My general research interests lie at the interface between genomics, evolutionary biology, and fisheries biology. Specific areas of research emphasis in my lab include the genetic architecture of complex traits, the evolution of locally adaptive phenotypes, and genomic analysis of behavioral variation in fish.  I employ two study systems to investigate these issues, the rainbow trout and the zebrafish.

My work on rainbow trout is focused on the genetics of local adaptation.  There are a wide variety of salmonid populations in the Pacific Northwest which harbor locally adaptive phenotypes in one or more behavioral, physiological, morphological, or life history traits.  This adaptive variation is often what conservation efforts are implicitly attempting to maintain, yet the primary genetic tools used in salmonid conservation are often neutral molecular markers.  Although these molecular techniques are extremely powerful for delineating population structure, and are an essential part of salmonid conservation, their link to adaptive variation is unclear.  An understanding of the genomic organization underlying adaptive variation is sorely needed, and could serve as an invaluable aid to conserving endangered salmonid populations as well as provide fundamental insights into the expression and inheritance of locally adaptive phenotypes.  To dissect the genetic architecture of these phenotypes, I employ modern methods in quantitative genetics to determine how trait expression interacts with the environment, to describe the evolutionary potential of the trait, and to identify potential constraints on phenotypic evolution.  In addition, I employ a variety of molecular methodologies to identify and describe quantitative trait loci (QTL) which underlie adaptive variation.

My work with zebrafish attempts to develop them as a model system for studying the genetics of behavior.  We have identified behavioral, morphological, and physiological polymorphisms among different strains of zebrafish, and we are in the process of investigating these polymorphisms to determine their genetic basis.  Of particular interest is the Nadia strain, a population of zebrafish obtained directly from their natural habitat in India.  When compared with this wild strain, standard lab strains of zebrafish have a faster growth rate, more sexual dimorphism, reduced predator avoidance behavior, and a greater degree of surface orientation.  Variation in these traits is presumably caused by adaptation to the laboratory environment and is consistent with the effects of domestication in other fish species, such as salmonids.

The rainbow trout and zebrafish components of my research complement each other in many ways.  The behavioral polymorphisms we have identified among zebrafish strains are remarkably similar to those observed in domesticated and wild populations of salmonids.  Genetic analysis of these behaviors in the zebrafish will provide candidate loci for studying the genetic effects of domestication in endangered populations of salmonids and other fish.  The zebrafish has one-twelfth the generation time of a typical salmonid, yet the types of experiments and manipulations possible in the two systems are remarkably similar.  Of particular interest is the fact that we can produced homozygous clonal lines in both species, as the availability of these clonal lines will greatly facilitate genomic analysis.  An overarching goal of my research is to use the genomics tools available in the zebrafish system to analyze the genetics of life history, behavioral, morphological, and physiological traits, ultimately applying the knowledge gained to the effective conservation of salmonid populations.

Selected Publications
 

Courses

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