Research in the Freshwater Fish Ecology Lab focuses on the population and community ecology of freshwater fishes, often linking environmental stressors (e.g., climate change, groundwater pumping, wildfire, invasive species) to freshwater fish population and assemblage dynamics across a variety of aquatic ecosystems. This research bridges the gap between basic and applied fisheries ecology, integrating quantitative ecological analyses, spatial statistical methods, landscape ecology and conservation biology to address conservation and management issues.
Below is a synopsis of selected past and current research in the FFEL. See "Publications" page for citations of peer-reviewed papers detailing our research.
Below is a synopsis of selected past and current research in the FFEL. See "Publications" page for citations of peer-reviewed papers detailing our research.
Landscape genetic diversity of native and invasive Northern pike (Esox lucius) in Alaska.This project will be the first to investigate the genetic and environmental landscape among introduced populations of Northern Pike (Esox lucius) in southcentral Alaska. First, we will examine genetic diversity among native and introduced populations of Northern Pike through the use of next generation sequencing. Genotyping-by-sequencing methods will allow for the creation of a multilocus genotype dataset expected to provide sufficient resolution for differentiation between native and introduced populations. Project goals are to test hypotheses regarding origins of invasive populations and inferred size of founding populations. Second, we will develop a Northern Pike distribution model for the Matanuska-Susitna Basin (MatSu, southcentral Alaska) using NetMap, an integrated set of watershed terrain parameters and analysis tools. Attributes representing climatic, hydrologic and topographic features will be generated across the MatSu Basin and used to characterize and rank habitat suitability for Northern Pike. Presence-absence data will be compiled from the Alaska Department of Fish and Game’s freshwater fish inventory database, sport fish harvest survey data, and maps of known and probable pike waters. These data will be used to parameterize and evaluate the accuracy of the habitat suitability model. Additionally, we will quantify habitat connectivity throughout the MatSu Basin to predict areas were Northern Pike are likely to invade. Finally, we will assess the potential impact of this invasion on salmon populations by comparing our Northern Pike habitat suitability model and among-habitat connectivity estimates to the known distribution of juvenile salmonid rearing habitats in the MatSu. This study is expected to increase our understanding of Northern Pike genetics across their native and invasive ranges, as well as our understanding of the abundance and dispersal abilities of this invader. Funding for this work has been provided by the Alaska Department of Fish and Game and the U. S. Geological Survey. Co-PI's: Peter Westley and Andres Lopez. Graduate student: Chase Jalbert (MS, in progress).
Pacific salmon population response to freshwater pressures in coastal Alaskan watersheds. Over the past decade, a growing body of evidence has demonstrated that hatchery salmon practices and climate-induced changes to stream flow and thermal regimes are impacting Pacific salmon in streams bordering the Gulf of Alaska. The broad goal of this research project is to assess increasing pressures on freshwater life stages of salmon and determine which have the potential for the greatest future population impact. Specific research questions will include: what types of streams bordering the Gulf of Alaska are at highest risk for current and future low dissolved oxygen events (hypoxia) due to low discharge, high salmon density, and/or warm summer water temperatures during upstream spawning migrations? Will the combination of periodic hypoxia, warmer thermal regimes, and shifting flow regimes change the future freshwater survival of juvenile and adult salmon in southern Alaska? And if so, will changes in freshwater survival affect population productivity? Our work will rely primarily on existing data sets and use modeling tools designed to predict current and future patterns in hydrology, physical habitat, and salmon life cycle productivity. In addition, we will engage local communities to ensure we analyze a sub-set of watersheds that have particular importance for subsistence harvest and other resource uses. Project results will help guide future watershed management and monitoring efforts throughout the Gulf of Alaska and further illuminate the effects of climate change on salmon populations. Graduate student: Chris Sergeant (PhD, in progress).
