Evolutionary ecological genomics of the great tit

大山雀的进化生态基因组学

• 批准号: NE/L005328/1
• 负责人: Kai Zeng
• 金额: $ 42.28万
• 依托单位: University of Sheffield
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FL005328%2F1
• 关键词: Evolutionary; ecological; genomics; great; tit

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.

适应是达尔文进化论的核心。多年来，生物学家一直试图确定“适应性基因”，这些基因负责使生物体适应其环境的表型变化。这项研究不仅对理解达尔文进化论是如何产生的很重要，而且对实践也很重要。例如，在环境迅速变化的时期，了解适应的机制和遗传基础对于评估野生生物应对选择压力的潜力至关重要。然而，研究适应性是一个挑战。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生物体的基因组如何随着时间的推移而演变，并确定由于参与最近的适应而与基因组的其他部分相比显示出不寻常特征的基因。到目前为止，这种以理论为基础的方法主要应用于几种经过充分研究的生物体，如人类和果蝇，这些生物体具有必要的资源。最近，高通量DNA测序技术的快速发展使得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。在本研究中，我们将使用理论为基础的方法来研究一种野生鸣禽，大山雀（Parus major）。大山雀一直是整个欧洲经典长期生态研究的焦点，并被用于研究关键主题，如繁殖时间何时以及如何应对气候变化。我们将使用高通量测序技术获得多个大山雀个体的基因组序列。通过利用和进一步发展最先进的理论模型，我们将详细了解遗传变异如何分布在大山雀基因组中，以及什么样的进化力量影响了这种分布。这些知识将使我们能够寻找负责最近适应的基因，并将帮助我们回答一些重要的问题，例如影响生态重要性状（如繁殖时间）的基因是否参与了最近的适应。此外，我们将研究大山雀基因组与其他鸟类（如斑胸草雀）基因组的差异程度，以了解感兴趣基因的长期进化历史。这些结果将帮助我们弥合我们对野生大山雀适应和基因组进化的知识差距。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，我们的研究将引起从事广泛主题的生物学家的兴趣。

项目成果

The Effects of Background and Interference Selection on Patterns of Genetic Variation in Subdivided Populations.

背景和干扰选择对细分群体遗传变异模式的影响。

• DOI: 10.1534/genetics.115.178558
• 发表时间: 2015
• 期刊: Genetics
• 影响因子: 3.3
• 作者: Zeng K

Determinants of the Efficacy of Natural Selection on Coding and Noncoding Variability in Two Passerine Species.

• DOI: 10.1093/gbe/evx213
• 发表时间: 2017-11-01
• 期刊: Genome biology and evolution
• 影响因子: 3.3
• 作者: Corcoran P;Gossmann TI;Barton HJ;Great Tit HapMap Consortium;Slate J;Zeng K
• 通讯作者: Zeng K

New Methods for Inferring the Distribution of Fitness Effects for INDELs and SNPs.

• DOI: 10.1093/molbev/msy054
• 发表时间: 2018-06-01
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Barton HJ;Zeng K
• 通讯作者: Zeng K

A supergene determines highly divergent male reproductive morphs in the ruff.

• DOI: 10.1038/ng.3443
• 发表时间: 2016-01
• 期刊: NATURE GENETICS
• 影响因子: 30.8
• 作者: Kuepper, Clemens;Stocks, Michael;Risse, Judith E.;dos Remedios, Natalie;Farrell, Lindsay L.;Mcrae, Susan B.;Morgan, Tawna C.;Karlionova, Natalia;Pinchuk, Pavel;Verkuil, Yvonne I.;Kitaysky, Alexander S.;Wingfield, John C.;Piersma, Theunis;Zeng, Kai;Slate, Jon;Blaxter, Mark;Lank, David B.;Burke, Terry
• 通讯作者: Burke, Terry

Evolutionary signals of selection on cognition from the great tit genome and methylome.

• DOI: 10.1038/ncomms10474
• 发表时间: 2016-01-25
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Laine VN;Gossmann TI;Schachtschneider KM;Garroway CJ;Madsen O;Verhoeven KJ;de Jager V;Megens HJ;Warren WC;Minx P;Crooijmans RP;Corcoran P;Great Tit HapMap Consortium;Sheldon BC;Slate J;Zeng K;van Oers K;Visser ME;Groenen MA
• 通讯作者: Groenen MA