Data from: Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

PREMISE OF STUDY: The carnivorous members of the large, hyperdiverse Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes 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.

METHODS: 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.

KEY RESULTS: 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.

CONCLUSIONS: 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.

研究背景：物种丰富度极高的大型石竹目（Caryophyllales）中的肉食性类群（如捕蝇草、茅膏菜及猪笼草），或许是现存肉食植物中起源最早、多样性最高的演化支系。然而，尽管已有诸多研究试图阐明其演化亲缘关系，但该类群早期分化的亲缘关系仍未得到明确解析。

研究方法：为探究系统基因组数据集在解析肉食性石竹目类群亲缘关系中的应用价值，本研究对10个转录组（transcriptomes）进行了测序，涵盖了除稀有西非木质藤本双钩叶科（Dioncophyllaceae）之外的所有肉食性属。本研究采用多种方法开展物种树推断、基因树冲突检测及古多倍化事件（paleopolyploidy events）推断。

主要结果：系统基因组分析结果支持肉食性石竹目为单系群（monophyly），其冠群分化时间为6800万至8300万年前。与既往研究结果不同，本研究发现剩余的非核心石竹目类群并非单系群，尽管支撑该亲缘关系的节点存在显著的基因树冲突（gene tree discordance）。本研究提供的证据显示：该演化支至少发生过7次独立的古多倍化事件；既往文献中未得到解析的节点存在高度基因树冲突；且无论采用溯祖法（coalescent methods）还是超级矩阵法（supermatrix methods），类群取样都会对系统基因组数据集的拓扑结构产生影响。

研究结论：本研究数据证实，在系统基因组分析中，审慎考量基因树冲突与类群取样策略具有重要意义。此外，本研究为被子植物（angiosperms）中古多倍化的发生倾向提供了极具说服力的实例：在一个物种数量不足2500个的演化支中，至少发生了7次古多倍化事件。