Shifting Adaptations: Genomics of Adaptation and Speciation with Gene Flow

新的理论模型和越来越强大的方法来解开基因组中包含的进化信息，正在挑战适应和物种形成的经典模型。传统上，人们认为种群适应当地环境的潜力主要取决于选择、遗传变异、基因流动和遗传漂变。然而，最近的研究表明，局部适应的潜力取决于两个额外的关键因素：1)遗传变异的来源（新突变与“常存遗传变异”——种群中已经存在的变异）；2)“基因组结构”（控制一个性状的基因数量，以及它们之间的物理和功能关系）。基因流动、基因组结构和适应之间的相互作用在理论上是复杂的，在自然种群中很大程度上尚未被探索。在目前的应用中，我建议使用全基因组测序和靶向基因测序的新组合来测试基因流动对本地适应和物种形成过程中站立遗传变异和基因组结构的影响。我提出的项目有两个主题，以海鸟为模型系统：

New theoretical models and increasingly powerful methods for unlocking the evolutionary information contained in genomes are challenging the classical models of adaptation and speciation. Traditionally, the potential for populations to adapt to the local environment was thought to depend primarily on selection, genetic variation, gene flow and genetic drift. However, recent research suggests that the potential for local adaptation depends on two additional critical factors: 1) the source of genetic variation (new mutations versus “standing genetic variation”- variation that already exists in a population); and 2) “genomic architecture” (the number of genes controlling a trait, and the physical and functional relationships among them). The interactions among gene flow, genomic architecture and adaptation are complex in theory, and largely unexplored in natural populations. In the present application, I propose to use a novel combination of whole genome sequencing and targeted gene sequencing to test the effect of gene flow on standing genetic variation and genomic architecture during local adaptation and speciation. My proposed program has two themes, using seabirds as model systems: Theme I will test the role of standing variation in adaptation and speciation by allochrony - differences in breeding time. In several archipelagos worldwide, morphologically different conspecific populations of storm-petrels (Hydrobates spp.) breed in the same colonies in warm versus cool seasons. We will test the hypothesis that seasonal adaptations on different archipelagoes arose from standing genetic variation, as opposed to independent mutations or recent gene flow between archipelagoes. We will also test the hypothesis that genomic architecture changes during the divergence process. Theme II tests the contribution of inter-species gene flow to adaptation in peripheral populations. Specifically, we will test whether 1) adaptive introgression from ground-nesting Kittlitz's murrelets (Brachyramphus brevirostris) enabled tree-nesting marbled murrelets (B. marmoratus) to expand their range into treeless areas; and 2) speciation in white-headed gulls (Larus spp.) entailed repeated isolation and secondary contact (gene flow) between ancestral populations during the Pleistocene glaciations. Understanding the effects of gene flow on standing variation and genomic architecture during adaptation is arguably one of the most important gaps in our understanding of evolution, since it affects all aspects of biological organization from behaviour through population dynamics to speciation. It also is integral to our ability to predict, and hopefully mitigate, the effects of anthropogenic change on biodiversity. The proposed work will provide training in genomics, bioinformatics, and field ecology for 3 PhD, 2 MSc and 10 BSc students.