Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
Departamento de Biologia, Universidad del Valle, Cali, Colombia.
Am J Bot. 2018 Nov;105(11):1888-1910. doi: 10.1002/ajb2.1178. Epub 2018 Oct 24.
We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification.
We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth.
Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large-scale accelerations in PACMAD-BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae-Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non-coding regions in identifying and supporting short, deep branches.
We provide the first resolved, well-supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome-scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).
本研究首次构建了涵盖所有 77 个单子叶植物科的质体基因组系统发育树，估算了分支支持率，并推断了单子叶植物的广泛分歧时间和物种多样化速率。
我们基于 545 种单子叶植物和 22 个外类群的 77 个质体基因进行了最大似然分析和 BAMM 多样化速率研究。我们量化了分支支持率和鉴定率如何随基因数量、分支长度和分支深度而变化。
基因组分析改变了 16 个科相对于基于四个质体基因的早期研究的位置，增加了七个科，将单子叶植物和木兰类植物+金鱼藻科的分歧时间确定为 136 百万年前，成功地确定了所有检查的菌根异养类群的位置，并支持将 Taccaceae 和 Thismiaceae 视为独立的科，Arecales 和 Dasypogonales 视为独立的目。只有 45%的科间分歧发生在白垩纪之后。净物种多样化在 PACMAD-BOP 禾本科、天门冬科姐妹科 Doryanthaceae、Orchidoideae-Epidendroideae 和天南星科姐妹科 Lemnoideae 中经历了四次大规模加速，每次都与特定的生态/形态变化相关。单子叶植物科间的分支鉴定率和支持率随基因数量和分支长度的增加而增加，随相对分支深度的增加而降低。对姜目植物全质体基因组的分析量化了非编码区域在识别和支持短而深的分支方面的重要性。
我们提供了第一个得到解决的、得到很好支持的单子叶植物系统发育树和时间线，涵盖了所有的科，并量化了质体基因组数据在解决短而深的分支方面的重要贡献。我们概述了一个单子叶植物及其诊断形态特征从水生祖先进化的新功能模型，这些特征中的许多在水生 Hydatellaceae（睡莲目）中都有趋同进化。
