Data from: Is morphology really at odds with molecules in estimating fern phylogeny?

Using a morphological dataset of 136 vegetative and reproductive characters, we infer the tracheophyte phylogeny with an emphasis on early divergences of ferns (monilophytes). The dataset comprises morphological, anatomical, biochemical, and some DNA structural characters for a taxon sample of 35 species, including representatives of all major lineages of vascular plants, especially ferns. Phylogenetic relationships among vascular plants are reconstructed using maximum parsimony and Bayesian inference. Both approaches yield similar relationships and provide evidence for three major lineages of extant vascular plants: lycophytes, ferns, and seed plants. Lycophytes are sister to the euphyllophyte clade, which comprises the fern and seed plant lineages. The fern lineage consists of five clades: horsetails, whisk ferns, ophioglossoids, marattioids, and leptosporangiate ferns. This lineage is supported by characters of the spore wall and has a parsimony bootstrap value of 76%, although the Bayesian posterior probability is only 0.53. Each of the five fern clades is well supported, but the relationships among them lack statistical support. Our independent phylogenetic analyses of morphological evidence recover the same deep phylogenetic relationships among tracheophytes as found in previous studies utilizing DNA sequence data, but differ in some ways within seed plants and within ferns. We discuss the extensive independent evolution of the five extant fern clades and the evidence for the placement of whisk ferns and horsetails in our morphological analyses.本研究依托包含136个营养与繁殖性状的形态学数据集，开展维管植物（tracheophyte）系统发育关系的推断工作，重点聚焦蕨类（monilophytes）的早期分化分支。本研究的类群采样涵盖35个物种，数据集包含这些物种的形态、解剖、生化及部分DNA结构性状，采样覆盖维管植物所有主要演化支的代表类群，尤以蕨类类群为核心。本研究采用最大简约法（maximum parsimony）与贝叶斯推断（Bayesian inference）重建维管植物的系统发育关系。两种分析方法得到的拓扑结构高度一致，证实现存维管植物可划分为三大主要演化支：石松类植物（lycophytes）、蕨类植物与种子植物（seed plants）。石松类植物为真叶植物演化支（euphyllophyte clade）的姊妹群，该演化支包含蕨类与种子植物两大演化支。蕨类演化支包含五个演化支：木贼类（horsetails）、松叶蕨类（whisk ferns）、瓶尔小草类（ophioglossoids）、莲座蕨类（marattioids）与薄囊蕨类（leptosporangiate ferns）。该蕨类演化支得到孢子壁性状的支持，其最大简约法自举支持值为76%，但贝叶斯后验概率仅为0.53。五个蕨类演化支各自均得到充分的统计支持，但各演化支之间的系统发育关系却缺乏统计学证据支撑。本研究基于形态学证据开展的独立系统发育分析，在维管植物的深层系统发育关系上与既往基于DNA序列数据的研究结果一致，但在种子植物内部以及蕨类植物内部的拓扑结构上存在部分差异。本研究还讨论了五个现存蕨类演化支的广泛独立演化过程，以及本研究形态学分析中支持松叶蕨类与木贼类类群归属的相关证据。