A Phylogenetic Analysis of Monocotyledons Based on the Chloroplast Gene rps4, Using Parsimony and a New Numerical Phenetics Method

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.

Section: Causes Of Ambiguitymentioning

confidence: 99%

Placing the Monocots: Conflicting Signal from Trigenomic Analyses

Duvall¹,

Matthews²,

Mohammad³

et al. 2006

“…Previous molecular studies have been inconclusive as to its phylogenetic position, either because of undersampling of Bambusoideae (e.g., Nadot et al 1995) or insufficient phylogenetic information (Clark et al 1995;GPWG 2001). More recent studies with broader sampling and additional morphological characters provide robust support for a North Temperate woody bamboo clade including Arundinaria, but the relationship of this clade to other lineages within the bamboos remains unresolved Ní Chonghaile 2002;Clark et al 2006).…”

Section: Arundinaria and Bambuseaementioning

confidence: 99%

Phylogeny of the Grasses (Poaceae) Revisited

Duvall¹,

Davis²,

Clark³

et al. 2007

The most robust previously published phylogeny for the overall structure of the grass family (Poaceae) shows three early diverging lineages and two major derived clades, the BEP clade and the PACCAD clade (Grass Phylogeny Working Group 2001). A few key taxa were incompletely sampled, however, and support for the BEP clade was moderate at best and relationships among the major lineages within the PACCAD clade remained unresolved. In addition, recent studies indicated that the sister group to Poaceae may be Joinvilleaceae and/or Ecdeiocoleaceae, the latter of which were not previously sampled. In this study, missing structural data were determined and analyzed as well as sequence data for ndhF and rbcL, the two most complete plastid sequence data sets. Sampling was increased with a particular focus on key taxa such as Danthoniopsis, Eriachne, Micraira, and Streptogyna and a representative of the outgroup, Ecdeiocoleaceae. A total of 61 ingroup and two outgroup taxa were analyzed using maximum parsimony for total data, and maximum parsimony, Bayesian inference, and neighbor joining for the molecular data. A strongly supported clade of ((Eriachneae, Isachne) Micraira) was recovered as a sister subfamily to Arundinoideae and excluded from Panicoideae. Arundinaria was strongly united with Bambusoideae. The position of Streptogyna was weakly supported among Ehrhartoideae, and is still unresolved. An outgroup effect on ingroup topology was observed demonstrating that highly divergent outgroups may unpredictably alter ingroup relationships.

“…Phylogenetic analyses based on morphology (Dahlgren and Rasmussen 1983;Dahlgren et al 1985; Donoghue and Doyle 1989;Loconte and Stevenson 1991;Doyle and Donoghue 1992;Stevenson and Loconte 1995), those based on molecular characters (Chase et al 1993Duvall et al 1993a, b;Qiu et al 1993Qiu et al , 2000Bharathan and Zimmer 1995;Nadot et al 1995;Nickrent and Soltis 1995;Davis et al 1996Davis et al , 1998Rice et al 1997;Soltis et al 1997Soltis et al , 1998Soltis et al , 1999Angiosperm Phylogeny Group (APG) 1998;Duvall 2000;Graham et al 2000Graham et al , 2006Savolainen et al 2000;APG II 2003;Borsch et al 2003;Duvall and Ervin 2004;Tamura et al 2004) and combined morphological and molecular analyses (Doyle et al 1994;Chase et al 1995;Doyle and Endress 2000;Stevenson et al 2000) all indicate that the monocots are nested deeply within the angiosperms. The placement of monocots within angiosperm phylogeny as a whole varies with the taxa and genes that are included in an analysis.…”

Section: Introductionmentioning

confidence: 99%

The Fossil Record of Basal Monocots

Stockey¹

2006

The fossil record of basal monocots (Acorales and Alismatales) extends back to the Cretaceous in the Northern Hemisphere. While many fossils were originally assigned to these basal groups, rigorous paleobotanical studies show many of them to be misidentified. Acarus fossils have been reliably reported from the Eocene while those of Alismatales extend back to the early Cretaceous. The fossil record of basal monocots is usually represented by leaves, fruits, and seeds; however, some localities preserve stems with attached leaves and roots and even whole plants. A detailed examination of leaf venation patterns in alismatids has recently allowed the description of a new taxon from the Upper Cretaceous of Alberta based on leaves attributed to Limnocharitaceae. Anatomically preserved alismatid petioles (Heleophyton helobiaeoides) and well-preserved flowers/fruits are known from the Middle Eocene Princeton chert of British Columbia. A complete developmental sequence from flower to fruit is known, and this material has good possibilities for whole plant reconstruction. The extinct floating aquatic Limnobiophyllum (Araceae!Lemnoideae) and the genus Pistia have been the subject of morphological cladistic analyses and competing hypotheses of relationships among aroids and duckweeds. The fossil record and recent molecular studies support separate origins of Pistia and the duckweeds from within Araceae. The fossil taxon "Pistia" corrugata has been reexamined in light of new evidence and indicates the presence of a new genus that shows leaf morphology unlike that seen in extant Pistia, but with a similar growth habit. Fossil evidence indicates that the floating aquatic habit probably arose at least three times within Araceae.