Oregon State University

Banks 2012-2013 Research Update

Marine Fisheries Genetics

Michael Banks, Associate Professor, Coastal Oregon Marine Experiment Station and Department of Fisheries and Wildlife

Our research in population genetics among Pacific salmon and other West-Coast fishery species seeks to determine how population structuring relates to the physical, biological and human components of the environment.  We develop methods to resolve differences among hybridized, admixed, or recently diverged populations, and statistical means for determining component estimates that are typically mixtures of various stocks or sub-populations. We apply candidate and population genomic tools to determine how fish sense and use smell (olfaction), electromagnetism (orientation), seasonal photoperiod changes (time) and other faculties to mediate migration and population structuring among stocks, environment and climate.  We also use genetic pedigrees to study population ecology.

Amelia Whitcomb, co-advised by Dr. Kathleen O’Malley, who recently completed her MS is now continuing work in sustainability of fish and wildlife resources in Olympia, in Washington Department of Fish and Wildlife’s Genetics Laboratory.  Her research findings, in which she used major histocompatibility complex (MHC) and non-MHC immunity markers to study evidence for mate choice differences among coho salmon that had either hatchery or wild ancestry, are currently being prepared for review for publication in Canadian Journal of Fisheries and Aquatic Sciences

Two manuscripts have been published in the journal Molecular Biology Reports, providing near-complete mtDNA genomes for krill species providing first fruits from the Roch 454 Junior Genome Sequencer recently installed in lab.  This work, in collaboration with HMSC resident NOAA Senior Scientist Bill Peterson, was achieved by post doc Mattias Johansson (now at University of Wisconsin-Milwaukee), graduate student Angie Scremba (PhD candidate studying with Scott Baker) and REU student Elizabeth Duda (hosted in our lab). 

Our work in discrimination among alternate Chinook runs of the Sacramento River system has produced two manuscripts.  One, senior-authored by Michael Banks, covers a blind test of three different microsatellite panels and s in review for Animal Genetics.  The second, senior-authored by Kathleen O’Malley, applies clock gene markers to spring and fall sub-population discrimination challenges on the Feather River and is in press for Evolutionary Applications.  

Likewise the Coast-wide Genetic Stock Identification Collaborative has produced manuscripts.  One, senior-authored by William Satterthwaite (from NOAA’s Southwest Fisheries Science Center), uses Genetic Stock Identification to compare Klamath River versus California Coastal Chinook salmon in terms of their ocean spatial distribution, size-at-age, and fishery exposure and is in press for Canadian Journal of Fisheries and Aquatic Sciences.  Two other manuscripts senior-authored by Reneee Bellinger utilize new methods to calibrate stock specific capture findings in the context of fishery effort as a means of assessing migration distribution patterns for Chinook salmon stocks encountered off the coast of Western North America; these are in revision. 

Our co-authored manuscript for the Canadian Journal for Fisheries and Aquatic Sciences that results from collaboration with the Genetic Analysis of Pacific Salmon group has been published.  Paul Moran of the Northwest Fisheries Science Center is senior author of this manuscript which is entitled: Traditional life-history “races’ in Chinook salmon are specific to the Columbia River and do not represent the species as a whole.

PhD students of Nick Sard and Chanté Davis have completed their course work, finalized their thesis committees and are now preparing their first research for peer review publication.  Nick’s covers findings from a pedigree study of four consecutive-year samples of juvenile Chinook that result from spawning among spring Chinook outplanted above Cougar dam.  Offspring from outplants in 2010 and 2011 provide insight into relative fitness of hatchery and wild hybrid offspring.  Chante’s work provides a first comprehensive study of population sub-structuring among Chinook salmon of the Siletz River. 

Incoming projects include a population sub-structuring study among steelhead from the Siletz River and how steelhead populations distributed further afield are affected by climate extremes.   Still pending is a yet to be funded study of population structuring among mullet sampled from marine waters nearby to Taiwan, Japan and the Philippines. 

Contact Info

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2030 SE Marine Science Drive
Newport, OR  97365
Tel:  541 867-0230
(at the Hatfield 
Marine Science Center)


2001 Marine Drive, Room 253
Astoria, OR  97103
503 325-4531
(at the Seafood Research 
& Education Center)