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Premise of the Study 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. Methods 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. Key Results 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. Conclusions 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).

Premise of the study: The Asparagales, with ca. 40% of all monocotyledons, include a host of commercially important ornamentals in families such as Orchidaceae, Alliaceae, and Iridaceae, and several important crop species in genera such as Allium, Aloe, Asparagus, Crocus, and Vanilla. Though the order is well defined, the number of recognized families, their circumscription, and relationships are somewhat controversial. Methods: Phylogenetic analyses of Asparagales were based on parsimony and maximum likelihood using nucleotide sequence variation in three plastid genes (matK, ndhF, and rbcL) and two mitochondrial genes (atpl and cob). Branch support was assessed using both jackknife analysis implementing strict-consensus (SC) and bootstrap analysis implementing frequencywithin-replicates (FWR). The contribution of edited sites in the mitochondrial genes to topology and branch support was investigated. Key results: The topologies recovered largely agree with previous results, though some clades remain poorly resolved (e.g., Ruscaceae). When the edited sites were included in the analysis, the plastid and mitochondrial genes were highly incongruent. However, when the edited sites were removed, the two partitions became congruent. Conclusions: Some deeper nodes in the Asparagales tree remain poorly resolved or unresolved as do the relationships of certain monogeneric families (e.g., Aphyllanthaceae, Ixioliriaceae, Doryanthaceae), whereas support for many families increases.煎However, the increased support is dominated by plastid data, and the potential influence of mitochondrial and biparentially inherited single or low-copy nuclear genes should be investigated.

A morphological cladistic analysis is presented of the lilioid order Asparagales, with emphasis on relationships within the “lower” asparagoids, in the context of recent new data on both floral and vegetative structures. The analysis retrieved a monophyletic “lower” asparagoid clade, in contrast to molecular analyses, in which lower asparagoids invariably form a grade. However, limited outgroup sampling in the current analysis is a significant factor in this “inside-out” topology; if the morphological tree is rerooted with Orchidaceae as the outgroup, the result is a topology broadly similar to the molecular one. The relatively low resolution of the “lower” asparagoid clade identified here is a result of high homoplasy in several characters, which could be regarded as iterative evolutionary themes within Asparagales, notably (among floral characters) epigyny and zygomorphy. Close relationships between some family pairs were inferred, including Orchidaceae and Hypoxidaceae, Boryaceae and Blandfordiaceae, Asphodelaceae and Hemerocallidaceae, and Iridaceae and Doryanthaceae. The small South African genus Pauridia, which differs from other Hypoxidaceae in that it lacks the outer stamen whorl, was placed as sister to Orchidaceae rather than being embedded in Hypoxidaceae as in molecular analyses, because despite some significant similarities with other Hypoxidaceae (e.g., mucilage canals), it shares some characters with Orchidaceae, notably the presence of a gynostemium and pontoperculate pollen. Xanthorrhoea and Lanaria were wild-card taxa in the context of this analysis, with characters in common with more than one different group.