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

AbstractWhile 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.摘要：尽管物种丰富的真骨鱼类（teleost fish）的演化繁盛被归因于该类群基部发生的一次古老基因组复制事件，但多倍体化（polyploidy）对鱼类演化与多样化的更广泛影响仍不甚明晰。本研究针对多个鱼类支系开展探究，以解析多倍体化与物种多样化之间的关联：涉及的类群包括鲟科（Acipenseridae: Acipenseriformes）、鳅科（Botiidae: Cypriniformes）的沙鳅类、鲤亚科（Cyprininae: Cyprinidae: Cypriniformes）鱼类以及鲑形目（Salmonidae: Salmoniformes）。我们采用基于似然法的进化分析方法，联合估算了多倍体与二倍体鱼类支系对应的物种形成速率与灭绝速率。对鲟科与鳅科的科水平分析显示，多倍体类群与其二倍体近缘类群的多样化速率无显著差异；而针对鲤亚科的亚科水平分析则发现，多倍体类群的多样化速率更高。此外，针对多倍体鲑形目与其二倍体姐妹群（sister clade）狗鱼目（Esociformes）开展的目水平分析，未支持两类群间净多样化速率存在显著差异。综合上述结果，本研究表明多倍体化总体上并未与鱼类的多样化速率降低相关联——这一模式与此前在植物中观测到的结果形成鲜明对比。尽管两项研究所考察的时间框架存在显著差异，但我们的结果提示，在真核生物生命之树的两大主要分支中，多倍体化所关联的多样化模式存在明显不同。