Eric Danner | University of California, Santa Cruz (original) (raw)

Papers by Eric Danner

Ecological Modelling, 2019

In highly regulated systems, like large dammed rivers, conservation legislation requires that sys... more In highly regulated systems, like large dammed rivers, conservation legislation requires that systems are managed, in part, to avoid adverse impacts on endangered species. However, multiple endangered species can occur in the same system, and management actions that benefit one species may be detrimental to another species. The current water management strategies in the Sacramento River basin are an example of this conflict. Cold-water releases from Shasta Reservoir during the summer and fall months are aimed at protecting Sacramento River winter-run Chinook (SRWRC) salmon by providing suitable incubation temperatures for their eggs. However, the effects of these regulated water temperature releases on another threatened species, green sturgeon, are less well understood. In this study, we applied a simplified dynamic energy budget (DEB) model (aka DEBkiss) to explore the effect of food limitation and water temperature on the growth rates of green sturgeon. This model captures these effects and able to predict the growth of green sturgeon at different food levels and temperature conditions. We then linked the DEB model with a physically-based water temperature model. We applied the DEB-water temperature linked model for green sturgeon along with a temperature-dependent egg to fry survival model for SRWRC salmon to quantify the consequences of managing water temperatures to improve salmon eggs survival on the growth rate of green sturgeon. We found that mean temperature-dependent egg-to-fry survival of salmon increased across a modeled environmental gradient from critically dry to wet water year types, while the fractional growth rate of juvenile green sturgeon showed the opposite trend, and decreased as water years transitioned from dry to wet conditions. We also found a non-linear negative correlation between temperaturedependent mean growth rate of green sturgeon and mean temperature-dependent egg-to-fry survival of salmon, which indicated there is a river temperature related trade-off between early growth rate of green sturgeon and embryonic stage survival of salmon. However, the relatively small gains in the growth rate of green sturgeon achieved in years when temperature criteria for SRWRC salmon eggs were not met came at the cost of large reduction in temperature-dependent egg-to-fry survival of salmon. Thus, we concluded the current Sacramento River water-temperature management for the eggs of the endangered SRWRC salmon eggs have a relatively small impact on the growth rate of green sturgeon.

Canadian Journal of Fisheries and Aquatic Sciences, 2017

Thermal refuges form important habitat for cold-water fishes in the face of rising temperatures. ... more 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 ...

Journal of Animal Ecology, 2017

1. Fish, even of the same species, can exhibit substantial variation in energy density (energy pe... more 1. Fish, even of the same species, can exhibit substantial variation in energy density (energy per unit wet weight). Most of this variation is due to differences in the amount of storage lipids. In addition to their importance as energy reserves for reproduction and for survival during unfavourable conditions, the accumulation of lipids represents a large energetic flux for many species, so figuring out how this energy flux is integrated with other major energy fluxes (growth, reproduction) is critical for any general theory of organismal energetics. 2. Here, we synthesize data from a wide range of fish species and identify patterns of intraspecific variation in energy storage, and use these patterns to formulate a general model of energy allocation between growth, lipid storage and reproduction in fishes. 3. From the compiled data we identified two patterns: (1) energy density increases with body size during the juvenile period, but is invariant with body size within the adult size range for most species, and (2) energy density changes across seasons, with depletion over winter, but increases fastest in periods of transition between favourable and unfavourable conditions for growth (i.e. fall). 4. Based on these patterns we propose DEBlipid, a simple, general model of energy allocation that is closely related to a simplified version of Dynamic Energy Budget theory, DEBkiss. The crux of the model is that assimilated energy is partitioned, with j fraction of energy allocated to pay maintenance costs first, and the surplus allocated to growth, and 1 À j fraction of assimilated energy is allocated to accumulating storage lipids during the juvenile phase, and later to reproduction as adults. This mechanism, in addition to capturing the two patterns that motivated the model, was able to predict lipid dynamics in a novel context, the migration of anadromous fish from low-food freshwater to high-food marine environments. Furthermore, the model was used to explain intra and interspecific variation in reproductive output based on patterns of lipid accumulation as juveniles. 5. Our results suggest that many seemingly complex, adaptive energy allocation strategies in response to ontogeny, seasonality and habitat quality can emerge from a simple physiological heuristic.

Ecology Letters, 2016

Predicting species responses to climate change is a central challenge in ecology. These predictio... more Predicting species responses to climate change is a central challenge in ecology. These predictions are often based on lab-derived phenomenological relationships between temperature and fitness metrics. We tested one of these relationships using the embryonic stage of a Chinook salmon population. We parameterised the model with laboratory data, applied it to predict survival in the field, and found that it significantly underestimated field-derived estimates of thermal mortality. We used a biophysical model based on mass transfer theory to show that the discrepancy was due to the differences in water flow velocities between the lab and the field. This mechanistic approach provides testable predictions for how the thermal tolerance of embryos depends on egg size and flow velocity of the surrounding water. We found support for these predictions across more than 180 fish species, suggesting that flow and temperature mediated oxygen limitation is a general mechanism underlying the thermal tolerance of embryos.

