Genomics of hybridization, speciation, and phenotypic evolution in wheatears

大自然的形态和色彩都有着惊人的多样性，但我们才开始揭开复杂的分子和进化机制，这些机制支撑着物种和个体之间的许多差异。由于最近的技术革命，我们现在可以前所未有地获得全基因组的分子多样性，因此，可以开始解决有关这种生物多样性进化的一些最相关的问题：物种边界和表型适应的遗传结构是什么？在表型和适应的进化中，祖先与新的遗传变异以及杂交后的基因渗入的作用是什么？后者是如何维持的？特别是，趋同表型背后的遗传变异的起源是什么？我在这里提出的研究旨在为这些问题提供一个独特的见解，但在遗传上基本上未经研究的系统的颜色多态鸣禽-黑耳和麦穗（Oenanthe hispanica和O。pleshanka）。利用在三个地理区域重复的这些物种之间的普遍杂交所提供的自然实验室，我的目标是：·使用新的比较种群基因组框架和混合物作图来确定参与物种和颜色表型进化的候选基因组区域。确定可能参与生殖隔离的所有杂交区中抵抗基因流动的基因组区域。·推断杂交的结果是否在杂交区之间存在差异（Sensu Gompert et al. 2016）。·推断基因流和选择在表型杂交区结构进化中的作用。在整个水芹属中复制了明显的颜色表型，反映了在两个主要研究物种中发现的多态性。这种暗示趋同进化的模式，以及对整个属的候选区域的追踪，使分析能够：·推断被鉴定为参与物种或表型进化的遗传变异是否代表祖先、渐渗或新的变异。推断相同的基因组区域是否被重复用于趋同表型的进化。最后，历史样本的可用性提供了对杂交区之一的表型和基因组组成的时间动态的见解。时间分析可以提供证据来证实特定的基因组区域参与物种进化，并提供对系统朝着或远离物种屏障完成的进化的见解。以及一种综合方法，补充了比较群体基因组框架（Burri 2017 a）和具有比较和时间视角的混合作图。

Nature is home to a splendid diversity in form and coloration, yet we only begin to unravel the complex molecular and evolutionary mechanisms underpinning the many ways in which species and individuals differ among each other. Owing to recent technological revolutions, we now have unprecedented access to genome-wide molecular diversity and, consequently, can start tackling some of the most pertinent questions regarding the evolution of this biodiversity:• What is the genetic architecture of species‘ boundaries and phenotypic adaptation?• What are the roles of ancestral vs new genetic variants, and of introgression upon hybridization in the evolution of phenotypes and adaptation, and how are the latter maintained?• In particular, what are the origins of genetic variation underlying convergent phenotypes?My research proposed here is designed to provide insights into these questions in a unique, yet genetically largely unstudied system of colour-polymorphic songbirds – black-eared and pied wheatears (Oenanthe hispanica and O. pleschanka). Making use of the natural laboratory provided by pervasive hybridization between these species repeated in three geographic regions, I aim to:• Identify candidate genomic regions involved in the evolution of species and colour phenotypes using a novel comparative population genomic framework and admixture mapping.• Determine genomic regions resisting gene flow in all hybrid zones that are likely involved in reproductive isolation.• Infer whether the outcome of hybridization varies among hybrid zones (sensu Gompert et al. 2016).• Infer the roles of gene flow and selection in the evolution of phenotypic hybrid zone structure.Conspicuous colour phenotypes are replicated across the entire genus Oenanthe, mirroring the polymorphism found in the two main study species. This pattern suggestive of convergent evolution, and the tracing of candidate regions across the genus empowers analyses to:• Infer whether genetic variants identified to be involved in species or phenotype evolution represent ancestral, introgressed, or novel variation.• Infer whether the same genomic regions are reused for the evolution of convergent phenotypes.Finally, the availability of a historical sample provides insights into the temporal dynamics of the phenotypic and genomic composition in one of the hybrid zones. Temporal analyses may provide evidence to corroborate particular genomic regions‘ involvement in species evolution and provide insights into the system‘s evolution towards or away from the completion of species barriers.The proposed research sets itself apart from similar studies by unique opportunities offered by the novel study system, and an integrative approach complementing a comparative population genomic framework (Burri 2017a) and admixture mapping with comparative and temporal perspectives.