Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
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DOI：
10.1073/pnas.1719358115
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发表时间：
2018-06-12
影响因子：
11.1
通讯作者：
Shi, Qiong
中科院分区：
文献类型：
--
作者：
Hughes, Lily C.;Orti, Guillermo;Shi, Qiong
通过对少量基因的分析，我们对硬骨鱼类系统发育关系的理解已经发生了变化，但关键节点周围仍然存在不确定性。迄今为止，基因组规模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个转录组来研究鱼类的进化，数据规模无与伦比：来自303个物种的1，105个正向外显子序列的>0.5 Mb，代表72个鳍鱼目中的66个。我们应用系统发育测试，旨在跟踪全基因组重复事件对基因树的影响，并使用生物信息学方法找到无旁系同源位点。全基因组的数据支持的结构的鱼的遗传，和假设检验程序适用于基因组数据集，使用明确的基因谱系询问解决一些长期存在的不确定性，如分支顺序在基地的硬骨鱼和早期真硬骨鱼，和姐妹谱系的棘形和percomorph辐射。全面的化石校准确定了所有主要鱼类谱系在白垩纪末之前的起源。
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. Genomescale 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.