Ecology Letters, 2016

Predicting species responses to climate change is a central challenge in ecology. These predictio... more Predicting species responses to climate change is a central challenge in ecology. These predictions are often based on lab-derived phenomenological relationships between temperature and fitness metrics. We tested one of these relationships using the embryonic stage of a Chinook salmon population. We parameterised the model with laboratory data, applied it to predict survival in the field, and found that it significantly underestimated field-derived estimates of thermal mortality. We used a biophysical model based on mass transfer theory to show that the discrepancy was due to the differences in water flow velocities between the lab and the field. This mechanistic approach provides testable predictions for how the thermal tolerance of embryos depends on egg size and flow velocity of the surrounding water. We found support for these predictions across more than 180 fish species, suggesting that flow and temperature mediated oxygen limitation is a general mechanism underlying the thermal tolerance of embryos.

Stream temperature is a critical indicator of habitat quality for endangered salmonid species and... more Stream temperature is a critical indicator of habitat quality for endangered salmonid species and affects re-licensing of major water projects and dam operations worth billions of dollars. The Central Valley Project (CVP) in California currently relies upon a monthly mean temperature standard for fisheries related decisions. Improving the spatial and temporal resolution of stream temperature forecasts allows for evaluation of habitat impacts at appropriate scales, anticipation of extreme water temperature events, and mitigation of adverse impacts to salmon through targeted water releases. In this study, we present a preliminary high-resolution stream temperature model (sub-hourly time step, 1km spatial resolution) developed for the Upper Sacramento River, spanning from Keswick Dam at the upstream end to Red Bluff Diversion Dam approximately 100km downstream. The model uses a heat budget approach to calculate the rate of heat transfer to/from the river, considering shortwave, longwave, evaporative, and conductive heat fluxes. Inputs for the heat budget formulation are atmospheric variables provided by the Weather Research and Forecasting (WRF) model, including: air temperature, relative humidity, atmospheric pressure, wind speed, and cloud cover. Water temperature is calculated using a 1dimensional advection-diffusion ("bulk flow") equation in a Lagrangian framework. Modeled temperatures for a test period (August-October, 2004) provided a substantially better estimate of the temperature dynamics than the current DSS standard monthly mean. Modeled values closely approximate both the magnitude and the phase of measured water temperatures for much of the test period. The spatiotemporal scale of our model also allows for the examination of critical temperature dynamics that would not otherwise be detected using monthly mean temperature standard. Specifically, our current model output reveals important longitudinal patterns in diel temperature variation that are unique to regulated rivers, and may be critical to salmon physiology. Ultimately, end users will be able to access the model over the internet, run various scenarios of water discharge and temperature under forecasted weather conditions to make informed decisions about water releases and subsequent impacts on fish and habitat.

Late summer and early fall water temperatures on the Klamath River can reach levels that are phys... more Late summer and early fall water temperatures on the Klamath River can reach levels that are physiologically stressful to endangered and threatened salmonids. At the limits of their thermal tolerance, salmonids may behaviorally thermoregulate by moving to localized patches of colder water, or thermal refugia. The presence of these refugia may be key to salmonid survival, especially during periods of elevated mainstem temperatures when refugia may be the only usable habitat available. However, the dynamics and importance of thermal refugia are not thoroughly understood. While fish obtain thermal benefits by using refugia, potential trade-offs include lower food availability, decreased growth rates, and increased risk of disease due to high fish densities. The interplay between these factors influences how much time a fish chooses to spend in the mainstem river versus the refugia. My research focuses on defining the mechanisms driving steelhead thermal refugia use at both landscape an...

As climate change and land-use impacts drive increases in river temperatures, thermal refugia cre... more As climate change and land-use impacts drive increases in river temperatures, thermal refugia created by coolwater tributary inputs are becoming increasingly important habitat for coldwater fish species. Summer mainstem temperatures on the Klamath River in northern California often reach physiologically stressful levels (~22-26°C) for native salmonid populations, driving juvenile salmonids into thermal refugia. These refugia are dynamic environments, and habitat quality may fluctuate in the refuge as well as in the surrounding sub-optimal mainstem habitat. The goal of this study was to determine which environmental factors are driving juvenile steelhead use of thermal refugia, and the timescale at which fish are shifting between thermal environments, in order to gain a better understanding of when these areas become critical habitat and how to effectively manage and restore thermal refugia on warming rivers. I used an innovative approach, taking advantage of relatively new radio tag...

