Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.

通过对少数基因的分析，我们对骨鱼之间的系统发育关系的理解已经转变，但是关键节点周围仍然存在不确定性。到目前为止，基因组规模的推断仅对有限数量的分类单元和基因进行了采样。在这里，我们利用144个基因组和159个转录组，以无与伦比的数据规模来研究鱼类的进化：来自303个物种的1,105个直系外显子序列中的> 0.5 Mb，代表了72条有鳍鱼类的66条。我们应用系统发育测试，旨在追踪全基因组复制事件对基因树的影响，并使用生物信息学方法找到无寄生虫的基因座。全基因组数据支持鱼类系统发育的结构，以及适用于使用显性基因谱系询问进行系统发育数据集的假设检验程序，解决了一些长期存在的不确定性，例如硬骨鱼基部和早期雌性硬皮动物之间的分支顺序，以及棘皮动物和percomorph辐射的姐妹谱系。全面的化石定标可以追溯到白垩纪末期所有主要鱼类谱系的起源。