Collaborative Research: Phylogenomics of palaeognathous birds and the genomic basis of flightlessness

合作研究：古颌鸟类的系统基因组学和不会飞的基因组基础

• 批准号: 1355343
• 负责人: Scott Edwards
• 金额: $ 60万
• 依托单位: Harvard University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-06-15 至 2018-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1355343&HistoricalAwards=false
• 关键词: Collaborative; Research; Phylogenomics; palaeognathous; birds

Flightless birds, including species such as the ostrich and emu (which belong to a bird group called the ratites), present a remarkable series of traits related to their loss of flight. Such traits include shortening of the bones in the forelimbs, extreme increases or decreases in body size, loss of the breast bone to which the flight muscles attach, and many other modifications. Moreover, recent research suggests that this suite of traits may have evolved multiple times within the ratites. By studying the evolution of such traits and determining which regions of the genome likely underlie them, we can gain insight into how evolution occurs in parallel in the natural world. We can also gain a better understanding of the types of genes that change when morphological traits are lost in the way they have been in the ratites. Ultimately, a better understanding of links between genotype and phenotype can help us understand the genetic basis for variation in the human phenotype. We expect that some human malformations, including the loss of digits, bones in the hand or forelimbs, likely occur because of mutations in some of the same genes or regulatory regions that underlie flightlessness in the ratites. In fact, one way we will attempt to find the genetic underpinnings of flightlessness in the ratites is to examine the evolution of ratite genes that are known from previous studies to cause similar morphologies in laboratory mice. Thus this study will forge important links between mutations known in developmental studies in the lab and natural variations we find in distantly related vertebrates. This project will use comparisons among the genomes of flightless birds, in combination with morphological studies and phylogenetic methods, to understand the genomic basis of traits contributing to flightlessness. Complete sequencing of the genomes of 8 ratite species will yield a robust genealogical tree of ratites and their relationships to the tinamous, a volant bird group closely related to, and likely embedded within, the ratites. This tree will in turn permit identification of conserved regulatory regions occurring near genes known to contribute to limb loss in better-studied models for development, such as chickens and mice. The timing of origin and loss of regulatory regions, such as conserved regions occurring outside of genes, will reveal important clues about the regulatory and genetic basis of trait evolution in flightless birds. Previous phylogenetic work in the strongly suggests that flight likely was lost independently in multiple lineages of ratites in parallel. This scenario will add statistical power to our inferences of the genomic underpinnings of morphological change, because it will allow us to identify genomic regions that have changed independently in flightless lineages. Thus, this project will also elucidate how convergent morphological changes occur at the genomic level. These themes will be used in a number of outreach activities, including an educational video, classroom teaching of undergraduates, and graduate student outreach in local K-12 schools.

无飞的鸟类，包括鸵鸟和EMU等物种（属于称为含量的鸟类），提出了与它们失去飞行有关的一系列非凡的特征。 这种特征包括缩短前肢中的骨骼，体大小的极大增加或减少，飞行肌肉附着的乳房损失以及许多其他修饰。 此外，最近的研究表明，这套特征可能已经在比例内多次发展。 通过研究此类特征的演变并确定基因组的哪些区域可能是它们的基础，我们可以深入了解自然世界中如何并行演变。 当形态学特征以其在等级中的方式中丢失时，我们还可以更好地理解改变形态特征的基因类型。 最终，对基因型与表型之间的联系的更好理解可以帮助我们了解人类表型变异的遗传基础。 我们预计，某些人类畸形，包括数字损失，手中或前肢的骨骼，可能是由于某些相同基因或构成无飞行的基因或调节区域的突变而发生的。 实际上，我们将尝试在比率中找到无飞行性的遗传基础的一种方法是检查级别基因的演变，这些基因的演变是从先前的研究中知道的，以引起实验室小鼠的类似形态。 因此，这项研究将建立在实验室中发育研究中已知的突变与我们在遥远相关的脊椎动物中发现的自然变异之间的重要联系。该项目将在无飞行鸟类的基因组中进行比较，结合形态学研究和系统发育方法，以了解有助于飞行无飞的特征的基因组基础。 对8种级别物种的基因组进行完整的测序将产生鲁棒的族谱树及其与Tinamous的关系，这是与含量鸟类群，与含量密切相关并可能嵌入在含量中。 这棵树反过来允许鉴定在已知的基因附近发生的保守调节区域，这会导致养殖模型（例如鸡和小鼠）的肢体损失。 起源和监管区域丧失的时间（例如基因之外的保守区域）将揭示有关无飞行鸟类性状进化的调节和遗传基础的重要线索。 以前的系统发育工作强烈表明，在平行的多个谱系中，飞行可能独立损失。 这种情况将为我们对形态变化的基因组基础的推论增添统计能力，因为它将使我们能够识别在无飞行谱系中独立变化的基因组区域。 因此，该项目还将阐明形态变化在基因组水平上的发生方式。 这些主题将用于许多外展活动，包括教育视频，本科生的课堂教学以及在本地K-12学校的研究生外展。