Ecosphere, 2014

Thermal refuges form potentially critical habitat for species at the limits of their thermal tole... more Thermal refuges form potentially critical habitat for species at the limits of their thermal tolerance, especially given large-scale habitat degradation and rising temperatures across ecosystems. The Klamath River is a highly altered system where summer mainstem temperatures reach levels that are physiologically stressful to threatened Pacific salmonid populations, making thermal refuges critical for over-summer survival when temperatures near upper thermal thresholds. Small changes in water temperature can have a large effect on salmonid growth and survival, and therefore fine-scale spatiotemporal temperature variation could influence when and where refuges are important for both individual survival and population persistence. In this study, we combined monitoring of environmental variables with measures of fish temperature (a proxy for refuge use) to quantify juvenile steelhead (Oncorhynchus mykiss) use of thermal refuges. We used a logistic mixed effects model to determine the relative influence of instantaneous mainstem temperature and flow, sub-daily temperature variation, body size, and time of day on steelhead refuge use. Mainstem temperature was the strongest predictor of refuge use; the majority (.80%) of juvenile steelhead moved into refuges when mainstem temperatures reached 22-238C, and all fish moved in by 258C. Fish were more likely to use refuges with increased diel mainstem temperature variation and larger temperature differential between the mainstem and tributary. In addition, steelhead exhibited a distinct diel behavioral shift in refuge use that varied with body size; smaller juveniles (;160 mm) were much more likely to use refuges during the night than day, whereas larger juveniles (;210 mm) exhibited a much less pronounced diel behavioral shift. Given impacts of watershed alteration and climate change and the growing importance of refuge habitat, these findings suggest that species persistence may depend on extremely fine-scale spatial and temporal temperature dynamics.

IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 2012

Humans have substantially altered the thermal regimes of freshwater habitats worldwide, with sign... more Humans have substantially altered the thermal regimes of freshwater habitats worldwide, with significant environmental consequences. There is a critical need for a comprehensive modeling framework for forecasting the downstream impacts of two of the most common anthropogenic structures that alter river water temperatures: 1) dams that selectively release water from thermally stratified reservoirs, and 2) power generating stations and industrial plants that use river water for once-through cooling. These facilities change the thermal dynamics of the downstream waters through a complex interaction of water release volume and temperature and the subsequent exchange with the environment downstream. In order to stay within the downstream temperature limits imposed by regulatory agencies, managers must monitor not just release volumes and temperatures, but also need to be able to forecast the thermal impacts of their day-today operations on habitat which may be hundreds of kilometers downstream. Here we describe a coupled modeling framework that links mesoscale weather and ecological models to generate inputs for a physically-based water temperature model for monitoring and forecasting river temperatures downstream from these facilities at fine spatiotemporal scales. We provide an example of how this modeling framework is being applied to a water allocation decision support system (DSS) for the management of Endangered Species Act (ESA) listed salmon species in the Sacramento River in California.

Proceedings of the National Academy of Sciences, 2003

Populations of seals, sea lions, and sea otters have sequentially collapsed over large areas of t... more Populations of seals, sea lions, and sea otters have sequentially collapsed over large areas of the northern North Pacific Ocean and southern Bering Sea during the last several decades. A bottom-up nutritional limitation mechanism induced by physical oceanographic change or competition with fisheries was long thought to be largely responsible for these declines. The current weight of evidence is more consistent with top-down forcing. Increased predation by killer whales probably drove the sea otter collapse and may have been responsible for the earlier pinniped declines as well. We propose that decimation of the great whales by post-World War II industrial whaling caused the great whales' foremost natural predators, killer whales, to begin feeding more intensively on the smaller marine mammals, thus “fishing-down” this element of the marine food web. The timing of these events, information on the abundance, diet, and foraging behavior of both predators and prey, and feasibility ...

