Walker Joseph F, Yang Ya, Moore Michael J, Mikenas Jessica, Timoneda Alfonso, Brockington Samuel F, Smith Stephen A
Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, Michigan 48109-1048 USA
Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, Michigan 48109-1048 USA.
Am J Bot. 2017 Jun;104(6):858-867. doi: 10.3732/ajb.1700083. Epub 2017 Jun 20.
The carnivorous members of the large, hyperdiverse Caryophyllales (e.g., Venus flytrap, sundews, and pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved.
To explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced 10 transcriptomes, including all the carnivorous genera except those in the rare West African liana family Dioncophyllaceae. We used a variety of methods to infer the species tree, examine gene tree conflict, and infer paleopolyploidy events.
Phylogenomic analyses supported the monophyly of the carnivorous Caryophyllales, with a crown age of 68-83 million years. In contrast to previous analyses, we recovered the remaining noncore Caryophyllales as nonmonophyletic, although the node supporting this relationship contained a significant amount of gene tree discordance. We present evidence that the clade contains at least seven independent paleopolyploidy events, previously unresolved nodes from the literature have high levels of gene tree conflict, and taxon sampling influences topology even in a phylogenomic data set, regardless of the use of coalescent or supermatrix methods.
Our data demonstrate the importance of carefully considering gene tree conflict and taxon sampling in phylogenomic analyses. Moreover, they provide a remarkable example of the propensity for paleopolyploidy in angiosperms, with at least seven such events in a clade of less than 2500 species.
石竹目（Caryophyllales）种类繁多且高度多样化，其中的肉食性成员（如捕蝇草、茅膏菜和猪笼草）可能代表了最古老且最多样化的食虫植物谱系。然而，尽管有众多研究试图阐明它们的进化关系，但早期分化的关系仍未得到解决。
为了探索系统发育基因组数据集在解析肉食性石竹目之间关系方面的效用，我们对10个转录组进行了测序，包括除稀有西非藤本植物科露叶茅膏菜科（Dioncophyllaceae）之外的所有肉食性属。我们使用了多种方法来推断物种树、检查基因树冲突并推断古多倍体事件。
系统发育基因组分析支持肉食性石竹目的单系性，其冠龄为6800万至8300万年。与之前的分析不同，我们发现其余的非核心石竹目并非单系的，尽管支持这种关系的节点存在大量基因树不一致性。我们提供的证据表明，该分支至少包含七个独立的古多倍体事件，文献中先前未解决的节点存在高水平的基因树冲突，并且分类群抽样即使在系统发育基因组数据集中也会影响拓扑结构，无论使用溯祖法还是超矩阵法。
我们的数据证明了在系统发育基因组分析中仔细考虑基因树冲突和分类群抽样的重要性。此外，它们提供了一个被子植物中古多倍体倾向的显著例子，在一个不到2500个物种的分支中至少有七个这样的事件。
