Data from: Rumbling orchids: how to assess divergent evolution between chloroplast endosymbionts and the nuclear host

Phylogenetic relationships inferred from multilocus organellar and nuclear DNA data are often difficult to resolve because of evolutionary conflicts among gene trees. However, conflicting or ‘outlier’ associations (i.e., linked pairs of Operational Terminal Units in two phylogenies) among these data sets often provide valuable information on evolutionary processes such as chloroplast capture following hybridization, incomplete lineage sorting, and horizontal gene transfer. Statistical tools that to date have been used in cophylogenetic studies only also have the potential to test for the degree of topological congruence between organellar and nuclear data sets and reliably detect outlier associations. Two distance-based methods, namely ParaFit and Procrustean Approach to Cophylogeny (PACo), were used in conjunction to detect those outliers contributing to conflicting phylogenies independently derived from chloroplast and nuclear sequence data. We explored their efficiency of retrieving outlier associations, and the impact of input data (unit branch length and additive trees) between data sets, by using several simulation approaches. In order to test their performance using real data sets, we additionally inferred the phylogenetic relationships within Neotropical Catasetinae (Epidendroideae, Orchidaceae), which is a suitable group to investigate phylogenetic incongruence because of hybridization processes between some of its constituent species. A comparison between trees derived from chloroplast and nuclear sequence data reflected strong, well supported incongruence within Catasetum, Cycnoches, and Mormodes. As a result, outliers among chloroplast and nuclear data sets, and in experimental simulations, were successfully detected by PACo when using patristic distance matrices obtained from phylograms, but not from unit branch length trees. The performance of ParaFit was overall inferior compared to PACo, using either phylograms or unit branch lengths as input data. Because workflows for applying cophylogenetic analyses are not standardized yet, we provide a pipeline for executing PACo and ParaFit as well as displaying outlier associations in plots and trees by using the software R. The pipeline renders a method to identify outliers with high reliability and to assess the combinability of the independently derived data sets by means of statistical analyses.

基于多位点细胞器DNA与核DNA数据推断的系统发育关系往往难以解析，这是因为不同基因树间存在进化冲突。然而，这些数据集间存在的冲突或‘异常’关联（即两棵系统发育树中配对的操作末端单元（Operational Terminal Units）），往往能为诸如杂交后的叶绿体捕获、不完全谱系分选以及水平基因转移等进化过程提供宝贵信息。迄今为止仅应用于共系统发育研究的统计工具，同样可用于检验细胞器与核DNA数据集间的拓扑一致性程度，并可靠地检测异常关联。本研究结合使用两种基于距离的方法——ParaFit与共系统发育普氏近似法（Procrustean Approach to Cophylogeny, PACo），以检测那些导致由叶绿体序列与核序列数据独立推导得到的系统发育树产生冲突的异常样本。我们通过多种模拟方法，探究了这两种方法检索异常关联的效能，以及输入数据（单位分支长度与加性树）对数据集间分析结果的影响。为了利用真实数据集检验其性能，我们额外对新热带区瓢唇兰亚族（树兰亚科，兰科）的系统发育关系进行了推断；该类群因部分组成物种间存在杂交过程，是研究系统发育不一致性的理想类群。对叶绿体与核序列数据推导得到的系统发育树进行比较后发现，瓢唇兰属（Catasetum）、天鹅兰属（Cycnoches）与魔帝兰属（Mormodes）内存在显著且支持度良好的系统发育不一致性。结果显示，当使用由谱系树（phylograms）得到的谱系距离矩阵时，PACo可成功检测到叶绿体与核DNA数据集间的异常关联，以及实验模拟中的异常关联；但使用单位分支长度树得到的矩阵时则无法实现。无论输入数据为谱系树还是单位分支长度树，ParaFit的整体性能均劣于PACo。由于当前共系统发育分析的工作流程尚未标准化，我们提供了一套可在R软件（R）中运行PACo与ParaFit，并通过绘图与系统发育树展示异常关联的分析流程。该流程可实现一种高可靠性的异常关联识别方法，并可通过统计分析评估独立推导得到的数据集的可组合性。