Marine Mammal Science, 2008

Marine Mammal Science, 2008

Ecological Monographs, 2006

The ramifying effects of top predators on food webs traditionally have been studied within the fr... more The ramifying effects of top predators on food webs traditionally have been studied within the framework of trophic cascades. Trophic cascades are compelling because they embody powerful indirect effects of predators on primary production. Although less studied, indirect effects of predators may occur via routes that are not exclusively trophic. We quantified how the introduction of foxes onto the Aleutian Islands transformed plant communities by reducing abundant seabird populations, thereby disrupting nutrient subsidies vectored by seabirds from sea to land. We compared soil and plant fertility, plant biomass and community composition, and stable isotopes of nitrogen in soil, plants, and other organisms on nine fox-infested and nine historically fox-free islands across the Aleutians. Additionally, we experimentally augmented nutrients on a fox-infested island to test whether differences in plant productivity and composition between fox-infested and foxfree islands could have arisen from differences in nutrient inputs between island types. Islands with historical fox infestations had soils low in phosphorus and nitrogen and plants low in tissue nitrogen. Soils, plants, slugs, flies, spiders, and bird droppings on these islands had low ␦ 15 N values indicating that these organisms obtained nitrogen from internally derived sources. In contrast, soils, plants, and higher trophic level organisms on fox-free islands had elevated ␦ 15 N signatures indicating that they utilized nutrients derived from the marine environment. Furthermore, soil phosphorus (but not nitrogen) and plant tissue nitrogen were higher on fox-free than fox-infested islands. Nutrient subsidized fox-free islands supported lush, high biomass plant communities dominated by graminoids. Fox-infested islands were less graminoid dominated and had higher cover and biomass of low-lying forbs and dwarf shrubs. While ␦ 15 N profiles of soils and plants and graminoid biomass varied with island size and distance from shore, after accounting for these effects differences between fox-infested and fox-free islands still existed. Fertilization over four years caused a 24-fold increase in graminoid biomass and a shift toward a more graminoid dominated plant community typical of fox-free islands. These results indicate that apex predators can influence plant productivity and composition through complex interaction web pathways involving both top-down forcing and bottom-up nutrient exchanges across systems.

The distributions and abundances of species and populations change almost continuously. Understan... more The distributions and abundances of species and populations change almost continuously. Understanding the processes responsible is perhaps ecologyʼs most fundamental challenge. Kelp-forest ecosystems in southwest Alaska have undergone several phase shifts between alga-and herbivore-dominated states in recent decades. Overhunting and recovery of sea otters caused the earlier shifts. Studies focusing on these changes demonstrate the importance of top-down forcing processes, a variety of indirect foodweb interactions associated with the otter-urchin-kelp trophic cascade, and the role of food-chain length in the coevolution of defense and resistance in plants and their herbivores. This system unexpectedly shifted back to an herbivore-dominated state during the 1990s, because of a sea-otter population collapse that apparently was driven by increased predation by killer whales. Reasons for this change remain uncertain but seem to be linked to the wholesale collapse of marine mammals in the North Pacific Ocean and southern Bering Sea. We hypothesize that killer whales sequentially "fished down" pinniped and sea-otter populations after their earlier prey, the great whales, were decimated by commercial whaling. The dynamics of kelp forests in southwest Alaska thus appears to have been influenced by an ecological chain reaction that encompassed numerous species and large scales of space and time.

Transactions of the American Fisheries Society, 2016

AbstractThe Wisconsin bioenergetics model is widely used to evaluate the effects of environmental... more AbstractThe Wisconsin bioenergetics model is widely used to evaluate the effects of environmental conditions, trophic interactions, and human-mediated alterations to physical and trophodynamic processes on the growth and survival of individual fish species. In particular, bioenergetics models are increasingly applied to evaluate conditions that vary on subdaily time steps, such as vertical migrations that influence thermal experience and fluvial alterations that increase diurnal temperature variability. However, because the algorithms that describe the relationship between temperature and physiological rates are often nonlinear, using inputs of daily mean temperatures can result in underestimation or overestimation of growth and energetic demand. We used simulations of daily and subdaily models of Chinook Salmon Oncorhynchus tshawytscha as an example to demonstrate that the nonlinear, temperature-dependent algorithms for consumption and respiration induce large differences in growth between constant- and ...

The “Wisconsin” bioenergetics model is widely used to evaluate the effects of environmental condi... more The “Wisconsin” bioenergetics model is widely used to evaluate the effects of environmental conditions, trophic interactions, and human-mediated alterations to physical and trophodynamic processes on the growth and survival of individual fish species. In particular, bioenergetics models are increasingly applied to evaluate conditions that vary on subdaily time-steps, such as vertical migrations that influence thermal experience or fluvial alterations that increase diurnal temperature variability. However, because the algorithms that describe the relationship between temperature and physiological rates are often non-linear, using inputs of daily mean temperatures can result in under- or overestimates of growth and energetic demand. Using simulations of daily and subdaily Chinook Salmon Oncorhynchus tshawytscha models as an example, we demonstrate that the non-linear temperature-dependent algorithms for consumption and respiration induce large differences in growth between constant and fluctuating temperature conditions (despite the same mean daily temperature), which increase with high diurnal variability and as temperatures approach the thermal optimum for the species. To correct for model bias in growth, we propose an integrated temperature-scaling algorithm that allows the daily model to be applied to systems where daily temperatures exhibit considerable subdaily variation. This approach can also be used for any bioenergetics model that includes non-linear temperature-dependent algorithms, and should be considered when modeled temperatures approach inflection points in non-linear relationships.

