Our research program is focused on the use of genetic approaches to characterizing fitness changes in populations, describing the evolution of fitness-related traits, and exploring conservation measures that may be implemented in order to preserve this fitness. Most of our current work is on Pacific salmon, but we have also started to work on marine turtles in South Africa, and have extensive experience on other aquatic organisms. We are very fortunate to have a number of great collaborators in other Academic institutions and in government agencies. Our research falls under three main categories.
1. Fitness consequences of population structure
It is widely recognized that relatedness between individuals across a species range can be described by a “breeding system continuum,” and that this continuum might predict offspring fitness following crosses between these individuals. Thus, at one end of the continuum, inbred crosses may result in a loss of fitness known as inbreeding depression; at the other end, unrelated crosses between populations may lead to the loss of fitness known as outbreeding depression. Predicting these outcomes is of significant importance in conservation; first, it is important to identify the relationship between inbreeding, population size, and loss of fitness, and subsequently, to make informed decision on the appropriate sources and numbers of individuals to introduce for population recovery. These issues are especially relevant to Pacific salmon, where many populations are small and declining, and where extensive hatchery programs have been established with the intention of recovering or compensating for demographic losses.
We are using a number of tools to study these effects. First, we create experimental populations to directly test the outcomes of inbreeding and outbreeding. Second, we use molecular tools to create long-term pedigrees, in order to measure the effective population size and the rates of inbreeding and migration in natural or hatchery populations. Third, we use species-specific markers to examine the consequences of hybridization. Finally, we have used population genetic analyses to examine the effects of numbers of individuals released on meta-population structure within a single Conservation Unit.
2. Human-induced evolution on correlated traits in fish populations
Many of the evolutionary changes induced by human activities (such as fishery selection, artificial propagation and global warming) are a challenge to study, because these changes affect quantitative traits that are directly related to fitness. To complicate matters further, these traits are usually correlated, and selection on one trait may elicit an unpredicted genetic response in others. For example, body size and growth rate typically affect other traits such as age at maturity, number of offspring and survivorship. In our research, we use both theoretical and empirical approaches to understand the effects of harvest and captive propagation on the evolution of salmon populations.
Fishing may cause evolutionary change in harvested populations, and this change might lead to reduced viability through a decrease in population fitness. However, it is usually difficult to separate environmental, demographic and genetic causes without control populations, which rarely exist in practise. We rely on the use of genetic variance-covariance (G) matrices based on empirical data to investigate the evolutionary response of populations under different management scenarios. Our aim is to identify those harvest strategies that have a minimal impact on the evolution of populations and to develop tools that can be integrated into forecasting.
Hatchery propagation of fishes imposes a form of artificial selection that can change traits related to fitness. Such domestication effects can pose genetic risks to natural populations if hatchery-origin adults spawn in the wild. However, theoretical studies have shown that integration of wild fish into hatchery broodstock might be one way to significantly reduce the incidence of domestication selection. We are empirically testing these predictions at our hatchery at Big Beef Creek, with the intention of further informing hatchery reform efforts and contributing to the field of supportive breeding as a whole.
3. Genome-based approaches to studying the evolution of quantitative traits
The many logistical challenges associated with traditional quantitative genetic approaches have generated much interest in the use of molecular approaches to studying functionally important genetic variation. If the genes underlying a fitness-related trait can be identified, then a more mechanistic approach to predicting evolutionary responses can be developed. We are using a range of approaches towards attaining these goals, and have initiated studies that examine the importance of such markers in an evolutionary context. Therefore, we have generated genome maps for Chinook and coho salmon, and have mapped quantitative trait loci (QTL) related to growth and development in these species. We have then surveyed patterns of diversification at these loci in wild populations. Our current research relies on recent innovations in sequencing – and we are using a number of approaches to investigate diversification in gene expression and gene sequences between evolutionary lineages of Chinook and coho salmon. Much of this work has been funded by Washington Sea Grant.