Ongoing Research

-->At the heart of the Pacific Northwest, the University of Washington in Seattle is an ideal location for studies on salmon and marine systems. Researchers based here work on populations of salmon and other marine life from Northern California through Oregon, the Columbia River Basin, Puget Sound, the Pacific Coast, all the way to Alaska. Their goal is to investigate how the environment affects these organisms, subsequently aiding our understanding of how changing climate will alter the biological world of salmon. The following researchers are thus dedicated, and here share their groundbreaking recent and ongoing work.

Associate Professor Lorenz Hauser

Lorenz Hauser: Associate Professor Lorenz Hauser is a population geneticist whose research uses genetic markers in DNA to look at the demographic history of populations. Some of his most recent work has involved comparative studies on species and populations, using the identification of unique regions of a group’s genetic makeup to identify susceptibility to climate change. Using genetic markers, his lab was able to determine species of shark that were most susceptible to the last ice age, which may indicate vulnerability to future accelerated climate change. While this requires some extrapolation of responses to a cooling climate and applying them to a warming climate, this identification of historic thermal weaknesses may highlight populations or species of particular concern in a once-again changing environment. Another such study involves genetic analysis of Pacific Cod populations to locate regions of the genome that are significantly different between those performing poorly in Puget Sound and those thriving in Alaska. Puget Sound Pacific Cod are most likely heat stressed, possibly leading to genotype-specific mortality; consequently, the degree of genetic variability present in the population will most likely determine whether they are capable of adapting to environmental change. Specific rearing experiments that involve raising Pacific Cod larvae in both warm and cold conditions will indicate, 1. whether there is enough such genetic variation to allow the fish to adapt and persist in a warming climate, and 2. how strong natural selection would be, predictive of what proportion of deaths would be attributed to temperature. Both techniques could, in theory, be applied to salmon to describe species extinction and expansion events in the past, as well as identify regions of the genome that may aid in the adaptation to changing climate [28].

Website: http://fish.washington.edu/people/hauser/
Relevant Publication(s): Canino MF, Spies IB, Cunningham KM, Hauser L, Grant WS (2010) Multiple ice age refugia in Pacific cod, Gadus macrocephalus. Molecular Ecology 19, 4339-4351

Associate Professor Nathan Mantua

Nathan Mantua: As co-director of the Climate Impacts Group, Associate Professor Nathan Mantua’s work focuses on making future climate projections relevant to the Pacific Northwest. By downscaling global climate projections, his group is able to produce a local picture of what climate change might look like for the PNW. Most notably, future predictions of temperature and precipitation are used to generate hydrologic features for watersheds across the region, in particular changes in snow pack, soil moisture, and stream flow – all of which will influence the future success of PNW salmon. Mantua’s current research with the Climate Impacts group focuses on how the above variables contribute to the creation of population bottlenecks in freshwater salmon habitat. The availability of cold water in the summer, determined primarily by snow pack accumulation and subsequent release, will be key to the success of salmon species whose life histories involve spawning in late summer and juveniles rearing for a year or more in fresh water. These species are subjected to the stress of elevated summer temperatures multiple times in a lifetime, and are thus most threatened by increasing temperature. A shift in winter precipitation from snow to rain increases opportunities for winter flooding events, which, if particularly intense, could scour salmon redds and wash incubating eggs and juveniles downstream. Such changes in flow regime may limit the overall success of spawning events, reducing the number of young salmon that migrate to the ocean as well as the ultimate number of adults returning to spawn of that generation [29].

Website: http://www.atmos.washington.edu/~mantua/
Relevant Publication(s): Mantua, N. J., Metzger, R., Crain, P., Brenkman, S., & Halofsky, J. E. (February 21, 2012). Climate change, fish, and fish habitat management at Olympic National Forest and Olympic National Park. Usda Forest Service - General Technical Report Pnw-Gtr, 844, 43-60.
            Mantua, N., Tohver, I., & Hamlet, A. (September 01, 2010). Climate change impacts on streamflow extremes and summertime stream temperature and their possible consequences for freshwater salmon habitat in Washington State. Climatic Change, 102. 
            Mantua, N. J. (January 01, 2009). Patterns of Change in Climate and Pacific Salmon Production. American Fisheries Society Symposium, 70, 1143-1158
            Lawson, P.W., E.A. Logerwell, N.J. Mantua, R.C. Francis, and V.N. Agostini. 2004. Environmental factors influencing freshwater survival and smolt production in Pacific Northwest coho salmon (Oncorhynchus kisutch). Canadian Journal of Fisheries and Aquatic Sciences, Vol 61, Number 3: 360-373.  

