Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences

Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted in concatenated, joint gene trees and species tree estimation and summary coalescent frameworks. All analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophy...

基于DNA序列证据的系统发育推断，在构建脊椎动物生命树稳定且支持度高的框架方面取得了重大进展。迄今为止，这些进展的大部分依赖于少数基因组区域的序列数据，但事实证明，这些数据无法为持续难以解决的系统发育问题提供满意答案。在此，我们利用超保守元件（ultraconserved elements）周边的DNA序列数据，重新审视了传统上归类于原棘鳍亚纲（Protacanthopterygii）的早期分化真骨鱼类支系之间的系统发育关系。我们报道并分析了一个包含34个操作分类单元（OTUs）的数据集，该数据集涵盖来自53个核基因座的17,957个比对后字符。系统发育分析在串联、联合基因树与物种树推断以及汇总溯祖框架下进行。