Data from: Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints. This phylogeny provides resolution for what has been classically referred to as the “bush at the top” of the teleost tree, and indicates acanthomorphs originated in the Early Cretaceous. Paleontological evidence suggests acanthomorphs exhibit a pulse of morphological diversification following the end Cretaceous mass extinction; however, the role of this event on the accumulation of living acanthomorph diversity remains unclear. Lineage diversification rates through time exhibit no shifts associated with the end Cretaceous mass extinction, but there is a global decrease in lineage diversification rates 50 Ma that occurs during a period when morphological disparity among fossil acanthomorphs increases sharply. Analysis of clade-specific shifts in diversification rates reveal that the hyperdiversity of living acanthomorphs is highlighted by several rapidly radiating lineages including tunas, gobies, blennies, snailfishes, and Afro-American cichlids. These lineages with high diversification rates are not associated with a single habitat type, such as coral reefs, indicating there is no single explanation for the success of acanthomorphs, as exceptional bouts of diversification have occurred across a wide array of marine and freshwater habitats.

棘鳍鱼类（acanthomorphs）占现存脊椎动物总数的近三分之一。尽管它们在水生生态系统中占据主导地位，但学界对棘鳍鱼类的演化历史及其多样化进程的认知仍较为匮乏。本研究基于包含520种棘鳍鱼类与37个化石年代约束的核基因超级矩阵，构建了分辨率较高的时间校准系统发育树，以此探究棘鳍鱼类的支系多样化模式。该系统发育树解决了硬骨鱼树经典上被称为「顶部灌木丛」的分类分辨率难题，并表明棘鳍鱼类起源于早白垩世。古生物学证据显示，白垩纪末大灭绝事件后，棘鳍鱼类曾出现一轮形态多样化爆发，但该事件对现存棘鳍鱼类多样性积累的作用仍不明确。支系多样化速率随时间的变化并未呈现出与白垩纪末大灭绝相关的偏移，但在距今50 Ma（百万年前）时，支系多样化速率出现全球性下降，这一时期恰好对应化石棘鳍鱼类的形态差异度急剧升高的阶段。对各演化支多样化速率偏移的分析显示，现存棘鳍鱼类的高度多样性由多个快速辐射演化的支系所主导，包括金枪鱼、鰕虎鱼、鳚鱼、狮子鱼以及非洲与美洲慈鲷。这些高多样化速率的支系并未局限于单一栖息地类型（如珊瑚礁），这表明棘鳍鱼类的演化成功并无单一解释——因为其显著的多样化爆发事件广泛发生于各类海洋与淡水生境中。