Phylogeny, Genome Size, and Chromosome Evolution of Asparagales

Abstract

Asparagales are a diverse monophyletic order that has numerous species (ca. 50% of monocots) including important crop plants such as Allium, Asparagus, and Vanilla, and a host of ornamentals such as irises, hyacinths, and orchids. Historically, Asparagales have been of interest partly because of their fascinating chromosomal evolution. We examine the evolutionary dynamics of Asparagales genomes in an updated phylogenetic framework that combines analyses of seven gene regions (atpl, atpB, matK, ndhF, rbcL, trnL intron, and trnL-F intergenic spacer) for 79 taxa of Asparagales and outgroups. Asparagales genomes are evolutionarily labile for many characters, including chromosome number and genome size. The history and causes of variation in chromosome number and genome size remain unclear, primarily because of the lack of data in small clades in the phylogenetic tree and the lack of comparative genetic maps, apart from Allium and Asparagus. Genomic tools such as bacterial artificial chromosome (BAC) libraries should be developed, as both molecular cytogenetic markers and a source of nuclear genes that can be widely used by evolutionary biologists and plant breeders alike to decipher mechanisms of chromosomal evolution.

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

“…A series of studies during the past decade resolved molecular phylogenetic relationships among a broad sample of representatives of Asparagales (e.g. Fay et al, 2000;Bogler et al, 2006;Givnish et al, 2006;Pires et al, 2006). All these studies are very much congruent with each other concerning topology and strong support for several terminal clades recognized as families as well as some internal relationships.…”

“…In contrast, Aloe and relatives are so firmly nested in the clade recognized as Asphodelaceae (e.g. Pires et al, 2006) that it is not feasible to recognize them as a separate family Aloaceae. Our suggestion for the classification of the diversity of succulent Asparagales families is congruent with the topologies published from molecular phylogenetic analyses and published phylogenetic classification systems (for references see above).…”

“…At least in some taxa, water storage in the roots appears to occur in mucilage-filled supra-endodermal spaces (Figueroa et al, 2008). Estimates of the number of succulent species of Orchids are difficult to determine, in line with the general disagreement about the total number of species for the family (18,000-35,000, Pires et al, 2006). The figure of 2,200 succulents (Eggli, 2007) is merely a first guess, and the actual number could easily be twice as high.…”

“…Therefore, we opt for continuing the usage of the more traditional splitters' classification of Asparagales. In the case of the very distinct genus Eriospermum, which all studies place as sister-group to the remaining taxa of the well supported clade recognized as Ruscaceae Rudall et al, 2000;Bogler et al, 2006;Pires et al, 2006), we opt to exclude them from Ruscaceae and to recognize Eriospermaceae as a distinct monotypic family. This renders Ruscaceae much more homogeneous (for further discussion of characters see below), and in this recircumscribed classification Ruscaceae now include the traditionally recognized families Dracaenaceae and Nolinaceae (e.g.…”

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

“…Their analyses showed that a subset of hypotheses are recovered rarely when used as model trees, while others may be recovered frequently when they are not used to simulate data (i.e., high potential for type I and II errors). We therefore performed two basic sets of analyses with Aphyllanthes L. included or excluded from consideration (for more on this problematic taxon, see Fay et al [2000]; Chase et al 2006;Pires et al 2006); Ceratophyllum and Chloranthaceae were included in both cases.…”