Ecological Modelling, 2019

In highly regulated systems, like large dammed rivers, conservation legislation requires that sys... more In highly regulated systems, like large dammed rivers, conservation legislation requires that systems are managed, in part, to avoid adverse impacts on endangered species. However, multiple endangered species can occur in the same system, and management actions that benefit one species may be detrimental to another species. The current water management strategies in the Sacramento River basin are an example of this conflict. Cold-water releases from Shasta Reservoir during the summer and fall months are aimed at protecting Sacramento River winter-run Chinook (SRWRC) salmon by providing suitable incubation temperatures for their eggs. However, the effects of these regulated water temperature releases on another threatened species, green sturgeon, are less well understood. In this study, we applied a simplified dynamic energy budget (DEB) model (aka DEBkiss) to explore the effect of food limitation and water temperature on the growth rates of green sturgeon. This model captures these effects and able to predict the growth of green sturgeon at different food levels and temperature conditions. We then linked the DEB model with a physically-based water temperature model. We applied the DEB-water temperature linked model for green sturgeon along with a temperature-dependent egg to fry survival model for SRWRC salmon to quantify the consequences of managing water temperatures to improve salmon eggs survival on the growth rate of green sturgeon. We found that mean temperature-dependent egg-to-fry survival of salmon increased across a modeled environmental gradient from critically dry to wet water year types, while the fractional growth rate of juvenile green sturgeon showed the opposite trend, and decreased as water years transitioned from dry to wet conditions. We also found a non-linear negative correlation between temperaturedependent mean growth rate of green sturgeon and mean temperature-dependent egg-to-fry survival of salmon, which indicated there is a river temperature related trade-off between early growth rate of green sturgeon and embryonic stage survival of salmon. However, the relatively small gains in the growth rate of green sturgeon achieved in years when temperature criteria for SRWRC salmon eggs were not met came at the cost of large reduction in temperature-dependent egg-to-fry survival of salmon. Thus, we concluded the current Sacramento River water-temperature management for the eggs of the endangered SRWRC salmon eggs have a relatively small impact on the growth rate of green sturgeon.

Canadian Journal of Fisheries and Aquatic Sciences, 2017

Thermal refuges form important habitat for cold-water fishes in the face of rising temperatures. ... more 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 ...

Journal of Animal Ecology, 2017

1. Fish, even of the same species, can exhibit substantial variation in energy density (energy pe... more 1. Fish, even of the same species, can exhibit substantial variation in energy density (energy per unit wet weight). Most of this variation is due to differences in the amount of storage lipids. In addition to their importance as energy reserves for reproduction and for survival during unfavourable conditions, the accumulation of lipids represents a large energetic flux for many species, so figuring out how this energy flux is integrated with other major energy fluxes (growth, reproduction) is critical for any general theory of organismal energetics. 2. Here, we synthesize data from a wide range of fish species and identify patterns of intraspecific variation in energy storage, and use these patterns to formulate a general model of energy allocation between growth, lipid storage and reproduction in fishes. 3. From the compiled data we identified two patterns: (1) energy density increases with body size during the juvenile period, but is invariant with body size within the adult size range for most species, and (2) energy density changes across seasons, with depletion over winter, but increases fastest in periods of transition between favourable and unfavourable conditions for growth (i.e. fall). 4. Based on these patterns we propose DEBlipid, a simple, general model of energy allocation that is closely related to a simplified version of Dynamic Energy Budget theory, DEBkiss. The crux of the model is that assimilated energy is partitioned, with j fraction of energy allocated to pay maintenance costs first, and the surplus allocated to growth, and 1 À j fraction of assimilated energy is allocated to accumulating storage lipids during the juvenile phase, and later to reproduction as adults. This mechanism, in addition to capturing the two patterns that motivated the model, was able to predict lipid dynamics in a novel context, the migration of anadromous fish from low-food freshwater to high-food marine environments. Furthermore, the model was used to explain intra and interspecific variation in reproductive output based on patterns of lipid accumulation as juveniles. 5. Our results suggest that many seemingly complex, adaptive energy allocation strategies in response to ontogeny, seasonality and habitat quality can emerge from a simple physiological heuristic.

Ecology Letters, 2016

Predicting species responses to climate change is a central challenge in ecology. These predictio... more Predicting species responses to climate change is a central challenge in ecology. These predictions are often based on lab-derived phenomenological relationships between temperature and fitness metrics. We tested one of these relationships using the embryonic stage of a Chinook salmon population. We parameterised the model with laboratory data, applied it to predict survival in the field, and found that it significantly underestimated field-derived estimates of thermal mortality. We used a biophysical model based on mass transfer theory to show that the discrepancy was due to the differences in water flow velocities between the lab and the field. This mechanistic approach provides testable predictions for how the thermal tolerance of embryos depends on egg size and flow velocity of the surrounding water. We found support for these predictions across more than 180 fish species, suggesting that flow and temperature mediated oxygen limitation is a general mechanism underlying the thermal tolerance of embryos.

