exceeds the marginal predation risk of displacement. If, during foraging/predator avoidance, the maximum current velocity rises above the swimming speed that maximizes growth, station holding is optimal; otherwise, appetitive movement, which carries greater predation risk, might be optimal. The two types of downstream movement predicted by the optimality model (appetitive movement and rapid downstream migration) describe the movements of the 'ocean-type' and 'stream-type' races of Chinook salmon populations of the Columbia River. In the Hanford Reach application, optimal movements begin with station holding, then switch to downstream appetitive movement or rapid downstream migration, depending on the maximum current velocity. Juveniles accelerate as they migrate downstream. I describe an experiment to test the influence of current velocity on foraging behaviour and a field study to characterize juvenile upstream migrations.

Contribution of warm habitat to cold‐water fisheries

Article

Full-text available

Feb 2022
CONSERV BIOL

A central tenet of landscape ecology is that mobile species depend on complementary habitats, which are insufficient in isolation, but combine to support animals through the full annual cycle. However, incorporating the dynamic needs of mobile species into conservation strategies remains a challenge, particularly in the context of climate adaptation planning. For cold‐water fishes, it is widely assumed that maximum temperatures are limiting and that summer data alone can predict refugia and population persistence. We tested these assumptions in populations of redband rainbow trout (Oncorhynchus mykiss newberrii) in an arid basin, where the dominance of hot, hyperproductive water in summer emulates threats of climate change predicted for cold‐water fish in other basins. We used telemetry to reveal seasonal patterns of movement and habitat use. Then, we compared contributions of hot and cool water to growth with empirical indicators of diet and condition (gut contents, weight–length ratios, electric phase angle, and stable isotope signatures) and a bioenergetics model. During summer, trout occurred only in cool tributaries or springs (<20 °C) and avoided Upper Klamath Lake (>25 °C). During spring and fall, ≥65% of trout migrated to the lake (5–50 km) to forage. Spring and fall growth (mean [SD] 0.58% per day [0.80%] and 0.34 per day [0.55%], respectively) compensated for a net loss of energy in cool summer refuges (–0.56% per day [0.55%]). In winter, ≥90% of trout returned to tributaries (25–150 km) to spawn. Thus, although perennially cool tributaries supported thermal refuge and spawning, foraging opportunities in the seasonally hot lake ultimately fueled these behaviors. Current approaches to climate adaptation would prioritize the tributaries for conservation but would devalue critical foraging habitat because the lake is unsuitable and unoccupied during summer. Our results empirically demonstrate that warm water can fuel cold‐water fisheries and challenge the common practice of identifying refugia based only on summer conditions.

Carmel River Fisheries Report 2021

Technical Report

Full-text available

Jun 2021

A meta‐analysis and model comparison of juvenile salmon growth across different habitat types

Article

Nov 2022

The size of an organism is an important factor for a variety of physiological and ecological processes. For fishes, larger size can increase long‐term survival and provide a population level benefit. Therefore, threatened and endangered species management often focuses on supporting high quality habitat that provides growth opportunities. There are numerous habitat characteristics that can affect growth, including food availability, temperature, and habitat complexity. Understanding how growth responds to habitat types of different quality is the first step in determining what could lead to increased growth and potentially increased individual survival. We use Bayesian techniques to determine which of the differing methods is best for modeling the effects of habitat type and temperature on growth. To apply this method, we gather data from previous studies of the growth benefits of differing habitats and temperature regimes on Chinook salmon on the Sacramento River, CA, USA. We find a consistent growth benefit of floodplain rearing across multiple studies and show that a Ratkowsky model is the best for modeling this growth data. This information can specifically help managers model and protect the endangered and threatened Chinook populations in this system and more generally understand fish growth across differing habitat types.

Preparing Aquatic Research for an Extreme Future: Call for Improved Definitions and Responsive, Multidisciplinary Approaches

Article

Full-text available

May 2022
BIOSCIENCE

Extreme events have increased in frequency globally, with a simultaneous surge in scientific interest about their ecological responses, particularly in sensitive freshwater, coastal, and marine ecosystems. We synthesized observational studies of extreme events in these aquatic ecosystems, finding that many studies do not use consistent definitions of extreme events. Furthermore, many studies do not capture ecological responses across the full spatial scale of the events. In contrast, sampling often extends across longer temporal scales than the event itself, highlighting the usefulness of long-term monitoring. Many ecological studies of extreme events measure biological responses but exclude chemical and physical responses, underscoring the need for integrative and multidisciplinary approaches. To advance extreme event research, we suggest prioritizing pre-and postevent data collection, including leveraging long-term monitoring; making intersite and cross-scale comparisons; adopting novel empirical and statistical approaches; and developing funding streams to support flexible and responsive data collection.