Dr. Ingrid Tohver

Ingrid Tohver: Dr. Tohver works with the Climate Impacts Group as a research scientist involved in the execution of a statewide assessment of Washington’s natural resource sectors and how they might be affected by climate change, as part of a legislative effort to devise an adaptation plan. Hired by Nathan Mantua, she conducted an analysis of water temperature and stream flow, focusing on how changes in these variables might affect salmon in the future. Air temperature projections (downscaled from global climate data) were used to predict consequent water temperatures via a regression model for each of 125 sites across the state. The result provided a comprehensive look at where in Washington state salmon may be threatened by warmer summer water temperatures in the future – information of importance as salmon are cold water species that may be deterred in reaching their spawning grounds by the creation of warm water thermal barriers. The analysis also included a stream flow component, in which changes in extreme stream flows, otherwise known as winter flooding events, were mapped around the state. This projection describes locations where 20-year and 100-year flooding events (floods of particular magnitude that statistically occur every 20 or 100 years) may become more severe. Increases in winter flooding are accompanied by lower summer flow, which, compounded with warmer air temperatures, can exasperate the problem of warming stream temperatures.

            Dr. Tohver has also been involved in Seattle City Light projects to investigate changing stream conditions as a precursor to the development of water management plans. Varies sites along the Skagit River and the tributaries of the Skagit headwaters were targeted to identify where salmon might be affected by climate in the future. While the tributaries themselves are kept cool by ground water input and glacial melt, the study found that mountainous slopes are differentially affected, depending on their east-west orientation. Slopes that face westward exhibit a mountainous effect, with increased warming due to more direct sun exposure than east facing slopes. Eastern slopes maintain their snowpack later into the summer, are glacier-fed, and ultimately stay cooler throughout the summer months. Eastern slopes in the Skagit River system thus provide better habitat for salmon. These results will be used by Seattle City Light to determine how they might alter their damming practices to meet increasing power demands while mitigating climate change for salmon [30].

Relevant Publication(s): Mantua, N., Tohver, I., & Hamlet, A. (September 01, 2010). Climate change impacts on streamflow extremes and summertime stream temperature and their possible consequences for freshwater salmon habitat in Washington State. Climatic Change, 102.

Associate Professor Kerry Naish

Kerry Naish: Associate Professor Kerry Naish works generally on the evolution of fitness traits, and specifically on salmon. Her research seeks to understand how traits related to reproductive success are inherited from one generation to another, such as number of offspring, adult size, and timing of spawning. Most of Naish’s work to date describes Puget Sound and Columbia River populations and utilizes pedigrees to quantify how much of a population’s genetic variation is passed from generation to generation. This involves catching all spawning adult salmon from one generation as well as all of their returning offspring of the next generation, then using forensic techniques to scrutinize their DNA and assign offspring to their parents. Pedigrees can then be used to determine the rates of inbreeding in a population to answer questions of how often related salmon are mating with one another, and if the original size of the population matters in determining this rate, as well as the effects of inbreeding and how it drives evolutionary change. Further, pedigrees can be enlisted to assess the effects of hybridization as a potential consequence of conservation effects to alleviate inbreeding stresses. The introduction of a new population to breed with an existing population could result in either maladapted or more fit offspring, and determining the likelihood of these results is key to ensuring the success of such management practices.

            From studying the inheritance of traits in this manner, predictions can be made on how a specific trait might evolve in the future with changing climate. The fitness of salmon populations in changing climatic conditions will be determined by their adaptation to the environment, or rather how the inheritance of fitness traits changes in response to environmental conditions. Such adaptive traits can be studied in depth by genome sequencing, which is part of Naish’s ongoing work. Though a complete baseline of a salmon genome is still lacking, sequences of salmon from populations with differential success in warm and cold stream temperatures can be compared to identify the genes that are involved in conferring advantages in particular stream conditions. Once the genes are identified, their prevalence and presence in different populations can be studied to assess genetic variation and the probable adaptations that will occur in response to changes in environmental drivers of evolution [31].

Website: http://fish.washington.edu/people/naish/index.html
Relevant Publication(s): McClelland EK, Naish K (in press) Quantitative trait locus analysis of hatch timing, weight, length and growth rate in coho salmon, Oncorhynchus kisutch. BMC Genomics.
            Naish KA, Hard JJ (2008) Bridging the gap between the phenotype and the genotype: linking genetic variation, selection, and adaptation in fishes. Fish and Fisheries 9, 396-422.
            McClelland EK, Naish KA (2007) What is the fitness outcome of crossing unrelated fish populations? A meta-analysis and an evaluation of future research directions. Conservation Genetics 8, 397-416.
 

Professor Thomas Quinn

Thomas Quinn: An evolutionary ecologist, Professor Thomas Quinn has a broad range of research interests that revolve around the behavior, ecology, evolution, and conservation of salmon species. Much of his long-term work has been based in Bristol Bay, Alaska, which is the center of distribution for sockeye salmon. The location is ideal for studying the adjacent lake systems that sockeye juveniles rely on for 1-2 years prior to their migration out to sea. The area has experienced visible warming, resulting from natural ocean system oscillations as well as the added influence of greenhouse gases. The consequential changing lake conditions have been the target of Quinn’s research. Investigations have sought to describe the size at which sockeye juveniles leave the lakes, what proportion of the populations migrate after 1 versus 2 years, how many years the salmon spend at sea before returning, and overall survival.

