Oregon State University

O'Malley 2012-2013 Research Update

Ecological and Conservation Genetics of Fishes

Kathleen O’Malley, Assistant Professor, Coastal Oregon Marine Experiment Station and Department of Fisheries and Wildlife

The Ecological and Conservation Genetics Laboratory (ECGL) is dedicated to the study of how genetic and environmental factors interact to shape life history variation among populations of marine and freshwater organisms, particularly salmon and Dungeness crab. The goal is to advance our understanding of the primary processes underlying genetic diversity within and among populations distributed along the West coast and assist fishery management and conservation efforts.   The ECGL employs cutting-edge molecular techniques as means to identify factors important to retaining genetically healthy populations.  Three primary areas of research are:

- Understanding the genetic basis of run timing in Pacific salmon                      

- Assessing the population genetic structure of Dungeness crab

- Evaluating fitness differences between hatchery and wild salmon

Run timing in Pacific salmon: To better understand the run time diversity observed within and among Pacific salmon species, the ECGL is working towards identifying the primary genes and environmental cues influencing the time at which adults return to spawn in their natal rivers.  Photoperiod (day length) is a long-term, stable environmental cue that animals can use to regulate seasonal behaviors (i.e. reproduction, dormancy and migration). Most plants and animals (including humans), have a daily molecular oscillator, known as the circadian clock, that is primarily entrained by photoperiod, and thus provides a genetic mechanism for long-term timekeeping to forecast optimal timing of these seasonal behaviors.

In collaboration with the MFGL (M. Banks), the ECGL recently identified variants in three circadian clock genes that discriminate between the fall and federally-listed threatened spring runs of Chinook salmon in the Feather River, California.  These three genetic markers will prove to be a valuable tool in managing and restoring the spring run in this river as well as guiding the reintroduction of spring run into other river systems.  Findings from this study, which was funded by the California Department of Water Resources, will be published in the journal Evolutionary Applications this year.

Population genetics of Dungeness crab: The Dungeness crab fishery is the most valuable 'single-species' fishery in Oregon.  Despite the high economic and social value of this species, no stock assessment work has been conducted on coastal Dungeness crab populations and the commercial fishery is managed based solely on a sex, size, and season strategy.  However, there has been increasing interest to collect more data and improve how the fishery is currently managed as indicated in the Oregon Nearshore Strategy Report (2005) and with the conditional sustainable certification of the Oregon commercial Dungeness crab fishery by the Marine Stewardship Council (MSC).  In response, the Oregon Department of Fish and Wildlife (ODFW) developed the Oregon Dungeness Crab Research and Monitoring Plan (2013) which outlines historical and current biological, ecological and socio-economic research and monitoring efforts on the Oregon Dungeness crab resource and future plans to address information gaps in each of the three areas. 

The EFGL is currently conducting a one year study to evaluate the population genetic structure of Dungeness crab off the Oregon coast.  In collaboration with the ODFW, tissue samples were collected from 800 Dungeness crabs distributed from Astoria south to Brookings during the 2011 Pre-Season Test Fishery.  Each crab has been genotyped at 10 microsatellite markers to estimate genetic diversity among samples. Since this is the first coast-wide population genetic study of Oregon Dungeness crab using microsatellite genetic markers, results from this study will provide important baseline information on the biology of one of Oregon’s most commercially valuable species and contribute to biological (e.g. stock structure) and soci-economic (e.g. marine spatial planning) research efforts identified in the new ODFW plan.  Findings from this study will also help fill three information gaps identified in the plan that would be of value to the management of the fishery: recruitment studies, movement studies, and connections between estuary and ocean populations.  Finally, the data generated from this research project can be used to help establish a “Limit Reference Point,” one of the five “conditions” associated with the Oregon Dungeness crab fishery’s recent MSC certification.

The EFGL plans to expand on this study, which was co-funded by the Oregon Wave Energy Trust Fund and the Oregon Dungeness Crab Commission, by examining samples from a broader geographic range and multiple years.  For example, over 4,000 Dungeness crab tissue samples were collected off the coasts of Washington, Oregon and California during the 2012 Pre-Season Test Fishery with assistance from each state fish and wildlife agency.  The EFGL is currently seeking funding from Oregon Sea Grant to analyze these samples at the same 10 microsatellite markers.  Understanding the inter-annual variation in genetic diversity among Dungeness crab from a broad geographical range will help inform decisions regarding ocean spatial planning, such as selection of wave energy development sites and marine reserves as well as long term management of Oregon’s most valuable single-species commercial fishery.

Fitness differences between hatchery and wild salmon: Recent studies have shown that naturally spawning hatchery fish have a lower reproductive success compared to wild fish.  This difference may result from lack of sexual selection (i.e. mate choice) in the hatchery. Parental mate choice is based on the premise of genetic compatibility to produce offspring of greater fitness.  Previous studies suggest that fish choose mates that are genetically dissimilar at genes critical to immune response using olfactory cues. Consequently, their offspring have increased variation at these immune-relevant genes and are able to mount an immune response against a larger array of pathogens; favoring their overall survival. 

This past November, Amelia Whitcomb, a master’s student co-advised by Drs. Kathleen O’Malley and Michael Banks, completed her thesis research investigating the genetic characteristics of parental mate choice in naturally spawning hatchery-reared and wild coho salmon.  Findings from this study suggest that increased diversity at genes involved in immune response may influence offspring survival.   Brynn Perales, an REU intern collaborating with A. Whitcomb, conducted a complementary study which examined how diversity at immune genes influences the reproductive success of male coho salmon that use an alternate “sneaker” mating strategy.  This research was funded by Oregon Sea Grant .

To experimentally test how diversity at immune genes affects survival, the EFGL initiated a collaborative project with the ODFW and NOAA to perform a disease challenge study on juvenile Chinook salmon.  The primary objective of this research is to test for relationships between pathogen resistance with hatchery/wild origin and variability at 10 immune genes.  This study is funded by the U.S. Army Corps of Engineers.

Service, Advising and Outreach:  

This past year, Kathleen has been an active member of the Center for Genome Research and Biocomputing (CGRB) faculty community. She served on the Search Committee for a new faculty hire in the area of Bioinformatics, is a member of the Scientific Program Committee for the CGRB Fall 2013 Conference and was recently appointed to the CGRB Scientific Advisory Board.  Kathleen continues to serve on four graduate student committees.  This past year, members of the ECGL presented their research at various meetings and conferences including the Oregon Hatchery Research Center’s Advisory Board Meetings, Oregon Sea Grant Scholars Day, Western Society of Naturalists Meeting, American Fisheries Society National Meeting, Salmon Coast-wide Genetics Meeting and HMSC’s Marine Science Day.

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)