Predator life history and prey ontogeny limit natural selection on the major armour gene, Eda, in threespine stickleback

Article

Oct 2021

Natural selection shapes the evolution of antipredator traits in prey. However, selection in the wild depends on ecological context, including features of predator and prey populations, making field studies of selection critical to understanding how predators shape selection on prey defences. Threespine stickleback (Gasterosteus aculeatus) is a classic system to study the effects of predators on the natural selection of prey. In lakes and rivers, fish predators have been shown to impose selection against low plated adult stickleback phenotypes and genotypes. We directly measured selection by predatory salmonids on the Ectodysplasin‐A (Eda) gene in estuary stickleback from California. Despite previous studies showing a positive correlation between predator presence and frequency of the Eda “complete” allele in estuary populations, we found that Eda “low” genotypes were not significantly more frequent in salmonid predator diets. Further, we found no evidence of changes in Eda genotype frequencies across generations that would suggest directional selection driven by predators. Prior selection studies have examined the effects of large resident trout on adult stickleback. In contrast, predators in this study were juvenile anadromous salmonids, which only ate juvenile stickleback whose plate phenotypes had not fully developed. Thus, in this case, predator life history and stickleback ontogeny may preclude strong selection on stickleback armour. Our results underscore the importance of selection studies in the wild for understanding the context‐dependent nature of selection in natural populations.

Evolution of phenology in a salmonid population: a potential adaptive response to climate change

Article

Full-text available

Jun 2017

Accumulating evidence has indicated that many fish populations are responding to climate change through shifts in migration time, but genetic data identifying the role of evolution in these shifts are rare. One of the first demonstrations of evolution of migration time was produced by monitoring allozyme alleles that were experimentally manipulated to genetically mark late-migrating pink salmon (Oncorhynchus gorbuscha). Here, we extend that research by using observations of the marker alleles in fry to demonstrate that these changes in migration time were caused by directional selection against the late-migrating phenotype during the oceanic phase of the salmonid life cycle. The selective event, which appeared to be driven by early vernal warming of the nearshore marine environment and consequent decreased survival of late-migrating fry relative to early-migrating fry, decreased the late-migrating phenotype from more than 50% to approximately 10% of the total fry abundance in only one generation. These demographic changes have persisted over the subsequent 13 generations and suggest that a larger trend toward earlier migration time in this population may reflect adaptation to warming sea-surface temperatures.

Abiotic habitat thresholds for salmonid over-summer survival in intermittent streams

Article

Full-text available

Feb 2017

Intermittent streams lose surface flow during part of the year but can provide important habitat for imperiled fishes in residual pools. However, extended intermittency can drive high mortality as pool contraction decreases pool quality, and some pools dry completely. We evaluated the influence of a suite of abiotic habitat characteristics on the over-summer survival of two imperiled salmonid fishes (coho salmon Oncorhynchus kisutch; steelhead trout Oncorhynchus mykiss) at four study sites on two tributaries of Salmon Creek (Sonoma County, California, USA) from 2012 to 2014, during deepening drought conditions. Study sites spanned an intermittency gradient from continuous flow to near-dry conditions, and included alluvial and bedrock stream reaches. We estimated over-summer survival at the pool scale from fish presence–absence data based on paired early-late summer snorkel surveys. We measured pool dimensions and water quality parameters monthly (more frequently during summer dry down) and, in 2013 and 2014, recorded water quality with continuous loggers in selected pools. We performed: (1) logistic regression in a generalized linear modeling framework to identify factors limiting over-summer survival and (2) classification trees using the random forests ensemble learning method to identify abiotic thresholds for sustaining salmonids. Results suggested that different factors governed mortality of the two species. Coho salmon, which tended to survive in large, deep pools, were limited by minimum dissolved oxygen (DO) concentrations. In contrast, steelhead trout, which tended to survive in pools with large surface area, were sensitive to pool geometry and temperature. Both species persisted for weeks in large pools with low DO levels, including in pools where at least part of the water column reached sublethal or lethal levels. Our results suggest that shallow, lateral hyporheic flow may be important for maintaining DO and temperatures suitable for sustaining salmonids in isolated pools, whereas groundwater discharge originating from deeper flow paths may generate low-DO conditions that inhibit salmonid persistence. Geomorphically complex watersheds with a variety of pool geometries and high rates of lateral hyporheic exchange are those most likely to serve as “sanctuary reaches” for imperiled Pacific salmonid populations in semi-arid regions in the context of a changing climate.