            Other interests have driven studies to understand the mechanisms and ecological processes of migration. The migration timing of salmon has evolved to accommodate differences between saltwater and freshwater habitat, allowing for some flexibility to account for environmental variation. The timing of migration then provides noticeable evidence of changes in climate. Past work on transplanting salmon to New Zealand drew on observations of the colonization of warm and cold rivers and the differentiation of migration timing to conclude that salmon have considerable capacity to evolve their migratory patterns in response to temperature. This supports the notion that genetic control over salmon spawning is strong, enabling evolution of spawning behavior to follow environmental change. More contemporary work on migration timing is being conducted in the Puget Sound. Conditions in the Sound appear to affect the proportion of juvenile salmon that remain within the estuarine system rather than migrating out to coastal waters. Quinn is in the process of investigating why significant numbers of coho and Chinook salmon end their migration in the salt water of the Puget Sound. The portion of salmon exhibiting this behavior seems to vary by year and may be influenced largely by climate, but also by fishing practices, habitat quality, and hatchery operations. Such work on the evolutionary ecology and migration timing of salmon holds implications for the potential changes in migratory and spawning behavior that may accompany changing climate [32].

Website: http://fish.washington.edu/people/tquinn/index.html
Relevant Publication(s): Quinn, TP, R Sharma. 2012. Linkages between life history type and migration pathways in freshwater and marine environments for Chinook salmon, Oncorhynchus tshawytscha. Acta Oecologica 41:1-13.
            Quinn, T. P., H. B. Rich, Jr., D. Gosse, and N. Schtickzelle. 2012. Population dynamics and asynchrony at fine spatial scales: A case history of sockeye salmon population structure in Alaska. Canadian Journal of Fisheries and Aquatic Sciences. 69: 297-306.
            Chamberlin, J. W., T. E. Essington, J. W. Ferguson, and T. P. Quinn. 2011. The influence of hatchery rearing practices on salmon migratory behavior:  Is the tendency of Chinook salmon to remain within Puget Sound affected by size and date of release? Transactions of the American Fisheries Society 140: 1398-1408.
            Quinn, T. P., M. J. Unwin and M. T. Kinnison. 2011. Contemporary divergence in migratory timing of naturalized populations of Chinook salmon, Oncorhynchus tshawytscha, in New Zealand. Evolutionary Ecology Research 13: 45-54
 

Research Professor Charles Simenstad

Charles A. Simenstad: Research Professor Charles Simenstad is an estuarine ecologist whose research investigates the habitat requirements of juvenile salmon migrating to the ocean. The life history traits of different species influence the degree of their dependence on estuarine habitat, so Simenstad’s work seeks to describe how important estuarine habitat is to the rearing of various species, as well as the mechanisms that promote their rearing. In the Columbia River, for example, his projects involve trying to identify habitat requirements and carry capacity to determine if humans have limited the productivity of threatened Chinook salmon by altering the quality of suitable habitat. Beyond the physical barrier dams pose to salmon migration and spawning, the development of the estuary and flow modifications may affect the ability of salmon to utilize available habitat. The research then looks to determine how these actions and conditions affect the development of juvenile salmon as well as the return of adults. The effects of estuary modification may be realized in the resultant resilience of salmon populations and their capacity to respond to both natural ocean variability and continued anthropogenic climate change.

            Another ongoing project in the Puget Sound is the maintenance of a database for the restoration of nearshore ecosystems. The database represents the habitat that was historically available to salmon in watersheds and estuaries. It provides a basis for the analysis of the degree to which salmon rely on remaining Sitka Spruce swamps for rearing, shrub shore systems, and emergent wetlands and marshes. The reality of climate change threats to the availability of estuarine habitat will further determine how salmon fare in the future. Rates of sea level rise and sediment discharge will dictate whether existing marshes will persist and whether new wetlands will be created. Simenstad proposes that combining projections of sea level rise and sediment discharge with the habitat database could empower conservationists to take advantage of climate change in management practices of estuarine habitat. Sediment delivery may outweigh sea level rise in some areas, which, if identified as suitable potential habitat and a location of significant salmon usage, could be considered as candidates for wetland conservation. Such land could then be purchased from private or public owners, have dikes and other man-made structures removed, and allowed to be flooded as sea level rises, eventually returning to natural wetland habitat [33]. 

Website: http://fish.washington.edu/people/simenstd/
Relevant Publication(s): Gray, A., C. A. Simenstad, D. L. Bottom and D. A. Beauchamp. In review. Bioenergetics modeling of wild
juvenile Chinook salmon performance: Determining relative success of restoring tidal wetlands at the Salmon River estuary, Oregon USA. N. Am. J. Fish. Mgmt.
            Miller, J. A., V. L. Butler, C. A. Simenstad, D. H. Backus, and A. J. R. Kent. 2011. Persistent life history variation in Columbia River Chinook salmon (Oncorhynchus tshawytscha): a comparison using modern and ~500 yr-old archaeological otoliths. Canadian J. Fish. Aquat. Sci. 68:603-617.
            Borja, A., D.M. Dauer, M. Elliott and C.A. Simenstad. 2010. Medium and long-term recovery of estuarine
and coastal marine ecosystems—an approach for new scenarios to restore ecological integrity. Est. Coasts 33: 1249-1260.