Shi Tian, He Jian
State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, China.
Front Plant Sci. 2025 Feb 24;16:1511582. doi: 10.3389/fpls.2025.1511582. eCollection 2025.
Accurate phylogenetic reconstruction is crucial for understanding evolutionary relationships and biodiversity. Despite advances in molecular systematics, the relationships within Pandanales-which include Cyclanthaceae, Pandanaceae, Stemonaceae, Triuridaceae, and Velloziaceae-remain unresolved. This study aims to clarify these relationships by analyzing transcriptomic and genomic data from these families.
We analyzed transcriptomic and genomic data from 20 samples representing all five families of Pandanales. Our approach involved assembling 2,668 single-copy orthologous genes (SCOGs) and conducting phylogenetic analyses using both coalescent- and concatenation-based methods, alongside plastid genome data. Additionally, we employed HyDe for gene flow analysis and conducted coalescent simulations and QuIBL analyses to explore sources of phylogenetic conflict. We also investigated whole-genome duplication (WGD) events within Pandanales.
The phylogenetic analyses produced strongly supported but topologically incongruent trees. Our gene flow analysis suggested that the concatenation-based topology likely reflects the true evolutionary history of Pandanales. We identified two significant ancient gene flow events: one between Velloziaceae and Triuridaceae, and another between Triuridaceae and the C-P clade (Cyclanthaceae + Pandanaceae). Furthermore, we detected five whole-genome duplication (WGD) events, including two that occurred before the Cretaceous-Paleogene boundary in Stemonaceae and Pandanaceae, one in Triuridaceae during the mid-Paleogene, and two within Velloziaceae near the Paleogene-Neogene boundary.
Our findings indicate that gene flow, rather than incomplete lineage sorting, is the primary source of phylogenetic conflict at certain nodes within Pandanales. The identified WGD events likely played a significant role in facilitating adaptation and diversification under changing environmental conditions. These results not only resolve long-standing phylogenetic conflicts but also enhance our understanding of the mechanisms driving plant diversification within this order.
准确的系统发育重建对于理解进化关系和生物多样性至关重要。尽管分子系统学取得了进展，但露兜树目（包括巴拿马草科、露兜树科、百部科、霉草科和翡若翠科）内部的关系仍未得到解决。本研究旨在通过分析这些科的转录组和基因组数据来阐明这些关系。
我们分析了代表露兜树目所有五个科的20个样本的转录组和基因组数据。我们的方法包括组装2668个单拷贝直系同源基因（SCOG），并使用基于溯祖和串联的方法以及质体基因组数据进行系统发育分析。此外，我们使用HyDe进行基因流分析，并进行溯祖模拟和QuIBL分析以探索系统发育冲突的来源。我们还研究了露兜树目内的全基因组复制（WGD）事件。
系统发育分析产生了支持度很高但拓扑结构不一致的树。我们的基因流分析表明基于串联的拓扑结构可能反映了露兜树目的真实进化历史。我们确定了两个重大的古代基因流事件：一个发生在翡若翠科和霉草科之间，另一个发生在霉草科和C-P分支（巴拿马草科+露兜树科）之间。此外，我们检测到五个全基因组复制（WGD）事件，包括两个发生在百部科和露兜树科白垩纪-古近纪边界之前，一个发生在古近纪中期的霉草科，以及两个发生在古近纪-新近纪边界附近的翡若翠科内。
我们的研究结果表明基因流而非不完全的谱系分选是露兜树目内某些节点系统发育冲突的主要来源。确定的WGD事件可能在促进不断变化的环境条件下的适应和多样化方面发挥了重要作用。这些结果不仅解决了长期存在的系统发育冲突，还增强了我们对驱动该目植物多样化机制的理解。
