Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China.
Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China.
Mol Phylogenet Evol. 2024 Nov;200:108184. doi: 10.1016/j.ympev.2024.108184. Epub 2024 Aug 30.
Poales, as one of the largest orders of angiosperm, holds crucial economic and ecological importance. Nevertheless, achieving a consensus topology has been challenging in previous studies due to limited molecular data and sparse taxon sampling. The uneven distribution of species diversity among families and the factors leading to elevated species richness in certain lineages have also been subjects of ongoing discussion and investigation. In this study, we conducted a comprehensive sampling, including representatives from all 14 families and 85 taxa of Poales, along with five additional outgroups. To reconstruct the phylogeny of Poales, we employed a combination of coalescent and concatenation methods on three nuclear gene sets (1093, 491, 143) and one plastid gene set (53), which were inferenced from genomic data. We also conducted phylogenetic hypothesis analyses to evaluate two major conflicting nodes detected in phylogenetic analyses. As a result, we successfully resolved the backbone of Poales and provided a timeline for its evolutionary history. We recovered the sister relationship between Typhaceae and Bromeliaceae as the earliest diverging families within Poales. The clade consisting of Ecdeiocoleaceae and Joinvilleaceae was recovered as the sister group of Poaceae. Within the xyrid clade, Mayacaceae and Erioaculaceae + Xyridaceae successively diverged along the backbone of Poales. The topology of [Aristidoideae, ((Micrairoideae, Panicoideae), (Arundinoideae, (Chloridoideae, Danthonioideae)))] within the PACMAD clade has received strong support from multiple findings. We also delved into the underlying biological factors that contributed to the conflicting nodes observed in the phylogenetic analysis. Apart from the uncertainty regarding the sister group of Poaceae caused by cytonuclear discordance, frequent hybridization and polyploidy may have contributed to other conflicting nodes. We identified 26 putative whole-genome duplication (WGD) events within Poales. However, apart from the σ-WGD and the ρ-WGD, we did not observe any potential polyploid events that could be directly linked to the species diversification in specific lineages. Furthermore, there was a significant increase in the net diversification rate of Poales following the K-Pg boundary.
Poales 是被子植物门中最大的一个目，具有重要的经济和生态意义。然而，由于分子数据有限且分类群取样稀疏，以前的研究中达成共识的拓扑结构一直具有挑战性。科间物种多样性的不均匀分布以及导致某些谱系物种丰富度增加的因素，也是正在讨论和研究的主题。在这项研究中，我们进行了全面的采样，包括 Poales 所有 14 个科和 85 个分类群的代表，以及另外 5 个外群。为了重建 Poales 的系统发育，我们使用了合并和连锁方法对三个核基因座（1093、491、143）和一个质体基因座（53）进行了推断，这些基因座是从基因组数据中推断出来的。我们还进行了系统发育假设分析，以评估在系统发育分析中检测到的两个主要冲突节点。结果，我们成功地解决了 Poales 的骨干，并提供了其进化历史的时间表。我们恢复了 Typhaceae 和 Bromeliaceae 作为 Poales 内最早分化的科的姐妹关系。由 Ecdeiocoleaceae 和 Joinvilleaceae 组成的分支被恢复为 Poaceae 的姐妹群。在 xyrid 分支中，Mayacaceae 和 Erioaculaceae + Xyridaceae 沿着 Poales 的骨干线相继分化。在 PACMAD 分支内的 [Aristidoideae，((Micrairoideae，Panicoideae)，(Arundinoideae，(Chloridoideae，Danthonioideae)))] 的拓扑结构得到了多种发现的强烈支持。我们还深入探讨了导致系统发育分析中观察到的冲突节点的潜在生物学因素。除了由于核质不和谐导致的对 Poaceae 姐妹群的不确定性之外，频繁的杂交和多倍体化可能导致了其他冲突节点。我们在 Poales 中鉴定了 26 个推定的全基因组复制 (WGD) 事件。然而，除了 σ-WGD 和 ρ-WGD 之外，我们没有观察到任何可能与特定谱系物种多样化直接相关的潜在多倍体事件。此外，在 K-Pg 边界之后，Poales 的净多样化率显著增加。
