Scott Baker is broadly interested in the evolutionary and ecological pattern and process in whales and dolphins, including their abundance, population structure, genetic diversity and systematic relationships. Scott is particularly interested in projects that bring together both molecular and demographic approaches to improve the conservation of these species. The advent of molecular genetics and the emerging fields of genomics and bioinformatics have provided powerful new tools to describe the hierarchical structure of biodiversity. These tools complement and extend, rather than replace, demographic methods used in animal ecology and conservation biology.

Current Research Topics include:

• Population structure and genetic diversity of whales, dolphins, sea lions and fur seals
• Demographic and genetic impacts of whaling
• Molecular taxonomy and applied bioinformatics for species identification
• Molecular monitoring of ‘whalemeat’ markets in Japan and Korea
• Social organization and kinship in whales and dolphins
• The evolution of Major Histocompatibility Complex (MHC) genes in cetaceans and pinniped

One of the recent initiatives of Scott’s research group has been to establish a web-based program for identification of whales, dolphins and porpoises using applied bioinformatics and a validated database of DNA sequences. Details are available at http://www.dna-surveillance.auckland.ac.nz. An exciting outcome of establishing this database was the discovery of a new species of beaked whales, Mesoplodon perrini (Dalebout et al. 2002) the first mammalian species recognised primarily by genetic characters and the first new species of cetaceans in 15 years.

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Michael Banks' program centers on the application of population genetic principles towards furthering basic knowledge and understanding of marine population processes. We are interested in i) genetic characterization of natural populations, fishery subjects and aquacultural species where we resolve hybridized, admixed, or recently diverged populations, and ii) statistical methods for determining component estimates for mixtures. We are particularly interested in evaluating the information content that can be gained from alternate genetic marker types and resolving links between genetic loci and life history variance.

Marine genetics projects in Banks' lab are diverse and include the following:

• Using molecular markers to resolve species of salmonid that predators (harbor seals, sea lions or marine birds) might be impacting;
• Extracting microsatellites or other genetic elements from marine organisms to provide resources for studying their population dynamics, ecology and life history variance;
• Determining population origin of juvenile salmonids captured in the ocean through microsatellite characterization and applying these techniques to determine the distribution of different life history types during ocean residence;
• Characterization of genetic traits associated with unique life history types among salmon or rockfish by applying a technique called suppressive subtractive hybridization to identify which gene expression patterns are unique to particular life history types;
• Genetic characterization of population characteristics and epidemiology of disease elements or other invasive species that may impact estuarine or marine systems;
• Genetic characterization of the relationships and dispersal patterns evident from a study of specific species across deep sea vent communities;
• Genetic research to establish successful restoration of native oyster bio-filter mechanisms in estuarine systems; and
• Characterization of genes associated with circadian rhythm control in chinook, coho salmon and the coelacanth.

http://marineresearch.oregonstate.edu/assets/page_folders/faculty_page/banks_hp.htm

Originally trained as a forest ecologist, Bryan has used tree ring data (dendrochronology) to reconstruct forest change, disturbance history, and climate. Bryan is now applying tree-ring techniques to the growth increments of long-lived marine organisms in order to address analogous topics in the northeast Pacific. Growth increments in the otoliths of long-lived Pacific rockfish can be treated in the same manner as tree rings and used to construct chronologies that span most of the past century. These rockfish chronologies correlate strongly with indices of ocean variability and quantify long-term trends in rockfish growth. Rockfish chronologies also relate to high elevation tree-ring chronologies from the Cascade Mountains and Sierra Nevada Mountains, showing the synchronous effects of climate in marine and terrestrial ecosystems. As an REU project, a student could develop a marine biochronology from rockfish or long-lived marine clams (geoducks), or develop a tree-ring chronology to relate to marine chronologies. The focus of any of these projects would be on climate variability, its effects on growth, and how it links marine and terrestrial ecosystems.

http://oregonstate.edu/~Blackbry/

Fisheries oceanography is the focus of work in George Boehlert's laboratory, where the effects of ocean variability on marine ecosystems are studied. Specific research includes long-term variability in fish growth related to regime-scale changes in the North Pacific and the use of archival tags to evaluate habitat use. An internship project could include analysis of fish otolith increments to determine growth patterns in differing environments and the response to climate variability.