Ecology Letters, 2016

Predicting species responses to climate change is a central challenge in ecology. These predictio... more Predicting species responses to climate change is a central challenge in ecology. These predictions are often based on lab-derived phenomenological relationships between temperature and fitness metrics. We tested one of these relationships using the embryonic stage of a Chinook salmon population. We parameterised the model with laboratory data, applied it to predict survival in the field, and found that it significantly underestimated field-derived estimates of thermal mortality. We used a biophysical model based on mass transfer theory to show that the discrepancy was due to the differences in water flow velocities between the lab and the field. This mechanistic approach provides testable predictions for how the thermal tolerance of embryos depends on egg size and flow velocity of the surrounding water. We found support for these predictions across more than 180 fish species, suggesting that flow and temperature mediated oxygen limitation is a general mechanism underlying the thermal tolerance of embryos.

Stream temperature is a critical indicator of habitat quality for endangered salmonid species and... more Stream temperature is a critical indicator of habitat quality for endangered salmonid species and affects re-licensing of major water projects and dam operations worth billions of dollars. The Central Valley Project (CVP) in California currently relies upon a monthly mean temperature standard for fisheries related decisions. Improving the spatial and temporal resolution of stream temperature forecasts allows for evaluation of habitat impacts at appropriate scales, anticipation of extreme water temperature events, and mitigation of adverse impacts to salmon through targeted water releases. In this study, we present a preliminary high-resolution stream temperature model (sub-hourly time step, 1km spatial resolution) developed for the Upper Sacramento River, spanning from Keswick Dam at the upstream end to Red Bluff Diversion Dam approximately 100km downstream. The model uses a heat budget approach to calculate the rate of heat transfer to/from the river, considering shortwave, longwave, evaporative, and conductive heat fluxes. Inputs for the heat budget formulation are atmospheric variables provided by the Weather Research and Forecasting (WRF) model, including: air temperature, relative humidity, atmospheric pressure, wind speed, and cloud cover. Water temperature is calculated using a 1dimensional advection-diffusion ("bulk flow") equation in a Lagrangian framework. Modeled temperatures for a test period (August-October, 2004) provided a substantially better estimate of the temperature dynamics than the current DSS standard monthly mean. Modeled values closely approximate both the magnitude and the phase of measured water temperatures for much of the test period. The spatiotemporal scale of our model also allows for the examination of critical temperature dynamics that would not otherwise be detected using monthly mean temperature standard. Specifically, our current model output reveals important longitudinal patterns in diel temperature variation that are unique to regulated rivers, and may be critical to salmon physiology. Ultimately, end users will be able to access the model over the internet, run various scenarios of water discharge and temperature under forecasted weather conditions to make informed decisions about water releases and subsequent impacts on fish and habitat.

Late summer and early fall water temperatures on the Klamath River can reach levels that are phys... more Late summer and early fall water temperatures on the Klamath River can reach levels that are physiologically stressful to endangered and threatened salmonids. At the limits of their thermal tolerance, salmonids may behaviorally thermoregulate by moving to localized patches of colder water, or thermal refugia. The presence of these refugia may be key to salmonid survival, especially during periods of elevated mainstem temperatures when refugia may be the only usable habitat available. However, the dynamics and importance of thermal refugia are not thoroughly understood. While fish obtain thermal benefits by using refugia, potential trade-offs include lower food availability, decreased growth rates, and increased risk of disease due to high fish densities. The interplay between these factors influences how much time a fish chooses to spend in the mainstem river versus the refugia. My research focuses on defining the mechanisms driving steelhead thermal refugia use at both landscape an...

As climate change and land-use impacts drive increases in river temperatures, thermal refugia cre... more As climate change and land-use impacts drive increases in river temperatures, thermal refugia created by coolwater tributary inputs are becoming increasingly important habitat for coldwater fish species. Summer mainstem temperatures on the Klamath River in northern California often reach physiologically stressful levels (~22-26°C) for native salmonid populations, driving juvenile salmonids into thermal refugia. These refugia are dynamic environments, and habitat quality may fluctuate in the refuge as well as in the surrounding sub-optimal mainstem habitat. The goal of this study was to determine which environmental factors are driving juvenile steelhead use of thermal refugia, and the timescale at which fish are shifting between thermal environments, in order to gain a better understanding of when these areas become critical habitat and how to effectively manage and restore thermal refugia on warming rivers. I used an innovative approach, taking advantage of relatively new radio tag...

