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.

恒温（Endothermy）在多个脊椎动物类群中独立演化，但在已知约36000种鱼类中仍属罕见。本研究整合了1051种辐鳍鱼类（ray-finned fishes）的系统基因组数据、体长、游泳模式等生态性状数据、化石数据，以及205种海洋脊椎动物的比较基因组分析结果，揭示出：在始新世-中新世时期，与鲸类（cetaceans）的竞争互作推动了辐鳍鱼类恒温性状的演化。系统发育比较分析显示，恒温性状的起源与大体型及特化游泳模式存在显著相关性（P < 0.05），同时对其他主流假说（如特化食性、分布深度拓展）提出了挑战。通过新开发的时间依赖性演化模型分析发现，鱼类恒温性状的演化与鲸类的辐射演化时间重合，而非与古气候事件同步。对894个直系同源基因（orthologous genes）的基因组分析共鉴定出51个与代谢、肌肉功能及神经响应相关的正选择基因座（loci），这些基因座在恒温海洋脊椎动物的主要类群中呈现趋同演化特征。关键基因包括参与代谢过程与肌肉功能的carnmt1和dcaf6。本研究结果加深了我们对生态互作与基因组创新如何共同塑造海洋恒温性状演化的理解。