Ric Brodeur works with the Fish Ecology (FE) Division on factors related to estuarine and ocean survival of salmon, examining aspects of growth, distribution, and health of juvenile, and predator-prey relationships within the ecosystem. Study sites range from small coastal estuaries near Newport, to larger estuaries such as the Columbia River, to the large coastal ecosystems of the California Current. Interns have worked with the Fish Ecology program on a variety of projects including understanding the distribution and life history of various species of plankton and fish. Ric recently worked with an undergraduate student to examine the food web relationships in the deepwater community of Astoria Canyon. The intern processed trawl samples, examined diets and stable isotopes for origins of food sources. She is a coauthor on a paper that was presented at an international meeting and is presently being published.

An example of a project that could be undertaken by a motivated undergraduate student would be to examine the distribution, trophic ecology, and parasite-host relationships of some non-commercial species that would potentially interact with species of interest such as salmon or endangered groundfish species. Some of these species may overlap substantially in diet and distribution and could be potential predators or prey on the targeted taxa. This project could involve going to sea on short research cruises, collect and take samples of the species of interest, and preserve them for later analysis. In the laboratory, the student would examine stomach contents and other biochemical measures of feeding and growth. The student would then analyze the results along with information on the environmental conditions where the species was caught to elucidate potential interactions. This could lead to a report and possible publication if the results were
conclusive.

http://oregonstate.edu/~brodeuri

Introduced species are one of the greatest environmental concerns of the new millennium. John is a pioneer of this field in marine and estuarine ecosystems. His studies include the geography, biology, ecology and history of introduced and native marine species. His research is conducted within the local areas surrounding the Hatfield Marine Science Center and the north Pacific and Atlantic. John's most recent REU collaboration involved the energetic costs of an isopod parasite introduced with ballast water to western US estuaries. The student measured the weight loss in its new mudshrimp hosts to estimate per gram energetic costs of this new parasite to its hosts. The student is senior author on a manuscript describing this work being prepared for the Journal of Crustacean Biology. He will present this work also at the international (ASLO) meeting in Hawaii in February 2006.

A strong science background is necessary but specific training and all necessary general information and materials required for independent projects are provided in the program. Possible projects could include the distribution, trophic ecology, or parasite-host relationships of introduced non-native species affecting native salmon or commercial oyster populations. These projects may require sampling trips to Pacific Northwest research areas or laboratory and field manipulations of introduced and native species to determine their interactions in marine and estuary ecosystems. Projects are mentored for completion in the allotted time, for quality and innovation sufficient for eventual publication and for sufficient general interest to warrant presentation at major scientific meetings.

Ted DeWitt is a part of EPA's Pacific Coastal Ecology Branch at HMSC, which aims to develop the scientific basis for assessing the condition and response of ecological resources of the US Pacific coast estuaries. EPA researchers explore linkages and feedbacks between habitats, fauna, and water quality in Pacific northwest estuaries. Ted is especially interested in the effects of nutrients (and other pollutants) on estuarine invertebrate communities and on critical ecosystem processes. Examples of internship projects include:

 

Two major research project’s are being addressed in Brett Dumbauld’s lab: 1) ecology of pests and predators affecting West coast marine shellfish aquaculture with a focus on the problem oyster growers are currently having with two species of burrowing shrimp that cause their crops to be smothered by estuarine sediments and die and 2) the role of shellfish aquaculture in West coast estuaries with a current focus on the effects of shellfish on eelgrass and other habitat and the use of these habitats including aquaculture beds by other marine organisms. Study sites include several West coast estuaries where shellfish aquaculture is important from Humboldt Bay, California to Willapa Bay, Washington with a focus on the latter, since this estuary produces over 10% of the nation’s oyster crop. Oyster growers in Washington state have historically applied a pesticide to the estuarine tideflats to kill burrowing shrimp and Brett’s research is designed to examine the life history and behavior of these shrimp to assist them in finding alternative control procedures and develop an integrated pest management plan. Pest control and other aquaculture practices certainly influence the estuarine environment, but aquaculture is a very important component of the local coastal economy and Brett’s research is designed to investigate this impact and determine whether these practices are environmentally and economically sustainable and how to keep them that way. Students can participate in on-going field studies in coastal estuaries and/or carry out experiments in the laboratory. REU projects might involve examining burrowing shrimp molting patterns and behavior, mating, or juvenile growth and behavior with a focus on determining whether there are vulnerable periods for control. Other projects could be related to several avenues of research into how juvenile fish and crab or other organisms utilize shellfish aquaculture areas. These projects have and will continue to offer opportunities to collaborate with other mentors, for example John Chapman with an investigation of how parasitic isopods might be used for biological control of burrowing shrimp or Cliff Ryer and Jessica Miller on fish behavior as it relates to shellfish as habitat.

