Data from: Comparative analysis reveals that polyploidy does not decelerate diversification in fish

While the proliferation of the species-rich teleost fish has been ascribed to an ancient genome duplication event at the base of this group, the broader impact of polyploidy on fish evolution and diversification remains poorly understood. Here, we investigate the association between polyploidy and diversification in several fish lineages: the sturgeons (Acipenseridae: Acipenseriformes), the botiid loaches (Botiidae: Cypriniformes), Cyprininae fishes (Cyprinidae: Cypriniformes) and the salmonids (Salmonidae: Salmoniformes). Using likelihood-based evolutionary methodologies, we co-estimate speciation and extinction rates associated with polyploid vs. diploid fish lineages. Family-level analysis of Acipenseridae and Botiidae revealed no significant difference in diversification rates between polyploid and diploid relatives, while analysis of the subfamily Cyprininae revealed higher polyploid diversification. Additionally, order-level analysis of the polyploid Salmoniformes and its diploid sister clade, the Esociformes, did not support a significantly different net diversification rate between the two groups. Taken together, our results suggest that polyploidy is generally not associated with decreased diversification in fish – a pattern that stands in contrast to that previously observed in plants. While there are notable differences in the time frame examined in the two studies, our results suggest that polyploidy is associated with different diversification patterns in these two major branches of the eukaryote tree of life.尽管物种丰富的真骨鱼类（teleost fish）的繁盛被归因于该类群基部发生的一次古全基因组复制事件，但多倍性（polyploidy）对鱼类演化与多样化的广泛影响仍未得到充分解析。本研究针对多个鱼类支系展开探究，以厘清多倍性与类群分化之间的关联：涵盖鲟科（Acipenseridae: Acipenseriformes）、鳅科（Botiidae: Cypriniformes）、鲤亚科鱼类（Cyprininae: Cyprinidae: Cypriniformes）以及鲑形目（Salmonidae: Salmoniformes）。研究采用基于似然法的演化分析手段，联合估算多倍体与二倍体鱼类支系的物种形成速率与灭绝速率。对鲟科与鳅科的科水平分析结果显示，多倍体类群与其二倍体近缘类群的分化速率并无显著差异；而针对鲤亚科的亚科水平分析则表明，多倍体类群的分化速率更高。此外，针对多倍体鲑形目及其二倍体姐妹支系狗鱼目（Esociformes）的目水平分析，未证实两类群间净分化速率存在显著差异。综合而言，本研究结果提示，多倍性通常并不与鱼类的分化速率降低相关——这一模式与此前在植物中观测到的结论相悖。尽管两项研究所考察的时间尺度存在显著差异，但我们的研究结果表明，多倍性在真核生物生命树的这两大主要分支中，呈现出截然不同的多样化模式。