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

不会飞的鸟类，包括鸵鸟和鸸鹋（它们属于一种叫做鼠的鸟类）等物种，表现出一系列与它们失去飞行能力相关的显著特征。这些特征包括前肢骨骼的缩短，身体大小的急剧增加或减少，飞行肌附着的胸骨的丧失，以及许多其他的变化。此外，最近的研究表明，这一套特征可能在比率内进化了多次。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是如何在自然界中并行发生的。我们还可以更好地理解，当形态特征丧失时，基因的类型会发生变化，就像在老鼠身上发生的那样。最终，更好地理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，人类的一些畸形，包括手指、手部骨骼或前肢的缺失，很可能是由于一些基因或调节区域的突变造成的，而这些基因或调节区域正是导致人类无法飞行的原因。事实上，我们将尝试找到鼠不会飞的遗传基础的一种方法是检查从先前的研究中已知的在实验室小鼠中引起类似形态的鼠基因的进化。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。该项目将通过比较不会飞的鸟类的基因组，结合形态学研究和系统发育方法，了解导致不会飞的性状的基因组基础。对8种扁鸟的基因组进行完整测序，将得到一份完整的扁鸟谱系树，以及它们与扁鸟之间的关系。扁鸟是一种与扁鸟密切相关的鸟类，很可能嵌在扁鸟内部。这棵树反过来将允许鉴定出在已知的在发育模型（如鸡和小鼠）中导致肢体丧失的基因附近发生的保守调控区域。调控区域（如发生在基因外的保守区域）的起源和丧失时间将揭示无飞行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，飞行可能是在平行的多个家鼠谱系中独立丧失的。这种情况将增加我们对形态变化的基因组基础的推断的统计能力，因为它将使我们能够确定在无飞行谱系中独立变化的基因组区域。因此，这个项目也将阐明如何收敛形态变化发生在基因组水平。这些主题将用于一些推广活动，包括教育视频，本科生的课堂教学，以及当地K-12学校的研究生推广。

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.