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The Acoustic Monitoring Project, managed by Bob Dziak, is a joint venture between Oregon State University and the NOAA Vents Program. The main research focus of the project’s faculty is to develop effective hydroacoustic methods for the detection of earthquakes associated with seafloor volcanic and tectonic activity. To accomplish this goal, researchers use hydrophone arrays that are part of the U.S. Navy's SOund SUrveillance System (SOSUS) that monitors northeast Pacific spreading centers in real time. Project personnel also have developed and deployed self-recording (autonomous) hydrophones used for regional experiments throughout the global oceans.

Undergraduate intern projects would involve utilizing the ocean earthquake database to study seafloor volcanic and tectonic processes. An example project would be to use a GIS (e.g. ARC-GIS, GMT, or other mapping tools) to plot earthquakes on a map of the seafloor and then develop a "movie" of how the earthquakes change through time, allowing for insights into the dynamics of short-term plate motion. Earthquake databases available for analysis cover the global oceans, from the northern Mid-Atlantic Ridge to the north and eastern equatorial Pacific Ocean, the Mariana Islands and will soon include the Scotia Sea off the Antarctic Peninsula. In addition, several ocean engineering, software development, and computer management undergraduate intern projects are available. We currently have a project underway to develop a “smart-hydrophone” within a float that can dynamically adjust its buoyancy. When the hydrophone detects a certain type of acoustic signal, the float rises from the seafloor to the sea-surface. Once at the sea-surface, the float transmits a copy of the acoustic signal to a satellite which then relays it to our laboratory for further analysis. We need an intern to develop the software communication (interface) between the hydrophone and the Digital Signal Processor on the float. Requirements for the intern include (1) knowledge of C or C++, and (2) familiarity with digital and analog electronics. The intern will acquire practical knowledge of how to build a DSP platform and gain familiarity with signal processing techniques.

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Geological research is also conducted in the Vents Program (NOAA/PMEL). This long-term effort began in 1984 and seeks to understand the dynamics of the global seafloor spreading system and the impact of its volcanic eruptions and hydrothermal vents systems on the ocean environment. Three specific projects are resident at HMSC. The acoustic monitoring project, headed by Bob Dziak, uses hydrophone arrays of the U.S. Navy's SOund SUrveillance System (SOSUS) to monitor northeast Pacific spreading centers in real time, and deploys self-recording hydrophones through out the global ocean. The seafloor imaging and monitoring team, led by Bob Embley and Bill Chadwick, uses a variety of deep-sea tools, including multibeam sonars, side scan sonars, deep-sea cameras, remotely operated vehicles, and manned submersibles such as ALVIN. The group also maintains seafloor pressure meters, acoustic ranging devices and temperature monitors at the NeMO site on Axial Volcano lying 500 km west of Newport. The ocean tracer project, led by John Lupton, uses an advanced mass spectrometer system to measure trace levels of He-3 and other noble elements in seawater. These data provide near-field measurements of hydrothermal activity and a long-term view of the mid-water circulation in the global ocean. In addition to this primary focus, there are also active research projects in marine mammal acoustics and essential fish habitat. A wide range of projects is potentially available for participation by REU interns. The Vents acoustic monitoring project has numerous acoustic recordings available for analysis of signals from earthquakes, volcanic activity, marine mammals, and general ocean noise. Seafloor imagery from both mid-ocean ridge and continental shelf regions is available for integration and interpretation in support of mid-ocean ridge and essential fish habitat research.

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Sarah works with the Northwest National Marine Renewable Energy Center, examining the ecological effects of wave energy development. Sarah's focus is on fishes and invertebrates associated with the sea floor and those that may become associated with wave energy devices following deployment. Work in Sarah's lab includes large-scale community surveys as well as targeted experiments.

