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

目的：采用分子、种群和定量遗传学方法，结合圈养繁殖实验和野外测量，划分遗传、表观遗传、GxE相互作用和环境效应对太平洋鲑鱼早期生活史性状变异的相对贡献。这项工作将最终寻求确定个体和群体之间与早期生活史特征差异相关的适应性差异的进化遗传基础。**建议的研究：鲑鱼是我建议的研究项目中非常重要的模式生物：它们在早期生活史特征上表现出极端的差异，这些特征会影响生命后期的关键繁殖和迁徙行为。一般来说，生命的早期阶段（受精到生命的第一年）经历了非常高的选择压力。早期生存、生长、迁徙行为和免疫功能的差异往往构成群体分化，并被引用为地方适应的证据。虽然过去的研究已经量化了这种变异的加性遗传基础，但探索非加性效应对适应性差异的潜在贡献的研究才刚刚出现。我提出的研究计划将利用我在鲑鱼遗传学，进化生态学和生理学方面的专业知识来描述鲑鱼种群的早期生活史特征变异。种群间进化分析的一个关键前提是对遗传隔离的评估。因此，我将使用新型NextGen测序方法对微卫星和单核苷酸多态性（SNP）基因分型来测量不同早期生活史人群之间的连通性。连通性也将使用功能基因多态性进行评估，因为这些标记可能导致鲑鱼遗传分化的不同模式。*为了评估“非传统”遗传机制（显性、上位、表观遗传学、转录修饰等）在鲑鱼快速本地适应和表型可塑性中的作用，我将与政府和水产养殖业养殖设施合作，使用育种实验、多种饲养环境和分子和定量遗传方法。cfi资助的GLIER EGF实验室为定制微阵列、qRT-PCR（标准和纳米流体）、NextGen RNAseq和miRNA测序提供集中的基础设施。将基因组学和转录组学分析与早期生活史性状变异的实地测量相结合，将为我提出的研究项目提供卓越的分析能力和独特的HQP培训机会。*拟议的研究将解决我们对鲑鱼生活史变异和局部适应进化的理解的核心问题：生活史变异是反映了对当地条件的传统适应，还是鲑鱼进化出了新的生活史可塑性形式？无论哪种方式，鲑鱼都是非常有能力的殖民者，并表现出大量的地方特征差异。重要的是，我们描述这种变化，不仅是为了理解和保护鲑鱼的多样性，也是为了保护所有脊椎动物的多样性。

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.