基于质体基因组的系统基因组学研究已经解决了各种植物之间的顽固关系,然而,由于质体基因冲突,Dennstaedtiaceae在家族和属水平上的系统发育仍未解决,有限的分子数据和不完整的分类单元采样以前的研究。本研究产生了30个Dennstaedtiaceae的新质体基因组(9属,29种),与42个公开可用的质体基因组(包括24个家族,27属,42种)探索Dennstaedtiaceae的进化。为了最大程度地减少系统误差对系统发育推断分辨率的影响,我们应用了六种策略来生成30个基于CDS的数据集,基因间间隔区,和整个塑物组,和两种树推断方法(最大似然,ML;和多物种聚结,MSC)以全面分析质体尺度数据。此外,使用ML框架对所有有争议的节点之间的系统发育信号进行量化,并对所有数据集之间的不同拓扑假设进行了测试。基于不同数据集和方法的树种树在多足蕨类植物的底部显示出明显的冲突。选择“CDS-密码子-比对-rm3”(删除第三个密码子的CDS)矩阵的拓扑结构作为主要参考或摘要树。最终的系统发育树支持Dennstaedtiaceae作为真核生物的姐妹组,Dennstaedtioideae在全力支持下分为四个分支。这种强大的重建的系统发育骨架为Dennstaedtiaceae分类的未来研究建立了框架,进化和多样化。本研究建议在使用质体基因组时考虑质体系统基因组冲突。从我们的结果来看,减少饱和基因或位点可以有效地减轻远缘相关分类群的树冲突。此外,基于氨基酸序列的系统发育树可以用作比较以验证基于核苷酸的树的置信度。
Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, intergenic spacers, and whole
plastome, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the
plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for controversial nodes using ML framework, and different topologies hypotheses among all datasets were tested. The species trees based on different datasets and methods revealed obvious conflicts at the base of the polypody ferns. The topology of the \"CDS-codon-align-rm3\" (CDS with the removal of the third codon) matrix was selected as the primary reference or summary tree. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtioideae was divided into four clades with full support. This robust reconstructed phylogenetic backbone establishes a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate tree conflicts for distantly related taxa. Moreover, phylogenetic trees based on amino acid sequences can be used as a comparison to verify the confidence of nucleotide-based trees.