Logjams and juvenile Chinook salmon (Onchorhynchus tshawystcha) habitat use in the Chena River, AK. Chinook salmon are an important commercial, subsistence, and recreational fishery resource in Alaska. Substantial declines in escapement from many Alaskan watersheds in recent years, including the Chena River in interior Alaska, have resulted in closure of Chinook salmon fisheries in more imperiled drainages and hardships for subsistence users. Body size influences survival rates for juvenile salmon during the freshwater rearing phase, and access to high quality rearing habitat provides a significant advantage for individuals to survive the winter. Large woody debris (e.g., logjams, rootwads; LWD) within the stream channel provides important rearing habitat for fishes, especially for juvenile Chinook salmon in interior Alaska rivers including the Chena River. For juvenile salmon, LWD offers cover from predation, refuge from high flow velocities, and high quality habitat for invertebrate prey items. However, the distribution, abundance, and characteristics of LWD, particularly within stream reaches where juvenile Chinook salmon are known to rear, have yet to be quantified in the Chena River basin. The overall goal of the project is to map the current distribution of LWD in the Chena River basin and estimate use of LWD by rearing juvenile Chinook Salmon. During summer 2017, we will 1) georeference and make simple measurements of LWD along the entire rearing distribution of juvenile Chinook Salmon in the upper Chena River, and potential rearing distribution in the lower river, 2) relate LWD characteristics use (i.e., presence) by juvenile Chinook Salmon for a subset of habitats, and 3) communicate the importance of LWD as juvenile Chinook Salmon habitat to the public. This project is funded by U.S. Fish and Wildlife Service Subsistence Management Program. Technicians: Nate Cathcart and Brian Crabill.
Migration patterns and energetics of adult Chinook salmon in Alaska rivers. The Stikine and Taku Rivers in Southeast Alaska are major producers of Chinook salmon, an ecological, cultural and economically important species to the region. The salmon from these transboundary rivers, with their headwaters in Canada, are jointly managed and harvested by American and Canadian shareholders. A radio telemetry study is being conducted on these rivers in order to better understand the behaviors of these fish, including spawning distribution, migration rates, temporal patterns and dropout rates. In addition to the telemetry information, bioelectrical impedance analysis is being measured on tagged fish to look at the relationship between migration patterns and body condition. One focus of this research will be on the success of fish passing a natural landslide that occurred on the Tahltan River, a tributary of the Stikine in which an estimated 50% of the Chinook salmon return. The May 2014 landslide created a velocity barrier resulting in many fish having to be assisted past the slide. Stationary data logging towers set at multiple locations within the river will collect information on the position and timing of individuals traveling up the rivers and aerial surveys will map the spawning distributions of tagged fish. Results from this project can be used to validate and inform current mark-recapture studies and escapement estimates and help fisheries managers set more accurate harvest limits for Chinook salmon in both American and Canadian fisheries. This project is funded by the Alaska Department of Fish and Game. Graduate student: Kristin Neuneker (MS, 2017).
Using remote sensing, occupancy estimation, and fine-scale habitat characterization to evaluate fall chum salmon spawning habitat usage in Arctic Alaska. An increase in mining exploration and the effects of climate change have raised concerns about the future of Chandalar River chum salmon among local community members and state and Federal fisheries managers. Yukon fall chum rely on systems that are spring fed or have geologically significant hyporheic groundwater upwellings, since these locations provide stable water temperatures for eggs and juveniles throughout the winter months. However, limited information is available on the spatial distribution and frequency of these upwellings on the Chandalar River. The goals of this project are to identify the longitudinal patterns of groundwater upwellings, as measured by thermal variability, and the relationship between the spatial distribution of spawning salmon and groundwater discharge patterns. This project is funded by U.S. Fish and Wildlife Service Subsistence Management Program. Graduate student: Chelsea Clawson (MS, 2017).
Lake trout (Salvelinus namaycush) otoliths as biochronological indicators of recent climate patterns in high Arctic lakes. High latitude ecosystems, such as Arctic Alaska, show increased effects of climate change. Due largely to costs and logistics associated with this region, long-term air temperature data only exists from a few locations. Lake temperature has only just begun to be more routinely monitored. Studies to obtain more spatially comprehensive data are needed. In terrestrial systems the use of tree-ring data and dendrochronolgy techniques are often used as a reliable proxy to reconstruct temperature regimes, however, most of Arctic Alaska is devoid of trees. These same dendrochronolgy techniques can be applied to growth-increment widths found in Lake Trout (Salvelinus namaycush) otoliths. Lake trout are present across the Arctic landscape and are a long-lived fish, thus may provide a reliable mulitdecadal proxy to reconstruct temperature regimes across the region. This project will focus on the Fish Creek and Ikpikpuk Sand Sea/Teshekpuk Lake watersheds which are experiencing the impacts of climate change as well as large-scale changes in land use involving oil and gas development. This project will provide valuable information with respect to these challenges. Graduate student: Eric Torvinen (MS, 2017)
