Molecular early burst associated with the diversification of birds at the K–Pg boundary

Complex patterns of genome and life-history evolution associated with the end-Cretaceous (K– Pg) mass extinction event limit our understanding of the early evolutionary history of crown group birds. Here, we assess molecular heterogeneity across living birds using a technique enabling inferred sequence substitution models to transition across the history of a clade. Our approach identifies contrasting patterns among exons, introns, untranslated regions, and mitochondrial genomes that reflect distinct regimes of molecular evolution. Up to fifteen shifts in the mode of avian molecular evolution map to rapidly diversifying clades near the Cretaceous-Palaeogene boundary, demonstrating a burst of genomic disparity early in the evolutionary history of crown birds. Using simulation and machine learning techniques, we show that shifts in developmental mode or adult body mass best explain transitions in the mode of nucleotide substitution. These patterns are related, in turn, to macroevolutionary shifts in the allometric scaling relationship between basal metabolic rate and body mass. In agreement with theoretical predictions, we show that this scaling relationship became weaker across the end-Cretaceous transition. Ultimately, our study provides evidence that the Chicxulub bolide impact triggered integrated patterns of evolution across avian genomes, physiology, and life history that structured the evolutionary potential of modern birds.