"Genetics of development, fitness, and life-history variability in 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 for gene silencing. Recent evidence suggests that this process is not random, in that genes regulating early development, with multifunctional properties, and those involved in disease defense may be more refractory to gene loss. My research examines the distribution of a class of DNA elements known as conserved non-coding elements (CNE). CNE regulate the expression of early development genes and are highly conserved across all vertebrate species. Hence these may be some of the most important elements that initiate and influence the developmental programs of vertebrates. I study the distribution and retention of CNE and functional genes across the duplicated chromosomes in the genomes of salmonid fishes (trout, salmon, charr). I do this because salmonids are the most recent vertebrate group to have undergone a WGD event in their ancestry, and for which we have the genomic resources available to study the consequences of WGD events. Of all the chromosomes in the bodies of salmonid fishes, there is one ancestral chromosome pair we have discovered that strongly influences their life-history and growth. Because of the WGD event in these fishes we can identify an 'A' and 'B' group for this pair. Chromosome set A appears to have greater regulatory effects on life-history variation (i.e., the timing of when females spawn, males mature, and how fast fish develop, etc.) in some species, while chromosome set B is more powerful in other species. My research asks why this should be so, by examining the retention and distribution of genes and CNE on these duplicated chromosomes, and whether each duplicated set differentially influences gene expression among the study species. This research will fundamentally enhance our knowledge of polyploidy as a force shaping evolution and speciation.