Collaborative Research: Comparative Genomics of Host-specific Adaptation and Life History Evolution of 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: 1754643
• 负责人: Jeffrey DaCosta
• 金额: $ 9.91万
• 依托单位: Boston College
• 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 2024-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1754643&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，其中相似的形态，行为或功能性状独立出现在不同的物种，提供了一个强有力的框架，检查在何种程度上的遗传变化的适应性进化是可预测的特异质，比较基因组学的一个基本问题。鸟类育雏寄生虫，鸟类不提供父母照顾他们的后代，而是把他们的蛋在其他物种的巢，代表了一个理想的模型系统进行比较分析，因为育雏寄生（和父母照顾行为的损失）独立进化七次在五个不同的鸟类家庭。该项目将表征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。研究结果还将为深入了解基因组进化的其他基本问题提供帮助，包括行为差异背后的遗传变化是否最常见于基因组的调控部分，或者是否代表基因本身的结构变化。在第二个相关的调查中，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雏寄生物种中编码在鸟类W染色体（类似于人类Y染色体）上。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。本科生研究经验（REU）部分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生产高质量的基因组组装，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新兴分子和种群基因组学领域课程的教育材料中。鸟类育雏寄生虫及其宿主，表现出惊人的行为，形态和生理适应和反适应多样性，已经成为研究共同进化的重要模型。最近发现的遗传分歧，主机特定的matrilines内的每三个不同的寄生物种，“适应无重组”的例子，提供了一个独特的机会，检查选择的影响，非重组，性别限制的染色体。同样，7个独立的起源专性寄生和相关的失去父母的照顾，育雏寄生虫提供了一个无与伦比的机会，探索全基因组的重大生活史转变的后果，提供更大的权力比其他最近分析的基因组基础的表型收敛的基因组收敛的测试。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约束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（目前仅适用于斑胸草雀和鸡）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W染色体的进化过程（例如，Hill-Robertson干扰、选择性清除、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;和2）检查所有七个寄生分支，幼虫寄生的进化（和父母照顾行为的丧失）导致基因组范围内的分子趋同特征和/或编码和/或基因表达的趋同变化。该奖项反映了NSF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。