Genomics of hybridization, speciation, and phenotypic evolution in wheatears

大自然是形态和色彩丰富多样的家园，然而，我们才刚刚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，我们现在有前所未有的机会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？•在表型和适应性的进化中，祖先遗传变异与新遗传变异的作用是什么，以及杂交的渗入是如何维持的？•特别是，趋同表型下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，但在遗传学上基本上没有研究过的颜色多态性鸣禽系统-黑耳和花斑小麦（Oenanthe hispanica和O. pleschanka）。利用在三个地理区域重复的这些物种之间普遍杂交提供的自然实验室，我的目标是：•使用新的比较种群基因组框架和混合图谱确定涉及物种和颜色表型进化的候选基因组区域。•确定所有杂交区域中可能与生殖隔离有关的抵抗基因流动的基因组区域。•推断杂交结果在杂交区之间是否存在差异（sensu Gompert et al. 2016）。•推断基因流动和选择在表型杂交带结构进化中的作用。明显的颜色表型在整个葡萄属中复制，反映了在两个主要研究物种中发现的多态性。这种模式暗示了趋同进化，并在整个属中追踪候选区域，从而使分析能够：•推断被确定参与物种或表型进化的遗传变异是否代表祖先的、渐渗的或新的变异。•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，证实特定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。拟议的研究通过新研究系统提供的独特机会，以及补充比较种群基因组框架（Burri 2017a）和具有比较和时间视角的混合绘图的综合方法，使其与类似研究区别开来。

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.