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/mfg-lab

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.

Understanding feeding habits of pelagic nekton is important in understanding their trophic position within the northern California current food web and potential changes expected under climate change scenarios. Dietary overlap of pelagic nekton with commercially important fishes such as juvenile salmon could identify the potential of competition for resources during a critical period of survival for salmon. Research into the feeding habits of pelagic nekton could be incorporated into multispecies food-web models and would be of interest to resource managers as they undertake an integrated ecosystem assessment of the California Current. A project exists within the NOAA Estuarine and Ocean Ecology project to analyze the diets of several common nekton species already collected along with new specimens collected this coming summer to look at diet overlap with salmon and compare to past studies done during different environmental conditions.

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 shellfish 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 the growers 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 affect burrowing shrimp populations 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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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 effect of ocean acidification on larval and juvenile stages of Alaskan fishes. Ocean acidification is caused by the dissolution of anthropogenically produced CO2 into the surface ocean, reducing the pH of the ocean. Research has shown that low pH can affect the growth, survival, and behavior of small fishes. The selected intern will take primary responsibility for conducting experiments on one of these responses while collaborating on examination of other responses. Ultimately this data will be used in conjunction with climate models of the Bering Sea Gulf of Alaska to determine the long term consequences of ocean acidification to fisheries production.

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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

 

Ben Laurel is a Research Fisheries Biologist with the Alaska Fisheries Science Center's Fisheries Behavioral Ecology Program. His interests include the behavioral and physiological ecology of larvae and juvenile fish species in coldwater marine systems. He is particularly interested in the role that behavior and physiology drive patterns of habitat use, survival and dispersal during these early life stages. He uses a combination of experimental and field approaches in his research.
Ben is currently examining settlement dynamics of larval northern rock sole in the laboratory. Like all flatfish, rock sole undergo a metamorphosis as they transition from a highly dispersive pelagic larval stage to a relatively sedentary benthic juvenile stage. The timing and location of settlement are critical to the survival of the fish, but it is uncertain whether larvae can control this process. The widely held view is that settlement in flatfish is a hard-wired size-dependent process, but new evidence suggests there is also a behavioral component. A potential intern project would be to examine these questions experimentally in the lab. These data could then be used to improve models of larval drift and nursery transport in this species.

http://www.afsc.noaa.gov/RACE/behavioral/default.php

 

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.

Kathleen O’Malley’s research interests focus on the evolutionary and ecological processes in freshwater and marine species and how they interact to shape life history variation within and among populations. The goal is to advance our understanding of population abundance and structure, genetic diversity, and the genetic mechanisms underlying life history trait variation and assist fishery management and conservation efforts. Kathleen’s research group uses cutting-edge molecular techniques as means to identify factors important to retaining genetically healthy populations.

Intern projects may focus on::

• Understanding the genetic basis of migration timing in Pacific salmon
• Assessing the population genetic structure of Dungeness crab
• Evaluating fitness differences between hatchery and wild salmon

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William Peterson
Professor
Oceanography, Plankton Ecology

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Clare Reimers
Professor
Biogeochemistry

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Shawn Rowe
Assistant Professor
Free Choice Learning