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

该项目将开发新的方法来描述基因如何多样化，并将使用这些方法来检测蝙蝠遗传多样化的适应性。基因如何多样化并进化出新的功能是进化生物学中鲜为人知的重要领域。哺乳动物的嗅觉是基因极度多样化的结果，这些基因编码着检测环境中化学物质的蛋白质。一些哺乳动物拥有1000多种这样的蛋白质，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到所涉及的过程：基因复制和丢失、突变以及基因拷贝的数量。该项目将开发数学工具，将这种复杂性结合起来，并测试关于具有不同专门饮食的蝙蝠物种感官进化的假设。该项目开发的方法将适用于许多类型的基因，包括涉及免疫功能和病原体识别的基因。通过Alan Alda传播科学中心的培训，研究团队将为公众设计一个短视频，解释了解气味进化的价值。他们还将实施一个暑期项目，让新泽西州长岛的高中生了解蝙蝠的感官系统。先前的研究已经确定了几种植物访视蝙蝠，它们通过基因复制进化出了新的嗅觉受体。饮食特异性和嗅觉受体之间的匹配为测试新进化的受体是否与依赖植物资源有关提供了一个理想的系统。蝙蝠祖先从食虫种群转变为以水果和花粉为食的种群，不仅需要新的形态适应以食用这些食物，还需要对化学感觉系统进行微调以发现这些植物资源。理解哺乳动物嗅觉基因家族分子进化的挑战阻碍了对这种模式的定量研究；该项目将开发新的方法来确定这种适应。焦点假说是基因拷贝保留和多样化的增加与新热带访植物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)确定嗅觉受体保留率是否与访花蝙蝠物种形成率的增加相关；(2)实证检验嗅觉基因复制是否在物种水平上具有适应性；(3)评估最近在访花蝙蝠中复制的受体的功能相似性和新颖性。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，以及密码子替代模型和蛋白质重建来检测选择如何影响这些高多样性基因的功能。

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.