Two conflicting morphological approaches to polyclad systematics highlight the relevance of molecular data for resolving the interrelationships of Polycladida. In the present study, phylogenetic trees were reconstructed based on a short alignment of the 28S rDNA marker gene with 118 polyclad terminals (24 new) including 100 different polyclad species from 44 genera and 22 families, as well as on a combined dataset using 18S and 28S rDNA genes with 27 polyclad terminals (19 new) covering 26 different polyclad species. In both approaches, Theamatidae and Cestoplanidae were included, two families that have previously been shown to switch from Acotylea to Cotylea. Three different alignment methods were used, both with and without alignment curation by Gblocks, and all alignments were subjected to Bayesian inference and maximum likelihood tree calculations. Over all trees of the combined dataset, an extended majority-rule consensus tree had weak support for Theamatidae and Cestoplanidae as acotyleans, and also the cotylean genera Boninia, Chromyella and Pericelis appeared as acotyleans. With the most inclusive short 28S dataset, on the other hand, there is good support for the aforementioned taxa as cotyleans. Especially with the short 28S matrix, taxon sampling, outgroup selection, alignment method and curation, as well as model choice were all decisive for tree topology. Well-supported parts of the phylogeny over all trees include Pseudocerotoidea, Prosthiostomoidea, Stylochoidea, Leptoplanoidea and Cryptoceloidea, the latter three with new definitions. Unstable positions in the tree were found not only for Theamatidae, Cestoplanidae, Boninia, Chromyella and Pericelis, but also for Anonymus, Chromoplana and Cycloporus.

中文翻译：

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Polyclad 系统发育仍然存在问题

Polyclad 系统学的两种相互冲突的形态学方法强调了分子数据对于解决 Polycladida 相互关系的相关性。在本研究中，基于 28S rDNA 标记基因与 118 个多枝末端（24 个新）的短比对重建系统发育树，包括来自 44 个属和 22 个科的 100 个不同的多枝物种，以及使用 18S 和28S rDNA 基因具有 27 个 polyclad 末端（19 个新），涵盖 26 个不同的 polyclad 物种。在这两种方法中，都包括 Theamatidae 和 Cestoplanidae，这两个家族以前已被证明从 Acotylea 转换为 Cotylea。使用了三种不同的对齐方法，有和没有 Gblocks 的对齐管理，并且所有比对都经过贝叶斯推理和最大似然树计算。在组合数据集的所有树中，扩展的多数规则共识树对作为子叶的 Theamatidae 和 Cestoplanidae 的支持较弱，而且子叶属 Boninia、Cromyella 和 Pericelis 作为子叶出现。另一方面，使用最具包容性的短 28S 数据集，可以很好地支持上述分类群作为子叶。特别是对于短的 28S 矩阵，分类单元采样、外群选择、对齐方法和管理以及模型选择都是树拓扑结构的决定性因素。所有树木的系统发育中得到充分支持的部分包括 Pseudocerotoidea、Prosthiostomoidea、Stylochoidea、Leptoplanoidea 和 Cryptoceloidea，后三个有新的定义。