Robust Inference of Monocot Deep Phylogeny Using an Expanded Multigene Plastid Data Set

Abstract

We use multiple photosynthetic, chlororespiratory, and plastid translation apparatus loci and their associated noncoding regions (ca. 16 kb per taxon, prior to alignment) to make strongly supported inferences of the deep internal branches of monocot phylogeny. Most monocot relationships are robust (an average of ca. 91 % bootstrap support per branch examined), including those poorly supported or unresolved in other studies. Our data strongly support a sister-group relationship between Asparagales and the commelinid monocots, the inclusion of the orchids in Asparagales, and the status of Petrosaviaceae as the sister group of all monocots except Acarus and Alismatales. The latter finding supports recognition of the order Petrosaviales. Also strongly supported is a placement of Petermannia disjunct from Colchicaceae (Liliales) and a sister-group relationship between Commelinales and Zingiberales. We highlight the remaining weak areas of monocot phylogeny, including the positions of Dioscoreales, Liliales, and Pandanales. Despite substantial variation in the overall rate of molecular evolution among lineages, inferred amounts of change among codon-position data partitions are correlated with each other across the monocot tree, consistent with low incongruence between these partitions. Ceratophyllum and Chloranthaceae appear to have a destabilizing effect on the position of the monocots among other angiosperms; the issue of monocot placement in broader angiosperm phylogeny remains problematic.

Ecdeiocoleaceae and Joinvilleaceae, sisters of Poaceae (Poales): evidence from rbcL and matK data

“…By contrast, the insufficiently resolved rbcL tree placed Flagellaria, Anarthriaceae and (JEP families + Restionaceae including Centrolepidaceae) at a trichotomy, a position for Flagellaria more in agreement with the results from combined data of morphology, atpA and rbcL (Michelangeli et al 2003). Graham et al (2006) and found Flagellaria to be sister to a clade including both Poaceae and Restionaceae. Data from rbcL, matK and trnL-F relevant to relationships within the restiid clade will be presented elsewhere.…”

“…strict. by Briggs et al (2000), Bremer (2002), Michelangeli et al (2003), Chase et al (2006) and Graham et al (2006). In particular, strongly supported clades here are (Poaceae, Ecdeiocoleaceae, Joinvilleaceae) and (Restionaceae, Centrolepidaceae).…”

“…Such long branch lengths in other Poales were noted by Bremer (2000) and are evident in the multi-gene analyses of Graham et al (2006), Chase et al (2006) and Givnish et al (2006). Branch lengths in Ecdeiocoleaceae are similarly long, unlike those of Joinvilleaceae (Fig.…”

Phylogeny, Genome Size, and Chromosome Evolution of Asparagales

“…2). McPherson et al (submitted) found strong bootstrap support for a sister relationship of lxioliriaceae and Tecophilaeaceae with molecular data; however, they did not sample Doryanthaceae (but see Graham et al 2006). Analyses of morphological data and base chromosome number support the sister relationship of Ixioliriaceae and Tecophilaeaceae (Stevenson and Loconte 1995) and place Doryanthes as sister to lridaceae (Rudall 2002b).…”

An up-to-date familial and suprafamilial classification of succulent plants

“…However, there is no doubt that Agavaceae belong to the "higher core Asparagales", together with Hyacinthaceae, Asparagaceae and Ruscaceae (see below, (6)) as well as further families without succulents. In a radical approach, all these families are treated as a much enlarged family Asparagaceae (APG 2003(APG , 2009Graham et al, 2006), circumscribed by racemose inflorescences (in comparison with the umbellate inflorescences of the "lower core Asparagales", but with numerous exceptions) (see below, (3)). …”