Evolutionary Genetics of Early Life History Variation in Salmon: Non-additive Genetic Effects and Local Adaptation

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OBJECTIVES: I propose to use molecular, population, and quantitative genetic methods combined with captive breeding experiments and field-based measurements to partition the relative contribution of genetic, epigenetic, GxE interactions and environmental effects to early life history trait variation in Pacific salmon. This work will ultimately seek to identify the evolutionary genetic basis of adaptive differences associated with early life history trait divergence among individuals and populations.PROPOSED RESEARCH: Salmon are remarkable model organisms for my proposed research program: they exhibit extreme variation in early life history traits that affect critical reproductive and migratory behaviours later in life. In general, the early life stages (fertilization through first year of life) experience very high selection pressures. Differences in early survival, growth, migratory behavior and immune function often constitute population differentiation, and are cited as evidence for local adaptation. While past studies have quantified the additive genetic basis of that variation, research exploring the potential contribution of non-additive effects to adaptive differences is just emerging. My proposed research program will capitalize on my expertise in salmon genetics, evolutionary ecology and physiology to characterize early life history trait variation among salmon populations. A key prerequisite for among-population evolutionary analyses is the assessment of genetic isolation. I will thus measure connectivity among populations that differ in early life history using novel NextGen sequencing approaches to microsatellite and single nucleotide polymorphism (SNP) genotyping. Connectivity will be also assessed using functional gene polymorphisms, as such markers may result in different patterns of genetic divergence in salmon. To assess the role of “non-traditional” genetic mechanisms (dominance, epistasis, epigenetics, transcriptional modification, etc.) in rapid local adaptation and phenotypic plasticity in salmon, I will use breeding experiments, multiple rearing environments and molecular and quantitative genetic methods in collaboration with government and aquaculture industry rearing facilities. The CFI-funded EGF lab at GLIER provides centralized infrastructure for custom microarrays, qRT-PCR (standard and nanofluidic) and NextGen RNAseq and miRNA sequencing. Integrating genomic and transcriptomic analyses with field measures of early life history trait variation will provide exceptional analytical power and unique HQP training opportunities in my proposed research program. The proposed research will address a question central to our understanding of the evolution of life history variation and local adaptation in salmon: does life history variation reflect traditional adaptation to local conditions, or have salmon evolved novel forms of life history plasticity? Either way, salmon are remarkably capable colonizers, and exhibit substantial local trait divergence. It is important that we characterize that variation to understand and conserve diversity not only in salmon, but in all vertebrates.