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 three spring Chinook salmon (O. tshawytscha) reintroduction programs:

  • North Santiam River

  • South Santiam River (Press release)

  • Fall Creek

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
Adaptation to a changing climate

Arctic climate impact assessment models project an increase in both temperature and precipitation, with the largest effect on areas above 60° North. As the only freshwater fish species on Svalbard (70°N), the Arctic charr (Salvelinus alpinus) is ideal for studying how environmental factors will affect life history strategies in fishes.  Anadromy (summer migration to sea for feeding), for example, is one strategy that can vary both within and among Arctic charr populations and is generally more frequent in cold than in warm, temperate latitudes. 

We use a combination of field and laboratory experiments to investigate the adaptation of Arctic charr to a changing polar climate through the study of behavior, physiology, and genomics.

Species or sex identification

Genetic markers are commonly used to distinguish species that look similar, especially during the early stages of development. Comparably, genetic markers are also used to determine the sex of reproductively immature individuals or in species where sex cannot be determined based on external characters.

We sample tissue nonlethally from individuals for species or sex identification.  Examples include:

  • Distinguishing between larval lamprey - Pacific lamprey (Entosphenus tridentatus) and Western Brook lamprey (Lampetra richardsoni)
  • Identifying sex of Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss)