Phylogenomics and the roles of chromosome architecture, recombination and hybridization on phylogenetic accuracy in the cat family (Felidae)

准确地确定地球物种进化史的模式和时间对于理解地质和环境力量如何推动物种的起源、多样化和灭绝是至关重要的。低成本基因组测序的出现彻底改变了系统学领域和利用遗传数据来推断生物体的进化关系。但是，产生基因组结构和变异数据的能力已经超过了如何使用它来推断进化史和物种关系的理解。该项目将分析基因组特征对猫科动物进化推断的影响。由于猫的物种关系被很好地理解，一些物种的基因组数据可用，并且可以使用遗传学工具进行详细分析，猫是研究染色体特征和基因组结构变化如何影响进化和进化史推断的绝佳系统。这项研究有望在系统学和进化生物学领域产生重大影响。这项研究对社会也有更广泛的影响。猫一直被认为是野生动物和动物保护中最具魅力和辨识度的象征，并为不同社会经济背景下的生物和进化提供了参与和学习的途径。最重要的项目成果之一将是由学生和研究人员开发一个网站，描述和整合研究成果与猫家族成员的信息，并将这些信息与公众联系起来。本项目将利用猫科动物家族Felidae的显著辐射作为模型系统，从所有现存物种中生成高质量的基因组序列，以确定染色体特征对物种树推断准确性的影响。将开发新的计算算法来搜索，排序和表征全基因组在拓扑，树形和发散时间上的变化，并将这种变化与物种树的预测基因组特征联系起来。最终目的是了解哪些染色体特征对准确的物种树估计有积极和消极的影响，以指导未来系统基因组学的原理和应用。由于家族内的高重组率和已建立的基因组工具和信息的存在，猫科动物是一个很好的模型系统。该奖项反映了美国国家科学基金会的法定使命，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。

Accurately determining the pattern and timing of the evolutionary history of Earth's species is essential to understand how geologic and environmental forces drive the origin, diversification, and extinction of species. The advent of low-cost genome sequencing has revolutionized the field of systematics and the use of genetic data to infer the evolutionary relationships of organisms. But the ability to generate data on genome structure and variation has outpaced understanding on how to use it to infer evolutionary history and species relationships. This project will analyze the impact of genomic features on evolutionary inference in the cat family. Because cat species relationships are well understood, genomic data are available for several species, and genetic tools are available that allow detailed analyses, cats are an excellent system to investigate how chromosome characteristics and structural variation in the genome affect evolution and the inference of evolutionary history. This study promises to have a large impact on the field of systematics and evolutionary biology. This study also has broader impacts on society. Cats are consistently ranked as the most charismatic and recognizable symbols of wildlife and animal conservation, and provide a gateway to engagement and learning about biology and evolution across diverse socioeconomic backgrounds. One of the most important project outcomes will be the development of a website by student recruits and researchers, describing and integrating research outcomes with information on the members of the cat family, and connecting these to the public.Using the remarkable radiation of the cat family Felidae as a model system, this project will generate high quality genome sequence assemblies from all living species to identify the impact of chromosomal characteristics on the accuracy of species tree inference. Novel computational algorithms will be developed to search, sort, and characterize genome-wide variation in topology, tree shape and divergence time, and connect this variation to genomic features predictive of the species tree. The ultimate goal is to understand which chromosomal features have positive and negative influences on accurate species tree estimation, to guide future principles and applications of phylogenomics. Felids are an excellent model system because of the high rate of recombination within the family and the existence of established genomic tools and information.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.