Department of Biological Sciences, The George Washington University, Washington, DC 20052;
National Museum of Natural History, Smithsonian Institution, Washington, DC 20560.
Proc Natl Acad Sci U S A. 2018 Jun 12;115(24):6249-6254. doi: 10.1073/pnas.1719358115. Epub 2018 May 14.
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.
我们对硬骨鱼类系统发育关系的理解已经通过对少数几个基因的分析发生了转变，但关键节点仍然存在不确定性。迄今为止，基于基因组规模的推断仅对有限数量的分类群和基因进行了采样。在这里，我们利用 144 个基因组和 159 个转录组，以前所未有的数据规模来研究鱼类进化：来自 303 个物种的 1105 个同源外显子序列的>0.5 Mb，代表了 72 个栉鳍鱼类目中的 66 个。我们应用了旨在追踪全基因组复制事件对基因树影响的系统发育检验，并使用生物信息学方法找到无并系的基因座。全基因组数据支持鱼类系统发育的结构，并且使用显式基因谱系询问的适合基因组数据集的假设检验程序解决了一些长期存在的不确定性，例如硬骨鱼类和早期真骨鱼类基部的分支顺序，以及棘鳍鱼类和鲈形鱼类辐射的姐妹谱系。全面的化石标定将所有主要鱼类谱系的起源日期定在白垩纪结束之前。
