Data from: Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements

Phylogenetics is undergoing a revolution as large-scale molecular datasets reveal unexpected but repeatable rearrangements of clades that were previously thought to be disparate lineages. One of the most unusual clades of fishes that has been found using large-scale molecular datasets is an expanded Syngnathiformes including traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), as well as a diverse set of largely benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae, Pegasidae) that were previously dispersed across three orders. The monophyly of this surprising clade of fishes has been upheld by recent studies utilizing both nuclear and mitogenomic data, but the relationships among major lineages within Syngnathiformes remain ambiguous; previous analyses have inconsistent topologies and are plagued by low support at deep divergences between the major lineages. In this study, we use a dataset of ultraconserved elements (UCEs) to conduct the first phylogenomic study of Syngnathiformes. UCEs have been effective markers for resolving deep phylogenetic relationships in fishes and, combined with increased taxon sampling, we expected UCEs to resolve problematic syngnathiform relationships. Overall, UCEs were effective at resolving relationships within Syngnathiformes at a range of evolutionary timescales. We find consistent support for the monophyly of traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), which better agrees with morphological hypotheses than previously published topologies from molecular data. This result was supported by all Bayesian and maximum likelihood analyses, was robust to differences in matrix completeness and potential sources of bias, and was highly supported in coalescent-based analyses in ASTRAL when matrices were filtered to contain the most phylogenetically informative loci. While Bayesian and maximum likelihood analyses found support for a benthic-associated clade (Callionymidae, Dactylopteridae, Mullidae, and Pegasidae) as sister to the long-snouted clade, this result was not replicated in the ASTRAL analyses. The base of our phylogeny is characterized by short internodes separating major syngnathiform lineages and is consistent with the hypothesis of an ancient rapid radiation at the base of Syngnathiformes. Syngnathiformes therefore present an exciting opportunity to study patterns of morphological variation and functional innovation arising from rapid but ancient radiation.

系统发育学（Phylogenetics）正经历一场变革：大规模分子数据集揭示了此前被认为属于不同演化支的支系（clades）出现了出人意料但可重复的重排。通过大规模分子数据集发现的最不同寻常的鱼类支系之一，是扩展后的海龙鱼目（Syngnathiformes）——该类群不仅包含传统的长吻海龙鱼目类群：管口鱼科（Aulostomidae）、玻甲鱼科（Centriscidae）、烟管鱼科（Fistulariidae）、剃刀鱼科（Solenostomidae）、海龙科（Syngnathidae），还涵盖了此前被划分至三个目中的多样底栖相关鱼类类群：䲗亚目（Callionymoidei）、飞角鱼科（Dactylopteridae）、羊鱼科（Mullidae）、海蛾鱼科（Pegasidae）。这一令人意外的鱼类支系的单系性（monophyly）已被近期同时利用核基因组与线粒体基因组数据的研究证实，但海龙鱼目内部主要类群间的演化关系仍不明确；此前的分析得到的拓扑结构不一致，且在主要类群间的深层分化节点处普遍存在支持度偏低的问题。本研究利用超保守元件（ultraconserved elements, UCEs）数据集，开展了首次针对海龙鱼目的系统发育组学研究。超保守元件已被证明是解决鱼类深层系统发育关系的有效分子标记，结合更广泛的类群采样，我们预期超保守元件能够解决此前悬而未决的海龙鱼目演化关系问题。总体而言，超保守元件可有效解析不同演化时间尺度下海龙鱼目内部的类群关系。我们的分析一致支持传统长吻海龙鱼目类群（管口鱼科、玻甲鱼科、烟管鱼科、剃刀鱼科、海龙科）的单系性，这一结果相较于此前已发表的分子数据拓扑结构，更符合形态学假说。该结果得到所有贝叶斯与最大似然分析的支持，对矩阵完整性差异及潜在偏倚来源具有鲁棒性；且在将矩阵过滤为仅保留最具系统发育信息的位点后，基于溯祖分析（coalescent-based analyses）的ASTRAL分析也给出了极高的支持度。尽管贝叶斯与最大似然分析发现，底栖相关类群（䲗科Callionymidae、飞角鱼科、羊鱼科与海蛾鱼科）作为长吻类群的姊妹支，但这一结果并未在ASTRAL分析中得到重复。我们的系统发育树基部以分隔海龙鱼目主要类群的短演化间隔为特征，这与海龙鱼目基部曾发生古老快速辐射演化的假说一致。因此，海龙鱼目为研究源自古老快速辐射的形态变异与功能创新模式提供了极具潜力的研究对象。