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 have also 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.

多基因座细胞器（organellar）DNA与核DNA数据推导的系统发育关系，常因基因树间的演化冲突而难以解析。然而，这些数据集间存在的冲突性或“异常（outlier）”关联（即两类系统发育树中配对的操作终端单元（Operational Terminal Units）），往往能为演化过程提供宝贵信息，例如杂交后的叶绿体捕获（chloroplast capture）、不完全谱系分选（incomplete lineage sorting）与水平基因转移（horizontal gene transfer）。迄今为止仅应用于协同系统发育（cophylogenetic）研究的统计工具，同样具备检验细胞器与核DNA数据集间拓扑一致性程度、并可靠识别异常关联的潜力。本研究联合使用两种基于距离的分析方法，即ParaFit与协同系统发育普氏方法（Procrustean Approach to Cophylogeny, PACo），以检测由叶绿体序列数据与核序列数据独立推导得到的冲突系统发育树中的异常关联。本研究通过多种模拟方法，探究了这两种方法识别异常关联的效能，以及输入数据（单位分支长度树与加性树）对数据集间分析结果的影响。为在真实数据集上检验这两种方法的性能，本研究额外推导了新热带卡特兰亚族（Neotropical Catasetinae，隶属于兰科（Orchidaceae）树兰亚科（Epidendroideae））的系统发育关系。该类群因部分物种间存在杂交过程，是研究系统发育不一致（phylogenetic incongruence）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，卡特兰属（Catasetum）、天鹅兰属（Cycnoches）与魔门兰属（Mormodes）内存在显著且支持度极高的系统发育不一致现象。实验模拟与真实数据集的分析结果均表明，当使用由系统发育树（phylograms）推导得到的谱系距离矩阵（patristic distance matrices）时，PACo可成功检测出叶绿体与核DNA数据集间的异常关联，而使用单位分支长度树时则无法实现这一点。无论以系统发育树还是单位分支长度树作为输入数据，ParaFit的整体性能均劣于PACo。由于当前协同系统发育分析的工作流程尚未标准化，本研究提供了一套基于R语言软件（R）的分析流程，可用于运行PACo与ParaFit分析，并以图表与系统发育树的形式展示异常关联结果。该分析流程可提供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。