Finnish Museum of Natural History (Botany), University of Helsinki, PO Box 7, FI-00014 Helsinki, Finland.
Unidad Ejecutora Lillo (CONICET-FML), Miguel Lillo 251, 4000 San Miguel de Tucumán, Tucumán, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo - Universidad Nacional de Tucumán, Miguel Lillo 205, 4000 San Miguel de Tucumán, Tucumán, Argentina.
Mol Phylogenet Evol. 2020 Feb;143:106662. doi: 10.1016/j.ympev.2019.106662. Epub 2019 Oct 29.
Morphological data has gained renewed attention and has been shown to be crucial in clarifying the phylogenetic relationship in a wide range of taxa. In the last decades, phylogenetic analyses of sequence-level data have radically modified the systematic schemes within bryophytes (early non-vascular land plants) and have revealed a widespread pattern of conflict with morphology-based classifications. Yet, a comprehensive evaluation of character conflict has not yet been performed in the context of combined matrices. In this study, we evaluate the impact of morphology on bryophyte phylogeny following a total-evidence approach across 10 published matrices. The analysed matrices span a wide range of bryophytes, taxonomic levels, gene sampling and number of morphological characters and taxa. Data conflict was addressed by measuring: (i) the topological congruence between individual partitions, (ii) changes in support values of the combined data relative to the molecular partition and (iii) clade stability. The association between these measures and the number of morphological characters per taxon (N/T ratio) and the proportion of non-fixed characters (i.e., inapplicable, polymorphic and missing data) was explored. In the individual partition analyses, the N/T ratio correlated positively with the topological congruence in six to seven datasets depending on the weighting scheme. The proportion of non-fixed cells had a minor influence on congruence between data partitions. The number of characters and proportion of non-fixed data varied significantly between morphological datasets that improved congruence between data types. This variation suggests that morphological datasets affect the results of combined analyses in different ways, depending on the taxa studied. Combined analyses revealed that, despite the low congruence values between partitions, integrating data types improves support values and stability. However, while non-fixed data had no negative effect on support values, stability was reduced as the proportion of non-fixed cells increased. N/T ratio was negatively associated with support values and it showed ambiguous responses in stability evaluations. Overall, the results indicate that adding morphology may contribute to the inference of phylogenetic relationships of bryophytes despite character conflict. Our findings suggest that merely comparing (a) morphology-based classifications with molecular phylogenies or (b) the outcome from individual data partitions can misestimate data conflict. These findings imply that analyses of combined data may provide conservative assessments of data conflict and, eventually, lead to an improved sampling of morphological characters in large-scale analyses of bryophytes.
形态学数据重新受到关注，并已被证明在阐明广泛类群的系统发育关系方面至关重要。在过去的几十年中，基于序列水平数据的系统发育分析极大地改变了苔藓植物（早期非维管束陆地植物）的系统分类方案，并揭示了与基于形态学分类的广泛冲突模式。然而，在组合矩阵的背景下，尚未对特征冲突进行全面评估。在这项研究中，我们通过跨 10 个已发表矩阵进行的全证据方法来评估形态学对苔藓植物系统发育的影响。分析的矩阵涵盖了广泛的苔藓植物、分类水平、基因采样以及形态特征和分类单元的数量。通过测量以下方法来解决数据冲突：（i）单个分区之间的拓扑一致性；（ii）相对于分子分区，组合数据的支持值变化；（iii）分支稳定性。探索了这些措施与每个分类单元的形态特征数量（N/T 比）和非固定特征（即不可应用、多态和缺失数据）的比例之间的关联。在单个分区分析中，N/T 比与六个到七个数据集的拓扑一致性呈正相关，具体取决于加权方案。非固定细胞的比例对数据分区之间的一致性影响较小。形态数据集之间的字符数量和非固定数据的比例差异很大，这提高了数据类型之间的一致性。这种变化表明，形态数据集以不同的方式影响组合分析的结果，具体取决于研究的分类单元。综合分析表明，尽管分区之间的一致性值较低，但整合数据类型可以提高支持值和稳定性。然而，虽然非固定数据对支持值没有负面影响，但随着非固定细胞比例的增加，稳定性会降低。N/T 比与支持值呈负相关，并且在稳定性评估中表现出模糊的反应。总的来说，这些结果表明，尽管存在特征冲突，但添加形态学可能有助于推断苔藓植物的系统发育关系。我们的研究结果表明，仅比较（a）基于形态学的分类与分子系统发育或（b）单个数据分区的结果可能会错误估计数据冲突。这些发现意味着，综合数据分析可能会对数据冲突进行保守评估，并最终导致在大规模苔藓植物分析中更好地采样形态学特征。