Projects for intern to undertake may include:

Tom Hurst is a Research Fisheries Biologist with the Alaska Fisheries Science Center's Fisheries Behavioral Ecology Program. Tom's research interests focus in the physiological ecology of fishes and how environmental variability affects the feeding, growth, and survival of early life stages of marine fishes. For example, a recent study compared the depth distribution, light requirements for feeding, and diets of three co-occurring flatfishes. Tom is particularly interested in the pervasive effects of temperature variation on fishes and communities. He recently completed a comprehensive review of the phenomenon of 'winter mortality' and is currently examining how temperature affects fish behavior, including schooling and vulnerability to predators. Species currently being researched are Pacific cod, walleye pollock, northern rock sole and Pacific halibut.

A current area of investigation that an intern would participate in is the behavior of Pacific cod larvae. The delivery of larval fish to nursery grounds suitable for growth and survival is dependent upon the interaction between the oceanographic flow field and the larvae's behavioral response to gradients in the environment. In this project, a student intern will conduct laboratory studies of the behavior of larval Pacific cod in vertical water columns. Factors that will be examined include the responses to light conditions, prey availability, water turbulence and water temperature. The selected intern will take primary responsibility for examining one or two of these factors while collaborating on examination of other factors. Ultimately this data will be used in conjunction with oceanographic models of the Bering Sea to determine patterns of larval transport and delivery to preferred nursery grounds.

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Kym Jacobson and members of her lab are interested in the ecology of host-parasite interactions.  Kym is zoologist with the Estuarine and Ocean Ecology program of NOAA Fisheries.  Her current research examines the ecology of host-parasite interactions of anadromous and marine fishes in the Columbia River estuary and the Northeast Pacific Ocean.  One area of research in her lab focuses on parasites of juvenile salmon as salmon make the transition from freshwater to estuarine and marine habitats to gain a better understanding of environmental factors that affect salmon-parasite relationships and the potential effects of parasites on growth and survival of salmon populations. Her research also examines parasites obtained through trophic interactions to gain a better understanding of fish diet, migration, and habitat use and conditions.  In addition to studying parasite communities of juvenile salmon her lab is also studying parasites of Pacific sardines to gain a better understanding of migration patterns and habitat use to help delineate potential stock separation.  Potential projects could examine any life stage of a parasite in fresh water, estuarine, or marine habitat.

 

The two major research themes being pursued in Chris Langdon's laboratory are: 1) genetic effects on growth, survival, disease resistance and morphology of Pacific oysters, and 2) nutritional requirements of altricial marine fish larvae. The oyster genetics program complements research in Michael Banks' laboratory. A major emphasis of this program is determination of genetic effects on life history traits of Pacific oysters (Crassostrea gigas). Banks and Langdon are also working to develop strategies to restore populations of the native oyster (Ostrea lurida) on the West coast by developing genetic markers for stock identification together with manipulation of culture conditions to maximize reproductive success. A research intern could i) determine physiological and behavioral traits in larval and juvenile oysters that are correlated with growth and survival of adults, ii) determine quantitative trait loci (QTL) that are correlated with growth, survival, disease resistance or morphological traits of oysters, or iii) determine microsatellite markers that allow identification of different genetic stocks of native oysters on the West coast.
For the altricial marine fish larvae research, experiments are currently underway to determine which dietary amino acids are important in triggering feeding responses in larvae and to evaluate nutritional requirements of larvae for dietary free amino acids versus peptides and proteins. A key component of this research project has been the establishment of a breeding colony of clown fish at HMSC that provides a regular and ample supply of larvae for experimentation. An intern could i) examine responses of marine fish larvae to various feeding stimulants delivered in microencapsulated diets or ii) develop optimal culture conditions for rearing larvae of different rockfish species.

http://marineresearch.oregonstate.edu/assets/page_folders/faculty_page/langdon_hp.htm

 

I am interested in the ecology and evolution of life history diversity in fishes and the development and maintenance of that diversity. My research focuses on dispersal and transport, population connectivity, and migratory behavior of marine and anadromous fishes. For example, I am interested in how juvenile salmon use coastal watersheds and how management and restoration activities affect those patterns. I have combined techniques, including otolith microchemistry, genetic, and time-series analyses, to provide novel information on these topics. Currently, I am continuing to use otolith microstructure and chemistry to identify patterns of mixing and migration in marine and anadromous and also working on the ecological assessment of estuarine restoration efforts. REU projects could involve reconstruction of migratory behavior in juvenile salmonids, estuarine field research on the impacts of native oyster restoration, or participation in laboratory experiments.

