Supplementary datasets for Interactions with cetaceans fueled the evolution of fish endothermy

Endothermy has independently evolved in several vertebrate lineages but remains rare among fishes. Using an integrated approach combining phylogenomic and ecomorphological data, including body size, swimming mode, depth range, and diet for 1,051 ray-finned fishes, coupled with a newly developed time-dependent evolutionary model and comparative genomic analyses of 205 marine vertebrates, we propose that ecological interactions with modern cetaceans coincided with the evolution of endothermy in ray-finned fishes during the Eocene–Miocene. This result is further supported by evidence of temporal and geographical overlap between cetaceans and endothermic fish lineages in the fossil record, as well as correlations between cetacean fossil and extant diversification patterns and the origin or endothermy in fishes. Phylogenetic comparative analyses also identified significant correlations between the origins of endothermy and large body sizes as well as specialized swimming modes while challenging hypotheses focusing on specialized diets and depth range expansion. Comparative genomic analyses identified 51 orthologous genes under positive selection related to metabolism, muscle function, and neural responses, showing convergence across major lineages of endothermic marine vertebrates, including key genes like carnmt1 and dcaf6. Our findings advance the understanding of how ecological interactions and genomic factors shape the evolution of innovative adaptations in the oceans.