Genomic Distortion of Jawed Vertebrate Phylogeny

Reconstructing patterns of evolution requires understanding the interrelationships of species, yet evolutionary relationships that defy resolution and calibration in time are commonplace across the Tree of Life. Here, we investigate the dynamics of temporal and topological uncertainty by generating a phylogeny of jawed vertebrates using 1105 exonic loci sampled for 540 species spanning all major orders and most families of gnathostomes. Across loci and DNA sequence sites, we observe rapid reductions in statistical support for the monophyly of jawed vertebrate clades that originated around the Cretaceous-Paleogene mass extinction. Phylogenetic signal was scrambled to different degrees during rapid successive divergences in multiple unrelated jawed vertebrate lineages that radiated in this interval, including birds, snakes, placental mammals, and acanthomorph fishes. In addition to showing that particular events have modified phylogenetic signal across the same loci in distantly related vertebrate clades, we also demonstrate how rates of genomic evolution affect our ability to infer the timescale of vertebrate evolution. By testing how the inclusion of lineages of ray-finned fishes with very fast and slow rates of molecular evolution changes inferences of the vertebrate evolutionary timescale, we show that the deepest divergences in ray-finned fishes may be impossible to accurately infer using sequence data and calibrations from a limited fossil record. These results hint at the macroevolutionary realities underlying topological and divergence time uncertainty across evolutionary trees.