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：******主题我将通过繁殖时间的异时性差异来测试直立变异在适应和物种形成中的作用。在世界范围内的几个群岛上，形态不同的风暴海燕（海燕属）在温暖和寒冷的季节在同一种群中繁殖。我们将测试不同群岛的季节性适应来自长期遗传变异的假设，而不是独立的突变或群岛之间最近的基因流动。我们还将检验基因组结构在分化过程中发生变化的假设。******主题II测试物种间基因流动对外围种群适应的贡献。具体来说，我们将测试1)地面筑巢的基特利茨小海豚（Brachyramphus brevirostris）的适应性渗入是否使树上筑巢的大理石小海豚（B. marmoratus）将其活动范围扩大到无树地区；2)在更新世冰川时期，白头鸥（Larus spp.）的物种形成需要祖先种群之间的反复分离和二次接触（基因流动）。******了解基因流对适应过程中站立变异和基因组结构的影响可以说是我们对进化的理解中最重要的空白之一，因为它影响生物组织的各个方面，从行为到种群动态再到物种形成。它也是我们预测、并有希望减轻人为变化对生物多样性影响的能力不可或缺的一部分。该项目将为3名博士、2名硕士和10名理学士提供基因组学、生物信息学和野外生态学方面的培训

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.***