SPATIAL STRUCTURE OF WATER-QUALITY IMPACTS AND FORAGING OPPORTUNITIES FOR STEELHEAD IN THE RUSSIAN RIVER ESTUARY: AN ENERGETICS PERSPECTIVE

Technical Report

Full-text available

Jan 2017

Estuaries along the California coast are recognized as critical rearing habitat for juvenile salmonids, particularly because they provide abundant feeding opportunities that support rapid growth. However, these estuaries exhibit a high degree of spatial and temporal variability in both food availability and elements of risk such as predation risk and mediocre water quality, varying greatly in response to natural seasonal changes as well as anthropogenic effects and management. Physical models—such as a quantified conceptual model (QCM) developed by UC Davis for the Russian River Estuary—can be used to predict the spatially explicit response of Estuary water quality and quantity to seasonal change and management interventions. These predictions take the form of depth-profiles of temperature, dissolved oxygen and salinity throughout the Estuary, calibrated to sonde measurements collected as part of regular monitoring. To aid in the interpretation of the outputs of such models, here we synthesize a categorical rating scheme for how water quality and spatial location in the Estuary affects rearing steelhead in terms of foraging opportunity, predation risk, and physiological impacts of water quality. We adopt a bioenergetics perspective as a conceptual framework because energy provides a unifying framework for thinking about how behavioral and physiological responses to predation risk, water quality, and foraging opportunity translate to somatic growth of rearing salmonids. However, our review and synthesis indicates that the tradeoffs posed to rearing salmonids by an estuary—among foraging opportunities and the different dimensions of waterquality impacts, for example—is multidimensional and complex. Rather than propose explicit quantitative models of behavior and physiology that capture all this complexity—which is outside our scope and in any case requires further work—for simplicity we develop a categorical (or qualitative) scheme to make sense of this complexity. It is our hope that this scheme will aid fisheries managers in interpreting the complex output of physical estuary models, and point the way toward more focused development of coupled behavioral-bioenergetics models of salmonids rearing in estuaries. Such models will need to address the spatial and temporal structure of the tradeoffs, as well as the important role of induced physiological tolerance for salinity and possibly hypoxic conditions, and its relationship to strategies for feeding, growth efficiency, and predator avoidance. For convenience the qualitative rating scheme is summarized in a short appendix at the end of the text.

Hot eats and cool creeks: juvenile Pacific salmonids use mainstem prey while in thermal refuges

Article

Full-text available

Jan 2017

Thermal refuges form important habitat for cold-water fishes in the face of rising temperatures. As fish become concentrated in refuges, food resources may become depleted. In this study, we used invertebrate drift sampling and fish density surveys to quantify potential in-refuge food limitation, temperature-sensitive radio-tagging studies to quantify thermal habitat use, and isotopic analyses to determine diet sources for juvenile Pacific salmonids using thermal refuges in California’s Klamath River. Juvenile salmonids using refuges formed by tributary junctions with the mainstem river obtained the majority (range = 47%–97%) of their diet from mainstem prey sources. Mean steelhead (Oncorhynchus mykiss) body temperatures were significantly cooler (∼3.5 °C) than diet-inferred foraging temperatures. Thus, while fish seek cooler habitat for physiological benefits, they rely primarily on mainstem prey. Moreover, consistently high densities of fish in refuges (mean = 3.5 fish·m⁻²) could lead to density-dependent food limitation. Thus, mobile consumers like fish can exploit existing heterogeneity associated with cold-water refuges by gaining thermal benefits from a food-limited cold-water habitat while deriving the majority of their prey from the warm mainstem river.

Steelhead abundance in seasonally closed estuaries estimated using mark recapture methods

Technical Report

Full-text available

Mar 2016

The Fate of Coho Salmon Nomads: The Story of an Estuarine-Rearing Strategy Promoting Resilience

Article

Full-text available

Jun 2009
ECOL SOC

K.V. Koski

The downstream movement of coho salmon nomads (age 0), conventionally considered surplus fry, has been an accepted characteristic of juvenile coho salmon for the past 40 to 50 yr. The fate of these nomads, however, was not known and they were assumed to perish in the ocean. Several studies and observations have recently provided new insights into the fate of nomads and the role of the stream-estuary ecotone and estuary in developing this life history strategy that promotes coho resilience. Chinook and sockeye salmon have developed the ocean-type life-history strategy to exploit the higher productivity of the estuarine environment and migrate to the ocean at age 0. Nomad coho can acclimate to brackish water, and survive and grow well in the stream-estuary ecotone and estuary, but instead of migrating to the ocean they return upstream into freshwater to overwinter before migrating to the ocean as smolts. Nomads may enter the estuarine environment from natal or non-natal streams, rear there throughout the summer, and then emigrate to a non-natal stream for overwintering and smolting in the spring. These estuarine and overwintering habitats have enabled coho to develop this unique nomad life history strategy that may help to ensure their resilience. Restoring estuarine habitats may be essential to the recovery of depressed populations of coho.

