Research Areas

Genetic monitoring pre- and post-dam removal

The world’s largest dam demolition has begun on the Klamath River. By the end of 2024, four hydroelectric dams spanning the California-Oregon state line will be gone reopening 400 miles of habitat for anadromous fishes including steelhead, salmon, and lamprey. This historic event presents a unique opportunity to study interactions between closely related species and changes in population structure within species before and after dam removal.  Currently, the lower Klamath River below the dams supports coastal steelhead (anadromous Oncorhynchus mykiss irideus); above the dams, Upper Klamath Lake and its tributaries support Klamath redband trout (O. m. newberii). Tissue samples were collected from O. mykiss throughout the basin pre-dam removal, and we used high-throughput DNA sequencing to document both neutral and adaptive genetic variation among redband trout and coastal steelhead. This information will serve as a genetic baseline to evaluate genetic diversity and population structure post-dam removal. Photo by Mark Hereford, ODFW. 

Reintroduction of threatened spring Chinook salmon

Alteration of the physical landscape through hydropower dam construction has adversely affected populations of Pacific (Oncorhynchus spp.) salmon and steelhead throughout the Northwestern United States. These dams block access to historical spawning habitat and disrupt natural river flows.  To mitigate for this habitat loss, hatcheries have been constructed in rivers systems throughout the Pacific Northwest. More recently, human-assisted reintroduction programs have been initiated to re-establish natural spawning populations in rivers above dam operations.

We use genetic parentage analysis to evaluate the contribution of reintroduced fish to the productivity of at-risk salmon populations. Currently, we are evaluating four spring Chinook salmon (O. tshawytscha) reintroduction programs:

  • North Santiam River

  • South Santiam River (Press release)

  • Fall Creek

  • South Fork McKenzie

Population connectivity in the marine environment


Connectivity broadly refers to the extent to which populations in different parts of a species’ range are linked by the exchange of larvae, recruits, juveniles or adults. Although both genetic (i.e. gene flow) and demographic (i.e. population growth) connectivity are important to developing effective management and conservation strategies, they are often poorly understood in most marine species. This is especially true for the Dungeness crab (Cancer magister) which supports the most valuable commercial fishery along the west coast of the United States. 

We are using genetic markers to evaluate the population structure and genetic diversity (i.e. vulnerability) in highly migratory marine species:

  • Dungeness crab (Cancer magister) (Press release)
  • Albacore tuna (Thunnus alalunga)
  • Deacon rockfish (Sebastes diaconus)
Genetic basis of migration timing

The seasonal timing of life history events is often under strong natural selection, requiring organisms to integrate and respond to multiple environmental cues. Fitness depends on forecasting the optimal timing of season-specific activities, such as migration and breeding, to exploit favorable conditions.  Photoperiod is a predictable environmental cue that organisms use to respond to seasonally varying conditions. The daily molecular oscillator, known as the circadian clock, senses changes in the photoperiod and mediates a diverse number of photoperiodic responses.

We study circadian clock gene evolution in salmonid fishes, which show considerable diversity in their temporal patterns of migration and breeding.  Photoperiod is one of the primary environmental cues influencing the timing of these seasonal events.  Species of interest to date include:

  • Chinook salmon (Oncorhynchus tshawytscha)
  • Coho salmon (Oncorhynchus kisutch)
  • Pink salmon (Oncorhynchus gorbuscha)
  • Chum salmon (Oncorhynchus keta)
  • Atlantic salmon (Salmo salar)
Fitness differences between hatchery and wild salmon

While it is well established that hatchery-reared fish have lower fitness than their wildborn counterparts when breeding in the wild, the question as to why remains unanswered.  Immune gene-dependent mate preference is one mechanism known to influence salmonid fitness.  Using an existing coho salmon genetic pedigree, we found no evidence for this phenomenon in wild spawning hatchery and wild mate pairs (WxW, WxH, HxH).  However, we did find an association between immune-gene diversity and increased fitness in WxW and WxH mate pairs but not in HxH mate pairs.

To expand on this research, we are currently using two existing spring Chinook salmon genetic pedigrees to:

  • Test for an association between immune gene diversity (e.g. Major Histocompatibility Complex) and fitness of reintroduced hatchery and wild salmon
  • Conduct a genome-wide association study to examine genetic and environmental variables as predictors of individual fitness of reintroduced hatchery and wild salmon