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个营养与生殖性状的形态学数据集，开展维管植物（tracheophyte）系统发育推断，重点聚焦蕨类植物（monilophytes）的早期分化事件。本数据集涵盖35个物种的类群样本的形态学、解剖学、生物化学及部分DNA结构性状，样本囊括维管植物所有主要演化支的代表类群，其中尤以蕨类类群为重点。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核心演化支：石松类植物（lycophytes）、蕨类植物以及种子植物。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支系。蕨类演化支包含五个独立演化支：木贼类、松叶蕨类、瓶尔小草类、合囊蕨类以及薄囊蕨类（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获得充分统计学支持，但各支系间的系统发育关系并未得到统计学支持。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此前利用DNA序列数据的研究结果一致，但在种子植物内部以及蕨类内部的系统发育关系上存在部分差异。本研究还讨论了现存五个蕨类演化支的广泛独立演化现象，以及本研究形态学分析中松叶蕨类与木贼类的系统发育位置相关证据。