Estimating the distribution of juvenile Chinook salmon (Oncorhynchus tshawytscha) using habitat modeling and eDNA in an interior Alaska river basin. In Alaska, it is estimated that less than 50% of waterbodies (e.g., streams, rivers or lakes) with the potential to support anadromous fishes have been documented. Identification and protection of these unsampled water bodies will be critical in light of increasing threats (e.g., climate change, fishing pressure, and land development) to fish populations, yet challenging when budgetary and logistical limitations are considered. Newly developed, non-invasive rapid-assessment techniques can reduce costs and sampling effort while increasing detectability (i.e., probability of observing an individual) across life stages. We are using a GIS-based habitat model to predict juvenile Chinook salmon habitat potential throughout the Chena River, a clear water tributary of the Yukon River located in interior Alaska. We will divide the Chena River into 149 tributary catchments (> 20 km2 surface area) and use the model and the State of Alaska Catalog of Anadromous Waters (AWC) to classify each tributary as high rearing potential, low rearing potential and known rearing habitat used by juvenile Chinook based on the AWC. Ten tributaries from each category will be randomly selected (N=30) for environmental DNA (eDNA) analysis and snorkel surveys. Three replicate water samples will be collected at each site, filtered and analyzed for presence of Chinook salmon DNA present in the environment. Snorkel surveys will also be conducted for visual confirmation of presence/absence and to quantify the range of juveniles within tributary habitats. Our results will provide tools for managers to rapidly and efficiently map critical rearing habitats and prioritize sampling efforts to expand the known distribution of juvenile salmon in interior Alaska streams. This project is funded by the State of Alaska and the Alaska Department of Fish and Game. Graduate student: Allison Martin (MS, 2016)
Temperature, phenology, and embryo survival in Western Alaska sockeye salmon populations: the potential for adaptation to a warming world? A fundamental ecological challenge is to understand and predict population responses to rapid environmental change. Viable sockeye salmon (Oncorhynchus nerka) populations are critical to the economy, culture, and freshwater ecosystems of Bristol Bay in Western Alaska, and it is unclear how populations might respond to warming temperatures during the critical life history stages of spawning and embryo incubation. Despite the importance of environmental factors in driving the evolution of locally-adapted populations, and the subsequent role of evolution in fishery sustainability, the patterns of population-specific responses to changes in the environment are largely unknown. The specific objectives of this study are 1) to use information on spawning timing and long-term water temperature records from the Kvichak watershed to predict the timing of juvenile hatching and emergence under the range of conditions observed in the past decades, 2) predict changes in water temperatures likely to be experienced by salmon populations in Iliamna Lake using a processed based one-dimensional hydrodynamics model, 3) conduct a controlled laboratory experiment to quantify Iliamna Lake population-specific functional responses between timing of hatching, emergence, and embryo survival under scenarios of freshwater warming determined in objective three, and 4) assess probabilities of persistence and likelihood for adaptation to warming temperatures for populations in the Kvichak watershed using individual-based eco-evolutionary models. This work will directly benefit resource managers as well as local communities that depend on sustainable sockeye salmon runs for their livelihoods and subsistence through an improved understanding of how salmon are likely to respond to a warming world. This project is funded by the Western Alaska Landscape Conservation Cooperative. Co-PIs: Peter Westley, Tom Quinn. Graduate student: Morgan Sparks (MS, 2016)
The role of environmental processes in structuring the distribution of Chinook salmon spawning and rearing habitats across a large Alaska river basin. Chinook salmon are an important subsistence, sport-fishing, and ecological resource in Alaska. Poor adult returns in recent years have resulted in fishery closures, leading to social and economic hardships for subsistence and sport users. Unfortunately, the mechanism(s) driving these declines are poorly understood. Uncertainty surrounding sources of mortality and their relative importance across life stages, habitat (e.g., freshwater vs. estuarine or ocean), and time is a major contributing factor. The objectives of this research are to, 1) develop spatially continuous metrics that describe historic, current, and future flow and temperature regimes within the Chena River basin and, 2) project derived flow and temperature metrics into the future under climate change scenarios in the context of Chinook salmon spawning and rearing habitat requirements and processes influencing juvenile mortality. A better understanding of past and contemporary relationships among hydrologic and thermal regimes and spawning and rearing habitat quality for Chinook salmon will greatly improve our ability to predict future states, and ultimately prioritize conservation and management action under a changing climate. Funding for this project has been provided by the State of Alaska. Brock Huntsman (Post-doc, 2014-2015)