Missing Values in Multivariate Analysis

Article

Sep 1975

This paper presents computational results for some alternative methods of analysing multivariate data with missing values. We recommend an algorithm due to Orchard and Woodbury (1972), which gives an estimator that is maximum likelihood when the data come from a multivariate normal population. We include a derivation of the estimator that does not assume a multivariate normal population, as an iterated form of Buck's (1960) method. We derive an approximate method of assigning standard errors to regression coefficients estimated from incomplete observations, and quote supporting evidence from simulation studies. A brief account is given of the application of these methods to some school examinations data.

Life history of coho salmon

Article

Jan 1991

F.K. Sandercock

Assessing estuaries as stopover habitats for juvenile Pacific salmon

Article

Nov 2016

Habitats along migratory routes may provide key resources for migratory specie (e.g. stopover habitat). For example, migratory juvenile salmon transit through estuaries on thei way from freshwaters out to the ocean, but they may also reside and feed in these habitats. Her we examined the amount of time that juvenile salmon feed and reside in the estuary of the Skeen River (British Columbia, Canada), the second-largest salmon-bearing watershed in Canada. W implemented a novel application of stable isotopes of sulfur, carbon, and nitrogen as clocks to estimat the days since estuary entry. Salmon estuary residency varied across species; 25% of individual spent at least 33, 22, 30, and 5 d in the estuary for Chinook Oncorhynchus tshawytscha coho O. kisutch, pink O. gorbuscha, and sockeye salmon O. nerka, respectively. Larger pink an Chinook salmon resided in the estuary for longer durations, growing at an estimated 0.2 an 0.5 mm d?1, respectively, evidence that estuary residency provides growth opportunities. A negativ relationship between size and estuary residency in coho salmon suggests the potential existenc of an estuary fry life history. Genetic stock assignment indicated that different population of sockeye salmon may reside in the estuary for different amounts of time. Collectively, thes results reveal that estuaries can represent stopover habitats for salmon, and that the extent varie across salmon species and populations. These data address a knowledge gap in assessment o environmental risks of proposed industrial developments. This study indicates the importance o considering the fundamental nature of habitats through which migratory species move.

Life History Diversity of Steelhead in Two Coastal Washington Watersheds

Article

Sep 2016

We used PIT tags implanted in juvenile Oncorhynchus mykiss to monitor movement into and out of two coastal Washington State rivers, East Twin River and West Twin River. Movement patterns revealed at least 18 life histories of steelhead O. mykiss with variations in age and seasonal migration of juveniles, juvenile use of the ocean prior to migration, years spent in the ocean, season of adult return, and iteroparity. While most migrants left the river in their first fall or winter, we did not detect any returning adults from these age-0 migrants. Adults were only produced from age-1 and older migrants, of which most were age-2 spring migrants that returned after two summers in the ocean. Our results indicated a positive relationship between fish length at tagging and the probability of being detected as a migrant, while the probability of a migrant leaving at age 1 and older decreased with increasing length at tagging among fish that were detected as migrants. We hypothesize that fish attaining a large enough size early in life to survive over the winter but not big enough to trigger migration at age 0 were more likely to remain in the river to become age-1 migrants, which were more likely to produce a returning adult steelhead. We also found evidence that density-dependent growth may influence juvenile steelhead migration patterns and production of migrants as evidenced by increasing contributing-adult steelhead escapement being negatively related to average cohort body size, probabilities of fish being detected as migrants, and production of age-1 and older migrants. We anticipate that the findings of this study can be used to inform the development of steelhead recovery strategies for East Twin and West Twin rivers, which have experienced recent declines in adult returns much like other North Pacific Ocean stocks. Received January 20, 2016; accepted May 18, 2016

The effects of early sandbar formation on the abundance and ecology of coho salmon (Oncorhynchus kisutch) and steelhead trout (Oncorhynchus mykiss) in a central California coastal lagoon

Abstract and Figures

Recommended publications

Mill Creek Salmonid Lifecycle Monitoring Station Juvenile Coho Salmon Outmigrant Trapping Project 20...

Use of a Floating Weir to Assess Salmonids in the Elwha River Prior to Dam Removal

Combining Proximate and Ultimate Approaches to Understand Life History Variation in Salmonids with A...

Competitive interactions among multiple non-native salmonids and two populations of Atlantic salmon