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

不会飞的鸟类，包括鸵鸟和鸵鸟(属于一种被称为ratites的鸟类)，呈现出一系列与它们失去飞行有关的显著特征。这些特征包括前肢骨骼的缩短，身体尺寸的极端增大或减小，飞行肌肉附着的胸骨的丢失，以及许多其他修改。此外，最近的研究表明，这一系列特征可能在这种比率内进化了多次。通过研究这些特征的进化并确定它们可能位于基因组的哪些区域，我们可以深入了解自然界的进化是如何平行发生的。我们还可以更好地了解当形态特征以其在比率中的方式丢失时发生变化的基因类型。最终，更好地了解基因型和表型之间的联系可以帮助我们理解人类表型变异的遗传基础。我们预计，一些人类畸形的发生，包括手指、手部骨骼或前肢的丢失，很可能是因为一些相同的基因或调控区域的突变，这些基因或调控区域是导致不能飞行的原因。事实上，我们试图找到Ratites中不能飞行的遗传基础的一种方法是检查Ratite基因的进化，这些基因从以前的研究中已知会导致实验室小鼠相似的形态。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亲脊椎动物中发现的自然变异之间建立重要的联系。这个项目将使用不会飞的鸟类基因组之间的比较，结合形态研究和系统发育方法，来了解导致不能飞的特征的基因组基础。对8个种的基因组进行完整的测序，将产生一个强大的家谱树，其中包括它们与八角鸟的关系，这是一个与八角鸟密切相关并可能嵌入其中的游荡性鸟类群体。这棵树反过来将允许识别发生在已知导致肢体丧失的基因附近的保守调控区域，这些基因在研究得更好的发育模型中，如鸡和老鼠。调节区的起源和丢失的时间，如发生在基因外的保守区，将揭示关于不能飞行的鸟类特征进化的调节和遗传基础的重要线索。以前的系统发育研究有力地表明，飞行很可能是在平行的多个比率谱系中独立消失的。这一情景将增加我们对形态变化的基因组基础的推断的统计学力量，因为它将使我们能够识别在不能飞行的谱系中独立发生变化的基因组区域。因此，这个项目还将阐明如何在基因组水平上发生趋同的形态变化。这些主题将用于一些外联活动，包括教育录像、本科生课堂教学以及在当地K-12学校的研究生外联活动。

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.