Characterization of resident rainbow trout (Oncorhynchus mykiss) seasonal habitats in Willow Creek, Alaska. Resident rainbow trout are an important ecological and fishery resource in the Susitna River basin, yet the distribution of their seasonal habitats is poorly understood. Variable spawning site fidelity, long-range movements, and potential land use and climate change effects add to the uncertainty surrounding conservation and management of this species. The objective of this project is to assess the availability and use of seasonal habitats by rainbow trout and to link habitat characteristics (physical habitat, water temperature, and flow) with fish location and movement. Habitat availability will be assessed by spatially-continuous mapping of geomorphic channel types and water temperature metrics, and will be conducted during summer 2013. Habitat use will be quantified by radio-tagging a sample of rainbow trout in 2013 and tracking them throughout the spawning and rearing seasons in 2014. The results from this research will be useful for prioritizing habitat protection efforts in light of anticipated future land use and climate change. This project is funded by the Alaska Department of Fish and Game, (Palmer Regional Office) who will also provide logistical support and collaborate on data analysis and interpretation, and the MatSu Basin Salmon Habitat Partnership. Graduate student: Kevin Fraley (MS, 2015)
Development and calibration of bioelectrical impedance analysis as a measure of energetic status of Arctic grayling (Thymallus arcticus). The objective of this research is to develop methods to accurately characterize the energetic condition of Arctic grayling. In doing so, we will further refine bioelectrical impedance analysis (BIA), a non-lethal method by which fish energy content is estimated in the field. Currently, proximate analysis is the most reliable means of estimating energy content. Under this method, fish are sacrificed, homogenized, and composition (lipid, protein, carbohydrates, water, and ash) is determined through chemical analysis. Before BIA can be employed extensively, statistical models specific to Arctic grayling must be developed which describe the relationship between BIA readings and estimates of energy content derived from proximate analysis. Development of BIA models for grayling will allow for rapid, precise, and non-lethal measures of individual energy density in lab or field situations. This pilot work will serve as a critical step towards future research on the biology and ecology of Arctic grayling. Funding: U.S. Geological Survey Cooperative Units Program.
Thermal criteria for Nevada coldwater stream fishes. Currently, a need exists to update and develop protective criteria and monitoring designs for thermal conditions that support coldwater stream fishes in the state of Nevada. To address these issues, we , 1) developed a matrix of recommended temperature standards for coldwater stream fishes in Nevada, and 2) reviewed approaches for monitoring thresholds that incorporate spatio-temporal variability in stream water temperatures. We conducted an extensive literature review of previously established thermal criteria for coldwater fishes that occur in Nevada and reviewed recent approaches for determining temperature criteria. Second, we developed supporting documentation along with recommended protocols for monitoring and assessing coldwater stream temperature criteria within water bodies. We also used existing temperature data, along with a subset of data collected specifically for this project, to develop new methods to quantify spatio-temporal patterns in stream temperatures. We worked closely with the Nevada Division of Environmental Protection who provided funding for the project.
Landscape-scale modeling of the distribution and abundance of steelhead redds: The objective of this study was to develop spatially-explicit models predicting redd occurrence and abundance for ESA-listed steelhead trout (Oncorhynchus mykiss) in the John Day River basin, Oregon. I and my collaborators at NOAA-Fisheries, United States Geological Survey, and the U.S. Forest Service developed innovative, landscape-scale, spatially continuous measures of important processes that influence growth and survival of steelhead across multiple life stages. Our goal was to use these measures to predict where steelhead spawn across a complex riverscape, based on empirical data collected during an ongoing spawning survey and monitoring program conducted by the Oregon Department of Fish and Wildlife.
Wildfire and population persistence of threatened fishes: The objective of this study was to develop new methodologies that can be used by forest and fire managers and planners to consider the potential effects of fire management (i.e., fuels reduction to post-fire restoration) on native stream fishes and their habitats across broad landscapes. The approach was demonstrated within a large river basin (Wenatchee, Washington, USA) home to several threatened fish species, including ESA-listed Chinook salmon (Oncorhynchus tshawytscha), steelhead, and bull trout (Salvelinus confluentus). We worked closely with managers and other stakeholders in the region to develop these tools, and the predictive framework that we developed will be useful for the problem assessment, design, and implementation stages of an adaptive management cycle.
Effects of groundwater withdrawal and drought on native fishes in Great Plains streams: My PhD research project under Dr. Kurt Fausch at Colorado State University was funded by the Colorado Division of Wildlife. Here I investigated the effects of groundwater withdrawal on stream fishes and their habitats in the Arikaree River, an eastern Colorado Great Plains stream.
Upstream effects of large reservoirs on prairie stream fish assemblages: My MS work under Dr. Keith Gido at Kansas State University was funded by the USGS Aquatic GAP Analysis Program and the Kansas Department of Wildlife and Parks. This research combined landscape-scale, GIS-derived data with field observations to investigate the upstream effects of large reservoirs on stream fish assemblages and their habitats.