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., Usage notesfish_polyploidyPhylogenetic and ploidy level data of 4 fish groups examined: Acipenseridae, Botiidae, Cyprininae, and Salmoniformes.

摘要：尽管物种多样性丰富的硬骨鱼（teleost fish）的辐射演化被归因于该类群基部发生的一次古老全基因组复制事件，但多倍化（polyploidy）对鱼类演化与物种多样化的更广泛影响仍有待深入研究。本研究针对多个鱼类支系展开分析，探讨多倍化与物种多样化之间的关联，涉及的类群包括：鲟科（Acipenseridae：鲟形目Acipenseriformes）、鳅科（Botiidae：鲤形目Cypriniformes）、鲤亚科鱼类（Cyprinidae：鲤形目Cypriniformes）以及鲑科鱼类（Salmonidae：鲑形目Salmoniformes）。
本研究采用基于似然法的演化分析方法，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物种多样化速率并无显著差异；而对鲤亚科的分析则发现，多倍体类群的多样化速率更高。此外，对多倍体鲑形目（Salmoniformes）及其二倍体姊妹群狗鱼目（Esociformes）的目水平分析也未发现两类群的净物种多样化速率存在显著差异。
综合来看，本研究结果表明，多倍化通常不会导致鱼类的物种多样化速率降低——这一结果与此前在植物中观测到的模式截然相反。尽管两项研究所考察的时间框架存在显著差异，但本研究结果表明，在真核生物生命树的这两大主要分支中，多倍化与不同的物种多样化模式相关联。
使用说明：数据集fish_polyploidy包含本次研究涉及的4个鱼类类群的系统发育数据与倍性水平数据，涉及类群分别为鲟科（Acipenseridae）、鳅科（Botiidae）、鲤亚科（Cyprininae）以及鲑科（Salmoniformes）。