Supplementary datasets for Ecological interactions and genomic innovations fueled evolution of fish endothermy

Endothermy has independently evolved in several vertebrate lineages but remains rare among the roughly 36,000 known fish species. Using an integrated approach combining phylogenomic data from 1,051 ray-finned fishes, ecological data on body size, swim mode and other traits, fossil data, and comparative genomic analyses of 205 marine vertebrates, we reveal that competitive interactions with cetaceans contributed to the evolution of endothermy in ray-finned fishes during the Eocene-Miocene. Phylogenetic comparative analyses identified significant correlations between the origins of endothermy and large body sizes as well as specialized swimming modes (P < 0.05) while challenging other prevailing hypotheses (e.g., specialized diets, depth range expansion). Implementation of a newly developed time-dependent evolutionary model showed that fish endothermy evolution coincided with the radiation of cetaceans but not with ancient climatic events. Genomic analyses of 894 orthologous genes identified 51 loci under positive selection related to metabolism, muscle function, and neural responses, showing convergence across major lineages of endothermic marine vertebrates. Key genes included carnmt1 and dcaf6 involved in metabolic processes and muscle function. These findings advance our understanding of how ecological interactions and genomic innovations interact to shape the evolution of endothermy in the oceans.