Evolutionary, developmental, and physiological genomics of salmonid fishes

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Whole genome duplication (WGD) events where all the chromosomes in each cell undergo a complete doubling to give rise to a completely identical set of genes are now recognized as being potential accelerators of evolutionary change in animals and plants. The fates of new genes that arise from WGD are varied, but most duplicated copies appear destined to become nonfunctional (silenced). We still do not understand why some genes are retained as duplicates for long periods of time as essentially identical copies of one another, while other duplicate genes diverge from one another and acquire new expression patterns and potentially new functions. I use salmonid fishes (trout, salmon, charr) to study the distribution and retention of duplicate genes because they are the most recent vertebrate group to have undergone a WGD event in their ancestry. I contrast the patterns of duplicate gene expression in Arctic charr (Salvelinus alpinus), a species whose chromosomes are more representative of the diploid fish ancestor with rainbow trout (Oncorhynchus mykiss) where some evolutionarily unrelated chromosome arms have fused. My research will examine the relationships between variation in pairing among duplicated chromosomes, DNA sequence similarity, and the relative proportion of nucleotide types, and how this variation may influence the expression of duplicate gene pairs from different functional categories. I will also determine if environmental change has different effects on the expression of duplicate genes involved with extracellular functions (e.g., stress-related genes) versus intracellular functional classes (e.g., development-regulating) and if mild stress experienced when the fish are young will influence gene expression responses to more severe stress later in life. If I find that different kinds of duplicate genes show varied responses to stress brought on by environmental change, I will test if one kind of change in DNA structure (methylation) explains the patterns observed. This research will fundamentally enhance our knowledge of polyploidy as a force shaping evolution and speciation.