Placing the Monocots: Conflicting Signal from Trigenomic Analyses

Abstract

Despite recent significant advances in understanding angiosperm phylogeny, the position of monocots remains uncertain. We present here a phylogeny inferred from four genes that unambiguously unite monocots with eumagnoliids. A well-supported position for the monocots was obtained only after we replaced the available nuclear 18S rDNA sequence data with data from phytochrome C in a matrix that also included plastid rbcL and ndhF and mitochondrial atp 1. Over 5000 base pairs of sequence data from 42 taxa were analyzed using Bayesian inference. The results of these analyses united monocots with the eumagnoliids in a well-supported clade. Although the substitution of phytochrome C for 18S data led to a highly supported position for the monocots, comparison with more densely sampled single-gene studies revealed conflict among data sets. This indicates that larger data sets from each genome should be explored explicitly to evaluate the position of the monocots, and that each of these larger data sets also should be investigated for insight into potential sources of conflict.

Integrating Early Cretaceous Fossils into the Phylogeny of Living Angiosperms: ANITA Lines and Relatives of Chloranthaceae

“…As already noted, in the combined morphological and molecular analysis of Doyle and Endress (2000) Chloranthaceae were sister to all other mesangiosperms, partly because they retain ascidiate carpels like those in the ANITA lines, and morphological data of Endress and Doyle (2009) grouped Ceratophyllum with them. The Chloranthaceae-Ceratophyllum clade has also been found in some molecular studies (Antonov et al 2000;Duvall et al 2006Duvall et al , 2008Qiu et al 2010;Moore et al 2011;Zhang et al 2012), although most indicate different relationships, such as analyses of whole chloroplast genomes (Jansen et al 2007;Moore et al 2007), in which Chloranthaceae are sister to the magnoliid clade and Ceratophyllum is sister to eudicots.…”

“…In this tree, Chloranthaceae and Ceratophyllum form a clade that is sister to all other mesangiosperms, while monocots are linked with magnoliids. The Chloranthaceae-Ceratophyllum clade is most strongly supported by morphology (Endress and Doyle 2009), but it has also been found in analyses of chloroplast ITS sequences (Antonov et al 2000); mitochondrial genes (Duvall et al 2006(Duvall et al , 2008Qiu et al 2010); chloroplast genes from the inverted repeat region (Moore et al 2011), which show a combination of a high proportion of informative sites and low rates of substitution that suggests they may be more reliable than average; and low-copy nuclear genes (Zhang et al 2012). In the "J/M" tree, based on analyses of nearly complete chloroplast genomes (Jansen et al 2007;Moore et al 2007), Chloranthaceae are linked with magnoliids and Ceratophyllum with eudicots, which together are sister to monocots.…”

Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms

“…Early molecular phylogenetic analyses confirmed that monocots were derived from a paraphyletic grade of ''dicots'' but did not resolve their position with high support. Molecular analyses have variously placed monocots as sister to all remaining angiosperms after the AmborellaNymphaeales-Austrobaileyales grade (11,15,17), as part of a clade with magnoliids and Chloranthaceae (7,15), or as sister to the magnoliids (15,24).…”

“…The phylogenetic position of monocots has also been problematic. In molecular phylogenetic studies, monocots have been recovered as sister to magnoliids, Ceratophyllum, or as part of a clade with magnoliids and Chloranthaceae, generally with low support (7,12,15,17,(19)(20)(21)(22)(23)(24). The unstable relationships exhibited among these five major lineages of angiosperms are likely due to a combination of the relatively ancient age of these taxa [at least four of which have fossil records that extend back Ͼ100 Mya to the Early Cretaceous (25)(26)(27)(28)(29)], the short evolutionary branches separating these lineages, and the relatively long branches leading to Ceratophyllum and to the basal lineages of monocots (2).…”

Ancestral traits and specializations in the flowers of the basal grade of living angiosperms

“…However, in the combined morphological and molecular analysis of Doyle & Endress (2000), which did not include Ceratophyllum, Chloranthaceae were the sister group of all other mesangiosperms, and when Endress & Doyle (2009) added Ceratophyllum to the tree it formed a clade with Chloranthaceae. This clade has also been found in a growing number of molecular analyses (Antonov & al., 2000;Duvall & al., 2006Duvall & al., , 2008Qiu & al., 2006Qiu & al., , 2010Moore & al., 2011;Zhang & al., 2012;Zeng & al., 2014;Sun & al., 2015), although its position varies greatly. At present, the relationships of these two groups are still unsettled.…”