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

Abstract

Although great progress has been made in clarifying deep-level angiosperm relationships, several early nodes in the angiosperm branch of the Tree of Life have proved difficult to resolve. Perhaps the last great question remaining in basal angiosperm phylogeny involves the branching order among the five major clades of mesangiosperms (Ceratophyllum, Chloranthaceae, eudicots, magnoliids, and monocots). Previous analyses have found no consistent support for relationships among these clades. In an effort to resolve these relationships, we performed phylogenetic analyses of 61 plastid genes (Ϸ42,000 bp) for 45 taxa, including members of all major basal angiosperm lineages. We also report the complete plastid genome sequence of Ceratophyllum demersum. Parsimony analyses of combined and partitioned data sets varied in the placement of several taxa, particularly Ceratophyllum, whereas maximum-likelihood (ML) trees were more topologically stable. Total evidence ML analyses recovered a clade of Chloranthaceae ؉ magnoliids as sister to a well supported clade of monocots ؉ (Ceratophyllum ؉ eudicots). ML bootstrap and Bayesian support values for these relationships were generally high, although approximately unbiased topology tests could not reject several alternative topologies. The extremely short branches separating these five lineages imply a rapid diversification estimated to have occurred between 143.8 ؎ 4.8 and 140.3 ؎ 4.8 Mya.

Identification of conserved Aquilegia coerulea microRNAs and their targets

“…We have identified 45 miRNAs belonging to 20 miRNA families and have determined that, in general, both the miRNA families and Liu, B., Li, P., Li, X., Liu, C., Cao, S., Chu, C., Cao, X. (Sanderson, 2003;Chaw et al, 2004;Sanderson et al, 2004;Moore et al, 2007;Qiu et al, 2007;Rensing et al, 2008). Major model systems associated with the various land plant lineages are listed.…”

“…The eudicot and monocot lineages are estimated to have diverged from one another approximately 140 Myr ago, while lineage containing Aquilegia diverged from other eudicots approximately 100 Myr ago ( Fig. 1) (Chaw et al, 2004;Sanderson et al, 2004;Moore et al, 2007). The Aquilegia miRNA dataset therefore helps to break up the large phylogenetic distance that separates major flowering plant lineages, particularly the monocots and dicots.…”

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

“…4) corresponds to the chloroplast genome trees of Jansen & al. (2007) and Moore & al. (2007), where Chloranthaceae are sister to magnoliids and Ceratophyllum is sister to eudicots, while the other ("D&E") (Figs.…”

“…A, most parsimonious course of evolution of carpel form on the D&E tree (see Fig. 3); B, evolution of carpel form on a tree with mesangiosperm relationships based on nearly complete chloroplast genomes (J/M tree; Jansen & al., 2007;Moore & al., 2007). -Abbreviations as in Fig.…”

“…1). For example, in analyses of nearly complete chloroplast genomes (Jansen & al., 2007;Moore & al., 2007), Chloranthaceae were sister to magnoliids…”