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: 1355292
• 负责人: Julia Clarke
• 金额: $ 35万
• 依托单位: University of Texas at Austin
• 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=1355292&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.

不会飞的鸟类，包括鸵鸟和鸸鹋（属于平胸鸟类）等物种，表现出一系列与它们失去飞行能力相关的显着特征。 这些特征包括前肢骨骼缩短、体型极度增大或减小、飞行肌肉附着的胸骨缺失以及许多其他改变。 此外，最近的研究表明，这套特征可能在平胸鸟体内进化了多次。 通过研究这些特征的进化并确定基因组的哪些区域可能是它们的基础，我们可以深入了解进化如何在自然世界中并行发生。 我们还可以更好地了解当平胸鸟的形态特征丢失时，基因类型会发生变化。 最终，更好地了解基因型和表型之间的联系可以帮助我们了解人类表型变异的遗传基础。 我们预计，一些人类畸形，包括手指、手骨或前肢的缺失，很可能是由于导致平胸鸟无法飞行的某些相同基因或调控区域发生突变而发生的。 事实上，我们试图找到平胸鸟不能飞的遗传基础的一种方法是检查平胸鸟基因的进化，从之前的研究中已知这些基因会在实验室小鼠中引起类似的形态。 因此，这项研究将在实验室发育研究中已知的突变与我们在远缘脊椎动物中发现的自然变异之间建立重要的联系。该项目将利用不会飞的鸟类的基因组比较，结合形态学研究和系统发育方法，来了解导致不会飞的性状的基因组基础。 对 8 个平胸鸟物种的基因组进行完整测序将产生一个稳健的平胸鸟谱系树及其与平胸鸟的关系，平胸鸟是一种与平胸鸟密切相关且可能嵌入其中的飞行鸟类。 反过来，这棵树将允许识别出现在已知导致在更好研究的发育模型（例如鸡和小鼠）中肢体丧失的基因附近的保守调节区域。 调控区域的起源和丢失时间，例如基因之外的保守区域，将揭示不会飞的鸟类性状进化的调控和遗传基础的重要线索。 先前的系统发育研究强烈表明，平胸鸟的多个谱系可能同时独立地丧失了飞行能力。 这种情况将为我们对形态变化的基因组基础的推断增加统计能力，因为它将使我们能够识别在不会飞行的谱系中独立变化的基因组区域。 因此，该项目还将阐明在基因组水平上如何发生趋同形态变化。 这些主题将用于许多外展活动，包括教育视频、本科生课堂教学以及当地 K-12 学校的研究生外展。