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

准确确定地球物种进化历史的模式和时间对于了解地质和环境力量如何驱动物种的起源、多样化和灭绝至关重要。低成本基因组测序的出现彻底改变了系统学领域和使用遗传数据来推断生物体进化关系的领域。但生成基因组结构和变异数据的能力已经超过了对如何使用它来推断进化历史和物种关系的理解。该项目将分析基因组特征对猫科进化推论的影响。由于猫的物种关系已被充分了解，多个物种的基因组数据可用，并且可以使用遗传工具进行详细分析，因此猫是研究染色体特征和基因组结构变异如何影响进化和进化历史推断的绝佳系统。这项研究有望对系统学和进化生物学领域产生巨大影响。这项研究还对社会产生更广泛的影响。猫一直被评为野生动物和动物保护领域最具魅力和最知名的象征，并为参与和了解不同社会经济背景的生物学和进化论提供了途径。最重要的项目成果之一将是由新招募的学生和研究人员开发一个网站，描述和整合研究成果与猫科成员的信息，并将其与公众联系起来。利用猫科动物的显着辐射作为模型系统，该项目将从所有生物物种中生成高质量的基因组序列组装，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、排序和表征拓扑、树形状和分化时间的全基因组变异，并将这种变异与预测物种树的基因组特征联系起来。最终目标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，以指导未来系统发育学的原理和应用。猫科动物是一个优秀的模型系统，因为家族内的重组率很高，并且存在已建立的基因组工具和信息。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力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.