Understanding the Co-Evolution of Phylogenomic Signal, Gene Linkage, and Recombination Rate Through Comparative Genomics

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One of the major themes that have emerged from the genetics literature from the past decade is that each species’ genome is a mosaic of many different genetic histories. A daunting challenge facing biologists is how to accurately interpret this large and complex collection of genetic histories to identify which of these most likely represent the true relationships among living and extinct species. The rate at which chromosomes exchange information (i.e., recombine) has been shown to be one of the most reliable predictors of which DNA sequences within chromosomes can best reconstruct ancient relationships of living species. Our goal is to retrace the evolution of mammalian chromosomes and their recombination rates across time, from the genomes of living species back to their inferred 100-million-year-old ancestor. We will identify those shared chromosome regions that have recombined at the slowest rates and provide the greatest fidelity to reconstructing mammalian evolutionary history. We will also determine whether specific genes preferentially evolve within regions of historically high or low rates of chromosomal change. Our findings will greatly benefit researchers seeking to resolve other parts of the Tree of Life, by leading to more efficient approaches for determining evolutionary history at both shallow and deep evolutionary timescales. We will create a new public web-database for mammalian genetic maps that allows researchers to browse chromosomes, genes, and recombination rates across the mammalian Tree of Life. This project will train a diverse cohort of scientists across multiple academic levels. Our proposal is predicated upon pairing new high-quality, chromosome-level mammalian genome assemblies with a recombination map. An explicit goal of this project is to generate a detailed history of mammalian genes and chromosomes annotated with their local recombination rates. We will create a novel, publicly accessible resource of recombination maps allowing researchers to trace the evolution of recombination rate and chromosome evolution across the mammalian tree of life, from the inferred ancestor to each living species. We will also generate the first mammalian phylogeny based on Y chromosome data, the only chromosome that contains regions that have historically lacked meiotic recombination. Our findings will contribute to the goal of resolving the mammalian tree of life and inform ongoing controversies surrounding the mode and tempo of early placental mammal evolution, while improving our understanding of the relationship between chromosome architecture, recombination, and local gene content.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.