Overview
Our research is driven primarily by questions relating to the conservation of genetic diversity in aquatic populations, and falls across four central themes:
- Understanding the genetic basis of local adaptation in wild populations
- Examining the fitness consequences of population structure
- Researching alternative strategies for reducing human-induced evolutionary changes in populations.
- Characterizing the evolution of the Pacific salmon genome following an ancient whole-genome duplication event.
For details on our research, please see our publications page. Here, we describe our current investigations.
Current and recent research projects
Testing alternative broodstock management approaches in Chinook salmon conservation hatcheries
A central goal of conservation-based enhancement is to reduce the genetic risk of hatchery fish to conspecific wild fish, so that populations can respond to ongoing environmental change. We have been collaborating with Tribal, State and Federal Biologists to determine whether using wild fish as a significant contributor to hatchery broodstock reduces genetic divergence from its founder population. The amount of divergence in this line is being compared to a fully segregated population founded from the same population four generations ago. We are currently using genome-based approaches to link markers to fitness traits such as growth and pathogen resistance, and to determine whether there is evidence for selection at these traits in the two lines. We aim to provide empirical evidence that can be used to inform the management of supportive breeding programs in the Pacific Northwest.
Ecological Drivers of IHNV transmission, emergence and displacement in steelhead trout
Changing uses in water has meant that characterizing the processes that drive aquatic pathogen emergence has become critical. Aquatic pathogens have unique transmission properties, and cultured individuals are often found in close proximity to their wild counterparts. We are collaborating with Federal and Academic virologists, immunologists, and ecological modelers to develop models of transmission dynamics for the salmon pathogen Infectious Hematopoietic Necrosis Virus, to examine approaches to reducing risks to salmon populations through informed disease control. Our group is specifically researching the genetic basis of pathogen resistance in steelhead populations using genomic approaches, and examining genotype by phenotype interactions in different environments. This information will be integrated with measures of factors influencing viral fitness and epidemics in the Pacific Northwest. This data in turn will inform models that will be used to predict emergence, and test control strategies.
Genomic and fitness consequences of hybridization between cutthroat and rainbow trout
Rainbow trout have been extensively introduced within the endemic range of Interior cutthroat trout, and where they come into contact the two species readily hybridize. Our collaborators at USGS Montana and University of Montana, Bozeman have shown that even a small amount of hybridization results in a dramatic loss of fitness beyond the second generation of hybridization. We are characterizing the reasons for this decline by mapping genomic regions linked to reproductive success in a population, and linking these regions to changes in the genome in early hybrids. We are also exploring the use of genomic data in identifying different classes of hybrids, and examining the relationship between these measures and changes in fitness. Our aim is to develop predictive approaches to the outcomes of hybridization for application in conservation of cutthroat trout.
Genetic basis of fitness traits in cultured coho salmon
Pacific salmon have a range of complex life histories that have resulted in extensive local adaptation across their range. While most traits have a genetic basis, they are also correlated and are influenced by the environment. Therefore, the range of phenotypes that might be expressed in a given environment might vary. We are interested in characterizing the genetic basis of temporal correlations between growth-related traits and the trade-off between growth and age at maturity in coho salmon. Very often, the fastest growing fish in a cohort mature earlier than their counterparts. We are using genome mapping of quantitative loci underlying these traits, and then examining how deliberate domestication in aquaculture might influence changes at these loci. These results can be used in aquaculture in selective breeding programs, and also to understand how domestication selection might act in supportive breeding.
Genetic basis of local adaptation in natural populations of Chinook salmon
One of the key steps in defining conservation units within a species is characterizing the evolutionary significance of life history trait variability. Many traits have a genetic basis, but they are also phenotypically plastic. Yet, it is important to protect genetic variability underlying a trait. Ascertaining the genetic basis of local adaptation life history traits across natural populations can be challenging, especially when it is not practical to measure them in laboratory settings. We have been developing analytical approaches aimed at identifying molecular markers linked to return timing in Chinook salmon, a key trait linked to ecological divergence between populations in the Columbia River. We have then used these markers to examine the basis of trait evolution between wild populations. The approaches we have developed provide a way to describe evolutionary important genetic variation in natural populations, facilitating the integration of genomics into conservation practice.