Ecosphere, 2014

Thermal refuges form potentially critical habitat for species at the limits of their thermal tole... more Thermal refuges form potentially critical habitat for species at the limits of their thermal tolerance, especially given large-scale habitat degradation and rising temperatures across ecosystems. The Klamath River is a highly altered system where summer mainstem temperatures reach levels that are physiologically stressful to threatened Pacific salmonid populations, making thermal refuges critical for over-summer survival when temperatures near upper thermal thresholds. Small changes in water temperature can have a large effect on salmonid growth and survival, and therefore fine-scale spatiotemporal temperature variation could influence when and where refuges are important for both individual survival and population persistence. In this study, we combined monitoring of environmental variables with measures of fish temperature (a proxy for refuge use) to quantify juvenile steelhead (Oncorhynchus mykiss) use of thermal refuges. We used a logistic mixed effects model to determine the relative influence of instantaneous mainstem temperature and flow, sub-daily temperature variation, body size, and time of day on steelhead refuge use. Mainstem temperature was the strongest predictor of refuge use; the majority (.80%) of juvenile steelhead moved into refuges when mainstem temperatures reached 22-238C, and all fish moved in by 258C. Fish were more likely to use refuges with increased diel mainstem temperature variation and larger temperature differential between the mainstem and tributary. In addition, steelhead exhibited a distinct diel behavioral shift in refuge use that varied with body size; smaller juveniles (;160 mm) were much more likely to use refuges during the night than day, whereas larger juveniles (;210 mm) exhibited a much less pronounced diel behavioral shift. Given impacts of watershed alteration and climate change and the growing importance of refuge habitat, these findings suggest that species persistence may depend on extremely fine-scale spatial and temporal temperature dynamics.

IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 2012

Humans have substantially altered the thermal regimes of freshwater habitats worldwide, with sign... more Humans have substantially altered the thermal regimes of freshwater habitats worldwide, with significant environmental consequences. There is a critical need for a comprehensive modeling framework for forecasting the downstream impacts of two of the most common anthropogenic structures that alter river water temperatures: 1) dams that selectively release water from thermally stratified reservoirs, and 2) power generating stations and industrial plants that use river water for once-through cooling. These facilities change the thermal dynamics of the downstream waters through a complex interaction of water release volume and temperature and the subsequent exchange with the environment downstream. In order to stay within the downstream temperature limits imposed by regulatory agencies, managers must monitor not just release volumes and temperatures, but also need to be able to forecast the thermal impacts of their day-today operations on habitat which may be hundreds of kilometers downstream. Here we describe a coupled modeling framework that links mesoscale weather and ecological models to generate inputs for a physically-based water temperature model for monitoring and forecasting river temperatures downstream from these facilities at fine spatiotemporal scales. We provide an example of how this modeling framework is being applied to a water allocation decision support system (DSS) for the management of Endangered Species Act (ESA) listed salmon species in the Sacramento River in California.

Proceedings of the National Academy of Sciences, 2003

Populations of seals, sea lions, and sea otters have sequentially collapsed over large areas of t... more Populations of seals, sea lions, and sea otters have sequentially collapsed over large areas of the northern North Pacific Ocean and southern Bering Sea during the last several decades. A bottom-up nutritional limitation mechanism induced by physical oceanographic change or competition with fisheries was long thought to be largely responsible for these declines. The current weight of evidence is more consistent with top-down forcing. Increased predation by killer whales probably drove the sea otter collapse and may have been responsible for the earlier pinniped declines as well. We propose that decimation of the great whales by post-World War II industrial whaling caused the great whales' foremost natural predators, killer whales, to begin feeding more intensively on the smaller marine mammals, thus “fishing-down” this element of the marine food web. The timing of these events, information on the abundance, diet, and foraging behavior of both predators and prey, and feasibility ...

Marine Mammal Science, 2008

Marine Mammal Science, 2008

Ecological Monographs, 2006

The ramifying effects of top predators on food webs traditionally have been studied within the fr... more The ramifying effects of top predators on food webs traditionally have been studied within the framework of trophic cascades. Trophic cascades are compelling because they embody powerful indirect effects of predators on primary production. Although less studied, indirect effects of predators may occur via routes that are not exclusively trophic. We quantified how the introduction of foxes onto the Aleutian Islands transformed plant communities by reducing abundant seabird populations, thereby disrupting nutrient subsidies vectored by seabirds from sea to land. We compared soil and plant fertility, plant biomass and community composition, and stable isotopes of nitrogen in soil, plants, and other organisms on nine fox-infested and nine historically fox-free islands across the Aleutians. Additionally, we experimentally augmented nutrients on a fox-infested island to test whether differences in plant productivity and composition between fox-infested and foxfree islands could have arisen from differences in nutrient inputs between island types. Islands with historical fox infestations had soils low in phosphorus and nitrogen and plants low in tissue nitrogen. Soils, plants, slugs, flies, spiders, and bird droppings on these islands had low ␦ 15 N values indicating that these organisms obtained nitrogen from internally derived sources. In contrast, soils, plants, and higher trophic level organisms on fox-free islands had elevated ␦ 15 N signatures indicating that they utilized nutrients derived from the marine environment. Furthermore, soil phosphorus (but not nitrogen) and plant tissue nitrogen were higher on fox-free than fox-infested islands. Nutrient subsidized fox-free islands supported lush, high biomass plant communities dominated by graminoids. Fox-infested islands were less graminoid dominated and had higher cover and biomass of low-lying forbs and dwarf shrubs. While ␦ 15 N profiles of soils and plants and graminoid biomass varied with island size and distance from shore, after accounting for these effects differences between fox-infested and fox-free islands still existed. Fertilization over four years caused a 24-fold increase in graminoid biomass and a shift toward a more graminoid dominated plant community typical of fox-free islands. These results indicate that apex predators can influence plant productivity and composition through complex interaction web pathways involving both top-down forcing and bottom-up nutrient exchanges across systems.

The distributions and abundances of species and populations change almost continuously. Understan... more The distributions and abundances of species and populations change almost continuously. Understanding the processes responsible is perhaps ecologyʼs most fundamental challenge. Kelp-forest ecosystems in southwest Alaska have undergone several phase shifts between alga-and herbivore-dominated states in recent decades. Overhunting and recovery of sea otters caused the earlier shifts. Studies focusing on these changes demonstrate the importance of top-down forcing processes, a variety of indirect foodweb interactions associated with the otter-urchin-kelp trophic cascade, and the role of food-chain length in the coevolution of defense and resistance in plants and their herbivores. This system unexpectedly shifted back to an herbivore-dominated state during the 1990s, because of a sea-otter population collapse that apparently was driven by increased predation by killer whales. Reasons for this change remain uncertain but seem to be linked to the wholesale collapse of marine mammals in the North Pacific Ocean and southern Bering Sea. We hypothesize that killer whales sequentially "fished down" pinniped and sea-otter populations after their earlier prey, the great whales, were decimated by commercial whaling. The dynamics of kelp forests in southwest Alaska thus appears to have been influenced by an ecological chain reaction that encompassed numerous species and large scales of space and time.

Transactions of the American Fisheries Society, 2016

AbstractThe Wisconsin bioenergetics model is widely used to evaluate the effects of environmental... more AbstractThe Wisconsin bioenergetics model is widely used to evaluate the effects of environmental conditions, trophic interactions, and human-mediated alterations to physical and trophodynamic processes on the growth and survival of individual fish species. In particular, bioenergetics models are increasingly applied to evaluate conditions that vary on subdaily time steps, such as vertical migrations that influence thermal experience and fluvial alterations that increase diurnal temperature variability. However, because the algorithms that describe the relationship between temperature and physiological rates are often nonlinear, using inputs of daily mean temperatures can result in underestimation or overestimation of growth and energetic demand. We used simulations of daily and subdaily models of Chinook Salmon Oncorhynchus tshawytscha as an example to demonstrate that the nonlinear, temperature-dependent algorithms for consumption and respiration induce large differences in growth between constant- and ...

The “Wisconsin” bioenergetics model is widely used to evaluate the effects of environmental condi... more The “Wisconsin” bioenergetics model is widely used to evaluate the effects of environmental conditions, trophic interactions, and human-mediated alterations to physical and trophodynamic processes on the growth and survival of individual fish species. In particular, bioenergetics models are increasingly applied to evaluate conditions that vary on subdaily time-steps, such as vertical migrations that influence thermal experience or fluvial alterations that increase diurnal temperature variability. However, because the algorithms that describe the relationship between temperature and physiological rates are often non-linear, using inputs of daily mean temperatures can result in under- or overestimates of growth and energetic demand. Using simulations of daily and subdaily Chinook Salmon Oncorhynchus tshawytscha models as an example, we demonstrate that the non-linear temperature-dependent algorithms for consumption and respiration induce large differences in growth between constant and fluctuating temperature conditions (despite the same mean daily temperature), which increase with high diurnal variability and as temperatures approach the thermal optimum for the species. To correct for model bias in growth, we propose an integrated temperature-scaling algorithm that allows the daily model to be applied to systems where daily temperatures exhibit considerable subdaily variation. This approach can also be used for any bioenergetics model that includes non-linear temperature-dependent algorithms, and should be considered when modeled temperatures approach inflection points in non-linear relationships.