Collaborative Research: Comparative Genomics of Host-specific Adaptation and Life History Evolution in Brood Parasitic Birds

合作研究：巢寄生鸟类宿主特异性适应和生活史进化的比较基因组学

• 批准号: 1754397
• 负责人: Timothy Sackton
• 金额: $ 14.96万
• 依托单位: Harvard University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-05-15 至 2024-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1754397&HistoricalAwards=false
• 关键词: Collaborative; Research; Comparative; Genomics; Host

Examples of convergent evolution, in which similar morphological, behavioral or functional traits arise independently in different species, provide a powerful framework for examining the extent to which the genetic changes underlying adaptive evolution are predictable versus idiosyncratic, a fundamental question in comparative genomics. Avian brood parasites, birds that provide no parental care to their offspring but instead lay their eggs in the nests of other species, represent an ideal model system for comparative analysis because brood parasitism (and the loss of parental care behavior) evolved independently seven times in five different avian families. This project will characterize patterns of genomic change in both parasitic and non-parasitic birds to test whether changes in the same specific genes and/or parallel patterns of genomic change have occurred in independent brood parasitic lineages. The results will also provide insight into other fundamental questions about genome evolution, including whether genetic changes underlying differences in behavior are most often in regulatory portions of the genome or represent structural changes to the genes themselves. In a second, related line of inquiry, the project will examine the unique evolutionary dynamics of the sex-determination chromosomes, leveraging recent research showing that specialized adaptations for exploiting particular host species are maternally inherited (passed from mother to daughter) and therefore encoded on the avian W-chromosome (analogous to the human Y-chromosome) in three different brood parasitic species. The project will also contribute to the training of scientists at various career stages including undergraduates, graduate students, and a postdoctoral fellow. A research experience for undergraduates (REU) component will provide an opportunity for two students from East Carolina University to receive training in bioinformatics at Harvard University. The project will produce high quality genome assemblies for additional bird species, supporting additional comparative analyses of genome evolution across vertebrates, and data from the project will be integrated into educational materials supporting courses in the emerging fields of molecular and population genomics.Avian brood parasites and their hosts, which exhibit a spectacular diversity of behavioral, morphological and physiological adaptations and counter-adaptations, have served as important models for the study of coevolution. Recent discoveries of genetically divergent, host-specific matrilines within each of three different parasitic species, examples of "adaptation without recombination", present a unique opportunity to examine the effects of selection on the non-recombining, sex-limited chromosome. Likewise, with seven independent origins of obligate parasitism and associated loss of parental care, brood parasites offer an unparalleled opportunity to explore the genome-wide consequences of a major life history transition, providing greater power for tests of genomic convergence than in other recent analyses of the genomic basis of phenotypic convergence. Results of the study will lend insight into basic questions about genome evolution, including the relative importance of determinism versus historical contingency, and the manner in which integration versus modularity of genetic networks constrains the outcomes of natural selection. In addition to increasing the number of high quality genome assemblies for birds (currently available for only zebra finch and chicken) and assembling W-chromosome sequences, the proposed study will test two major hypotheses: 1) that evolutionary processes influencing the non-recombining, sex-limited W-chromosome (e.g., Hill-Robertson interference, selective sweeps, genetic hitchhiking) are amplified in parasitic lineages that have maternally inherited host-specific adaptations; and 2) examining all seven parasitic clades, that the evolution of brood parasitism (and loss of parental care behavior) results in genome-wide signatures of molecular convergence and/or convergent changes in coding and/or regulatory regions associated with particular genetic pathways or functions.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

趋同进化的例子，即相似的形态、行为或功能特征在不同物种中独立出现，为研究适应进化的遗传变化在多大程度上是可预测的还是特殊的提供了一个强大的框架，这是比较基因组学的一个基本问题。鸟类的巢寄生，即不为后代提供亲代照顾，而是在其他物种的巢中产卵的鸟类，代表了一个理想的比较分析模型系统，因为在五个不同的鸟类科中，巢寄生（以及亲代照顾行为的丧失）独立进化了七次。该项目将描述寄生和非寄生鸟类的基因组变化模式，以测试在独立的育雏寄生谱系中是否发生了相同特定基因的变化和/或基因组变化的平行模式。这些结果还将为基因组进化的其他基本问题提供见解，包括行为差异背后的遗传变化是否最常发生在基因组的调控部分，还是代表基因本身的结构变化。在第二项相关的研究中，该项目将研究性别决定染色体的独特进化动力学，利用最近的研究表明，利用特定宿主物种的专门适应是母系遗传的（从母亲传给女儿），因此在三种不同的育成寄生物种中，鸟类的w染色体（类似于人类的y染色体）被编码。该项目还将有助于培养不同职业阶段的科学家，包括本科生、研究生和博士后。本科生研究经验（REU）组件将为来自东卡罗莱纳大学的两名学生提供在哈佛大学接受生物信息学培训的机会。该项目将为其他鸟类物种提供高质量的基因组组装，支持脊椎动物基因组进化的额外比较分析，项目数据将被整合到支持分子和种群基因组学新兴领域课程的教育材料中。鸟类幼虫寄生物及其寄主在行为、形态和生理上的适应和反适应方面表现出惊人的多样性，为共同进化研究提供了重要的模型。最近发现，在三种不同的寄生物种中，每一种都存在遗传上的分歧，宿主特有的母系，这是“不重组的适应”的例子，为研究选择对非重组、性别限制的染色体的影响提供了一个独特的机会。同样地，寄生物有7个独立的专性寄生起源和相关的亲代抚育缺失，这为探索重大生活史转变的全基因组后果提供了无与伦比的机会，为基因组趋同测试提供了比其他最近的表型趋同基因组基础分析更大的力量。这项研究的结果将有助于深入了解基因组进化的基本问题，包括决定论与历史偶然性的相对重要性，以及遗传网络的整合与模块化如何限制自然选择的结果。除了增加鸟类高质量基因组组装的数量（目前仅适用于斑马雀和鸡）和组装w染色体序列外，拟议的研究还将测试两个主要假设：1)影响非重组、性别限制的w染色体的进化过程（例如，Hill-Robertson干扰、选择性扫描、基因搭便车）在具有母体遗传宿主特异性适应性的寄生谱系中被放大；2)研究所有7个寄生支系，发现幼蜂寄生的进化（以及亲代抚育行为的丧失）导致了与特定遗传途径或功能相关的编码和/或调控区域的分子趋同和/或趋同变化的全基因组特征。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。