Data from: Phylogenetic relationships in Asarum (Aristolochiaceae): effect of data partitioning and a revised classification

Premise of the study: Generic boundaries and infrageneric relationships among the charismatic temperate magnoliid Asarum sensu lato have long been uncertain. Previous molecular phylogenetic analyses used either plastid or nuclear loci alone and varied greatly in their taxonomic implications for the genus. We analyze additional molecular markers from the nuclear and plastid genomes, reevaluate the possibility of a derived loss of autonomous self-pollination, and investigate the topological effects of matrix partitioning scheme choice. Methods: We sequenced seven plastid regions and the nuclear ITS1 - ITS2 region of 58 individuals representing all previously recognized Asarum s.l. segregate genera and the monotypic genus Saruma. Matrices were partitioned using common a priori partitioning schemes and PartitionFinder. Key results: Topologies recovered using a priori partitioning of matrices differed from those recovered using a PartitionFinder-selected scheme, and by analysis method. We recover six monophyletic groups that we circumscribe into three subgenera and six sections. Putative fungal mimic characters serve as synapomorphies only for subgenus Heterotropa. Subgenus Geotaenium, a new subgenus, is recovered as sister to the remainder of Asarum by ML analyses of highly partitioned datasets. Section Longistylis, also newly named, is sister to section Hexastylis. Conclusions: Our analyses do not unambiguously support a single origin for all fungal mimicry characters. Topologies recovered through the analysis of PartitionFinder-optimized matrices can differ drastically from those inferred from a priori partitioned matrices and by analytical method. We recommend that investigators evaluate the topological effects of matrix partitioning using multiple methods of phylogenetic reconstruction.

研究背景：广受关注的温带木兰类植物广义细辛属（Asarum sensu lato）的属级界限及其属下类群间的系统发育关系长期以来存在争议。此前的分子系统发育分析要么仅采用质体基因组位点，要么仅使用核基因组位点，且针对该属的分类学推论差异悬殊。本研究新增了来自核基因组与质体基因组的分子标记，重新评估了自主自交次生丢失的可能性，并探讨了矩阵分区方案选择对系统发育拓扑结构的影响。

研究方法：我们对覆盖所有此前认定的广义细辛属（Asarum s.l.）分立属以及单型属马蹄香属（Saruma）的58个个体，完成了7个质体区域与核基因组内转录间隔区1-内转录间隔区2（ITS1-ITS2）的测序。序列矩阵分别采用常见的先验分区方案以及PartitionFinder软件进行分区处理。

主要结果：基于先验矩阵分区得到的系统发育拓扑结构，与采用PartitionFinder筛选出的分区方案以及不同分析方法得到的拓扑结构均存在显著差异。本研究鉴定出6个单系类群，并将其划分为3个亚属与6个组。推测的真菌拟态性状仅为异莶细辛亚属（Heterotropa）的共有衍征。新建立的Geotaenium亚属经最大似然法（Maximum Likelihood, ML）对高度分区的数据集进行分析后，被确定为广义细辛属其余类群的姊妹群。新命名的Longistylis组与Hexastylis组互为姊妹群。

研究结论：本研究的分析结果并未明确支持所有真菌拟态性状起源于单次演化事件。采用PartitionFinder优化后的矩阵得到的拓扑结构，与基于先验分区矩阵得到的拓扑结构以及不同分析方法得到的结果均存在显著差异。因此我们建议研究者采用多种系统发育重建方法，评估矩阵分区方案对拓扑结构的影响。