A phylogeny aware analysis of gene function for the biodiversity genomics era

Abstract

In the biodiversity genomics era, vast gene catalogs have rapidly accumulated, but how gene functions map onto major evolutionary transitions remains vague. We integrated phylogenomics with functional annotations to trace the emergence of ∼4.5 million genes and their associated functions in 508 representative species across the tree of life. Using this top-down, function-centric approach, we mapped the evolutionary history of well-annotated biological functions, revealing key insights and widespread parallelism. For instance, major founder events—bursts of gene and function gain—aligned with key evolutionary transitions, including the origins of eukaryotes, animals, plants, and vertebrates. Independent transitions to multicellularity and terrestrial life showed convergent enrichment of analogous functions, often drawing on ancient gene families. Our framework enables scalable interpretation of new genomes in an evolutionary context and offers a roadmap for exploring the genomic basis of biodiversity.