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