Dr. Peterson's research in biological and fisheries oceanography encompasses several research programs, including research in the Northeast Pacific GLOBEC program. One of his main interests is how climate variability and climate change impact marine food webs and Pacific salmon. Towards that end, his laboratory maintains a long-term study of hydrography and plankton dynamics along a sampling line that crosses the continental shelf off Newport, OR and is sampled biweekly. These cruises have been conducted continuously since 1996, which provides the opportunity for projects related to long-term changes in the plankton community in relation to climate variability. Research cruises sample each of seven stations, using CTD casts, surface water samples, phytoplankton nets and zooplankton tows to collect data on physical, chemical and biological parameters. Live animals are collected and transported to the laboratory for experimental measurements of euphausiid (krill) egg production and molting rates, and copepod egg production rates. Undergraduate students can participate in oceanographic cruises and carry out laboratory experiments on living zooplankton and phytoplankton. Recent interests have focused on the impact of seasonal hypoxia on the development of zooplankton and on the potential effects of ocean acidification on pteropods (pelagic mollusks). Dr. Peterson's lab is also involved in research on harmful algal blooms (HAB) and is working on techniques to forecast their occurrence.

Dr. Peterson is also a principal investigator in a study that examines the effects of physical and biotic conditions on the distribution of zooplankton and fish, especially salmon. Research cruises are conducted in May, June and September to determine the distribution and abundance of zooplankton, juvenile salmon, and other fishes in relation to ocean conditions. One focus of this effort is on how changes in zooplankton community composition relate to salmon survival and growth rates, and how each is related to climate variability. This research has shown that zooplankton can be useful indicators of climate variability and that these lower trophic level organisms are good indicators of ecosystem health. These oceanographic data are applied to forecasting the returns of salmon to coastal rivers; these forecasts are available on the web at http://www.nwfsc.noaa.gov under "Ocean Index Tools".

REU students who have worked in the Peterson lab have studied habitat use of juvenile salmon, and compared catches of krill in different types of plankton nets. They have also conducted experiments with live zooplankton to measure vital rates of krill (growth, molting, feeding), and to examine the effects of low oxygen concentration (hypoxia) on hatching of copepod eggs and development of nauplii. All REU students have had the opportunity to participate in oceanographic cruises.

Clare Reimers conducts research in biogeochemistry and chemical oceanography from laboratories within HMSC. Her lab group employs novel electrochemical methods to study how chemical resources are utilized in diverse marine environments. In one recent project, different designs of microelectrodes were used to characterize distributions of pore water O2, Fe, Mn, H2S and pH around rhizomes and vertical roots of the seagrass Zostera marina. This work was in collaboration with plant physiologists and modelers from the EPA lab at HMSC. Electrochemical sensors are also being applied in situ as part of a study of biogeochemical processes associated with rippled sand beds on continental shelves. The sensors are used to detect dissolved iodide as a tracer of pore-fluid velocities under the influences of natural waves and currents. For a third project, electrochemical devices placed across the sediment-water interface are being developed to harvest low-levels of electrical power by using natural, continually renewed, chemical resources in sediment and at geochemical seeps as "fuel" and dissolved seawater oxygen as oxidant. This new technology functions much like a microbial fuel cell, taking advantage of the voltage gradient that occurs in the top few centimeters of the sediment column. Interns working in Reimers lab would be engaged in both field and laboratory aspects of these and other interdisciplinary studies. They would be taught analytical techniques and given the opportunity to collect and interpret data sets that reveal spatial and temporal variation in biogeochemical processes. The student may also develop a working model of a benthic microbial fuel cell for an exhibit in the HMSC Visitors Center and/or make exhibit improvements based on public responses.

Shawn joined the staff of Sea Grant Extension and the Department of Science and Math Education at OSU after receiving his Ph.D. from Washington University in St. Louis. His research combines methods for studying learning outside of school with tools for analyzing how groups make sense out of what they say and do. Along with Dr. Olga Rowe, he has carried out research in history and science museums both in the US and in Ukraine. His current position combines academic work on Free-choice learning with practice-based research in the OSU Hatfield Marine Science Visitor Center in Newport, OR.

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Clifford Ryer
Assistant Professor (NOAA)
Behavioral Ecology