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: 1940624
• 负责人: Wesley Warren
• 金额: $ 45.43万
• 依托单位: University of Missouri-Columbia
• 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: 2018-09-15 至 2024-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1940624&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.

收敛进化的例子，即相似的形态、行为或功能特征在不同物种中独立出现，为检验适应性进化背后的遗传变化在多大程度上是可预测的，而不是特有的，提供了一个强大的框架，这是比较基因组学中的一个基本问题。雏鸟寄生虫是一种不为后代提供父母照料的鸟类，而是在其他物种的巢中产卵，是比较分析的理想模型系统，因为雏鸟寄生虫(和失去父母照料行为)在五个不同的鸟类家族中独立进化了七次。这个项目将描述寄生和非寄生鸟类的基因组变化模式，以测试相同特定基因的变化和/或基因组变化的平行模式是否发生在独立的幼鸟寄生谱系中。这些结果还将提供对基因组进化的其他基本问题的洞察，包括行为差异背后的遗传变化最常见的是基因组的调控部分，还是代表基因本身的结构性变化。在第二个相关的研究领域，该项目将研究性别决定染色体的独特进化动态，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(从母亲传给女儿)，因此在三个不同的幼虫寄生物种中编码在鸟类的W染色体上(类似于人类的Y染色体)。该项目还将有助于培训处于不同职业阶段的科学家，包括本科生、研究生和博士后研究员。本科生(REU)部分的研究经验将为来自东卡罗来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。该项目将为更多的鸟类物种制作高质量的基因组组件，支持对脊椎动物基因组进化的额外比较分析，该项目的数据将被整合到支持分子和种群基因组新兴领域的课程的教育材料中。禽类寄生虫及其宿主表现出惊人的行为、形态和生理适应和反适应的多样性，已成为共同进化研究的重要模型。最近在三个不同寄生物种中发现了遗传上不同的、寄主特有的母系，例如“适应而不重组”，这为研究选择对非重组、性别受限染色体的影响提供了一个独特的机会。同样，由于专性寄生的七个独立来源和相关的父母照顾的丧失，幼虫提供了一个无与伦比的机会来探索重大生活史转变的全基因组后果，比最近对表型收敛的基因组基础的其他分析提供了更大的力量来测试基因组收敛。这项研究的结果将有助于洞察关于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限制自然选择结果的方式。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，拟议的研究还将检验两个主要假设：1)影响非重组、性别受限的W染色体的进化过程(例如Hill-Robertson干扰、选择性扫描、遗传搭便车)在具有母系遗传宿主特异性适应的寄生谱系中被放大；以及2)检查所有七个寄生分支，即幼虫寄生的进化(和父母照料行为的丧失)导致全基因组范围的分子收敛签名和/或与特定遗传途径或功能相关的编码和/或调节区的收敛变化。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。