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, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalaxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the majority of analyses. The concatenated and joint gene trees and species tree analysis types produce high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are also apparent within the otomorph and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny.

基于DNA序列证据的系统发育推断（Phylogenetic inference），已为脊椎动物生命之树构建稳定且支持度极高的框架取得了显著进展。迄今为止，此类进展大多依赖于少量基因组区域的序列数据，但这类数据已被证实无法为长期存在的顽固系统发育问题提供令人满意的解答。本研究基于围绕超保守元件（ultraconserved elements）的DNA序列数据，重新审视了经典归类于原棘鳍总目（Protacanthopterygii）的早期分化真骨鱼支系间的系统发育关系。本研究报道并分析了一套包含34个操作分类单元（Operational Taxonomic Units, OTUs）、来自53个核基因座、经比对后共17957个特征位点的数据集。本研究分别采用串联法、联合基因树与物种树估计法以及汇总式溯祖分析框架开展系统发育分析。所有分析框架均为现有亲缘关系假说提供了支持证据，包括鳞南乳鱼（Lepidogalaxias salamandroides）的系统位置、巨口鱼总目（Stomiatii）的单系性，以及狗鱼目+鲑形目演化支的存在。在多数分析中，鳞南乳鱼（Lepidogalaxias salamandroides）与狗鱼目+鲑形目类群依次作为其余所有真骨鱼的姊妹支系。串联法、联合基因树与物种树分析均为该拓扑结构提供了极高的支持率。但银汉鱼目（Argentiniformes）、巨口鱼总目（Stomiatii）与新真骨鱼亚部（Neoteleostei）之间的亲缘关系仍不明确：不同分析方法得到的结果存在差异，且均获得了较强但相互矛盾的支持指数。数据集内骨鳔总目（otomorph）与鲈形总目（percomorph）类群的拓扑结构差异也因分析方法不同而显现。本研究结果既明确了早期分化真骨鱼支系内部及支系间亲缘关系中存在高度支持的一致区域，同时也揭示了大型数据集仍无法彻底解析该系统发育其他方面问题的局限性。