DISSERTATION RESEARCH: Detecting adaptive evolution of gene duplication in olfactory receptors

论文研究：检测嗅觉受体基因复制的适应性进化

• 批准号: 1701414
• 负责人: Liliana Davalos
• 金额: $ 2.03万
• 依托单位: SUNY at Stony Brook
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-05-01 至 2019-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1701414&HistoricalAwards=false
• 关键词: DISSERTATION; RESEARCH; Detecting; adaptive; evolution

This project will develop novel methods to characterize how genes diversify and will use these methods to detect adaptation in genetic diversification in bats. How genes diversify and evolve new functions is a little understood but important area in evolutionary biology. The sense of smell in mammals is the result of extreme diversification of genes that code for proteins that detect chemicals in the environment. Some mammals possess over 1,000 such proteins and others only a few hundred. Quantifying the role of natural selection in this diversification is difficult because current models fail to fully account for the processes involved: gene duplication and loss, mutation, as well as the number of gene copies present. This project will develop mathematical tools that incorporate this complexity and test hypotheses about sensory evolution in bat species with divergent specialized diets. The methods developed in the project will be applicable to many types of genes, including those involved in immune function and pathogen recognition. Through training from the Alan Alda Center for Communicating Science, the research team will design a short video for the public explaining the value understanding the evolution of smell. They will also implement a summer program for underrepresented Long Island, NJ high school students to learn about bat sensory systems.Previous research has identified several species of plant-visiting bats that have evolved novel olfactory receptors via gene duplication. The match between dietary specialization and olfactory receptors provides an ideal system to test whether newly evolved receptors are related to a reliance on plant resources. A shift from an insectivorous ancestral bat population to a population that exploits fruit and pollen requires not only new morphological adaptations for consumption of these foods, but also fine-tuning of chemosensory systems to find these plant resources. The challenge of understanding the molecular evolution of the mammalian olfactory gene family has prevented a quantitative investigation of this pattern; this project will develop new methods to identify such adaptation. The focal hypothesis is that increased gene copy retention and diversification is connected to the rapid diversification of Neotropical plant-visiting bats. To test this hypothesis, this research involves three major objectives: (1) determine whether olfactory receptor retention rate is correlated with the increased speciation rate observed in plant-visiting bats, (2) empirically test whether olfactory gene duplicates are adaptive at the species level, and (3) evaluate the functional similarity and novelty of the receptors that have recently duplicated in plant-visiting bats. The project will make use of newly developed gene-tree/species tree reconciliation and gene retention models developed for recently diverged populations, as well as codon substitution models and protein reconstructions to detect how selection may be affecting the function of these hyperdiverse genes.

该项目将开发新的方法来表征基因如何多样化，并将使用这些方法来检测蝙蝠遗传多样性的适应性。基因如何多样化和进化新的功能是进化生物学中一个鲜为人知但却很重要的领域。哺乳动物的嗅觉是基因极度多样化的结果，这些基因编码的蛋白质可以检测环境中的化学物质。一些哺乳动物拥有超过1,000种这样的蛋白质，而另一些只有几百种。量化自然选择在这种多样化中的作用是困难的，因为目前的模型未能充分考虑所涉及的过程：基因复制和丢失，突变以及存在的基因拷贝数。该项目将开发数学工具，将这种复杂性和测试假设的感官进化蝙蝠物种不同的专门饮食。该项目开发的方法将适用于许多类型的基因，包括那些参与免疫功能和病原体识别的基因。通过Alan Alda交流科学中心的培训，研究团队将为公众设计一个简短的视频，解释理解气味进化的价值。他们还将实施一个夏季计划，为代表性不足的长岛，新泽西州高中学生了解蝙蝠的感觉系统。以前的研究已经确定了几种植物访问蝙蝠已经通过基因复制进化出新的嗅觉受体。饮食特化和嗅觉受体之间的匹配提供了一个理想的系统来测试新进化的受体是否与对植物资源的依赖有关。从一个食虫的祖先蝙蝠种群到一个利用水果和花粉的种群的转变，不仅需要新的形态适应这些食物的消费，而且还需要微调化学传感系统来寻找这些植物资源。理解哺乳动物嗅觉基因家族的分子进化的挑战阻止了对这种模式的定量研究;该项目将开发新的方法来识别这种适应。焦点假设是，增加基因拷贝保留和多样化与新热带植物访问蝙蝠的快速多样化有关。为了验证这一假设，本研究涉及三个主要目标：（1）确定嗅觉受体留存率是否与观察到的植物访问蝙蝠的物种形成率增加，（2）经验性测试嗅觉基因复制是否是适应在物种水平上，（3）评估最近复制的受体的功能相似性和新奇性在植物访问蝙蝠。该项目将利用新开发的基因树/物种树和解和基因保留模型，以及密码子替换模型和蛋白质重建来检测选择如何影响这些高度多样化基因的功能。

项目成果

Evaluating the performance of targeted sequence capture, RNA‐Seq, and degenerate‐primer PCR cloning for sequencing the largest mammalian multigene family

• DOI: 10.1111/1755-0998.13093
• 发表时间: 2020-01
• 期刊: Molecular Ecology Resources
• 影响因子: 7.7
• 作者: Laurel R. Yohe;Kalina T. J. Davies;N. Simmons;K. Sears;E. Dumont;S. Rossiter;Liliana M. Dávalos

Expressed Vomeronasal Type-1 Receptors (V1rs) in Bats Uncover Conserved Sequences Underlying Social Chemical Signaling

蝙蝠中表达的犁鼻 1 型受体 (V1rs) 揭示了社会化学信号传导背后的保守序列

• DOI: 10.1093/gbe/evz179
• 发表时间: 2019
• 期刊: Genome Biology and Evolution
• 影响因子: 3.3
• 作者: Yohe, Laurel R;Davies, Kalina T;Rossiter, Stephen J;Dávalos, Liliana M;Chang, Belinda
• 通讯作者: Chang, Belinda

Strength of selection on the Trpc2 gene predicts accessory olfactory bulb form in bat vomeronasal evolution

Trpc2基因的选择强度预测蝙蝠犁鼻进化中的副嗅球形状

• DOI: 10.1093/biolinnean/bly015
• 发表时间: 2018
• 期刊: Biological Journal of the Linnean Society
• 影响因子: 1.9
• 作者: Yohe, Laurel R;Dávalos, Liliana M
• 通讯作者: Dávalos, Liliana M

Protocols for the Molecular Evolutionary Analysis of Membrane Protein Gene Duplicates

膜蛋白基因重复分子进化分析方案

• DOI: 10.1007/978-1-4939-8736-8_3
• 发表时间: 2019
• 期刊: Computational Methods in Protein Evolution
• 作者: Yohe, Laurel R.;Liu, Liang;Davalos, Liliana M.;Liberles, David A.
• 通讯作者: Liberles, David A.

Tissue Collection of Bats for -Omics Analyses and Primary Cell Culture

收集蝙蝠组织用于组学分析和原代细胞培养

• DOI: 10.3791/59505
• 发表时间: 2019
• 期刊: Journal of Visualized Experiments
• 作者: Yohe, Laurel R.;Devanna, Paolo;Davies, Kalina T.J.;Potter, Joshua H.T.;Rossiter, Stephen J.;Teeling, Emma C.;Vernes, Sonja C.;Dávalos, Liliana M.
• 通讯作者: Dávalos, Liliana M.