Evolutionary ecological genomics of the great tit

适应是达尔文进化论的核心。多年来，生物学家一直试图找出“适应性基因”，这些基因负责使有机体适应环境的表型变化。这项研究不仅对理解达尔文进化论是如何产生的很重要，而且对于实际原因也很重要。例如，在环境快速变化的时代，了解适应的机制和遗传基础对于评估野生生物对选择压力做出反应的潜力至关重要。然而，研究适应是具有挑战性的。它需要使用严格的数学模型来分析基因组DNA序列，以帮助我们了解所讨论的有机体的基因组是如何随着时间的推移而进化的，并识别由于参与最近的适应而表现出与基因组其他部分相比的不同寻常的特征的基因。到目前为止，这种基于理论的方法主要应用于几种研究得很好的生物体，如人类和果蝇，在那里有必要的资源可用。最近，高通量DNA测序技术的快速发展使研究野生生物的基因组变得经济而有效，包括生态学家所研究的那些生物。在这个提案中，我们将使用基于理论的方法来研究一种野生鸣鸟--大山雀(Parus Major)。大山雀一直是整个欧洲经典的长期生态学研究的焦点，并被用来研究关键话题，如繁殖的时间和如何应对气候变化。我们将利用高通量测序技术获得多个大山雀个体的基因组序列。通过利用并进一步发展最先进的理论模型，我们将详细了解遗传变异是如何在大山雀基因组中分布的，以及是什么进化力量影响了这种分布。这些知识将使我们能够寻找导致最近适应的基因，并将帮助我们回答一些重要的问题，例如影响重要生态特征的基因是否与最近的适应有关，例如繁殖的时机。此外，我们将研究大山雀的基因组与斑马雀等其他鸟类的基因组有何不同，以了解感兴趣基因的较长期进化历史。这些结果将帮助我们弥合我们在野生大山雀适应和基因组进化方面的知识差距。更重要的是，我们采用的方法是通用的，可以用来研究其他野生生物。因此，我们的研究将对从事广泛主题工作的生物学家感兴趣。

Adaptation lies at the heart of Darwin's theory of evolution. For many years, biologists have tried to identify "adaptive genes" that are responsible for phenotypic changes that enable an organism to adapt to its environment. This research is important not only for understanding how Darwinian evolution comes about, but also for practical reasons. For instance, in a time of rapid environmental change, understanding the mechanisms and genetic basis of adaptation is critical to assessing the potential of wild organisms to respond to selective pressures. Studying adaptation is, however, challenging. It requires the use of rigorous mathematical models to analyse genomic DNA sequences, in order to help us understand how the genome of the organism in question evolves over time, and to identify genes showing unusual characteristics compared to the rest of the genome as a result of their involvement in recent adaptations. Thus far, this theory-based approach has mainly been applied to several well-studied organisms such as humans and fruit flies where the necessary resources are available. More recently, the rapid development of high-throughput DNA sequencing technologies has made it economical and efficient to study the genomes of wild organisms, including those studied by ecologists. In this proposal, we will use the theory-based approach to study a wild songbird, the great tit (Parus major). The great tit has been the focus of classical long-term ecological studies throughout Europe, and has been used to study key topics such as when and how the timing of breeding responds to climate change. We will use high-throughput sequencing technologies to obtain the genome sequences of multiple great tit individuals. By making use of, and further developing, state-of-the-art theoretical models, we will obtain a detailed understanding of how genetic variation is distributed across the great tit genome, and what evolutionary forces have influenced this distribution. This knowledge will enable us to search for genes that are responsible for recent adaptations, and will help us answer important questions such as whether genes affecting ecologically important traits such as the timing of breeding are involved in recent adaptations. In addition, we will examine to what extent the great tit genome differs from those of other birds such as the zebra finch, in order to understand the longer-term evolutionary history of genes of interest. These results will help us bridge the gaps in our knowledge of adaptation and genome evolution in wild great tits. More importantly, the methodology we employ is generic, and can be used to study other wild organisms. Thus, our research will be of interest to biologists working on a wide range of topics.