Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms

Abstract

Recent contributions from DNA sequences have revolutionized our concept of systematic relationships in angiosperms. However, parts of the angiosperm tree remain unclear. Previous studies have been based on coding or rDNA regions of relatively conserved genes. A phylogeny for basal angiosperms based on noncoding, fast-evolving sequences of the chloroplast genome region trnT-trnF is presented. The recognition of simple direct repeats allowed a robust alignment. Mutational hot spots appear to be confined to certain sectors, as in two stem-loop regions of the trnL intron secondary structure. Our highly resolved and well-supported phylogeny depicts the New Caledonian Amborella as the sister to all other angiosperms, followed by Nymphaeaceae and an Austrobaileya-Illicium-Schisandra clade. Ceratophyllum is substantiated as a close relative of monocots, as is a monophyletic eumagnoliid clade consisting of Piperales plus Winterales sister to Laurales plus Magnoliales. Possible reasons for the striking congruence between the trnT-trnF based phylogeny and phylogenies generated from combined multi-gene, multi-genome data are discussed.

Phylogenetic Analyses of Basal Angiosperms Based on Nine Plastid, Mitochondrial, and Nuclear Genes

“…In consideration of the variety of analyses we have conducted on our multigene data set in this and previous studies (Qiu et al , 2001, it is safe to conclude that the AmborellaNymphaeaceae-Austrobaileyales-basal topology of the angiosperm phylogeny has been rigorously tested. Moreover, the congruent topologies inferred from functionally and structurally different coding genes in this study and others (e.g., phytochromes: Donoghue 1999, 2000; floral MADS-box genes: Kim et al 2004) and noncoding DNAs in the analyses of Borsch et al (2003) and Lö hne and Borsch (2005) should make sufficiently clear that locus-inherent specific patterns of molecular evolution have not led to a spurious conclusion of the rooting of angiosperm phylogeny. …”

“…The impressively resolved overall topology with strong bootstrap support and a high degree of convergence of results from different research groups using different taxon and gene sampling schemes as well as different rooting strategies led to the realization that the earliest-diverging lineages of extant angiosperms had been identified. Subsequent analyses with different methods and new data have further confirmed and reinforced this consensus (Qiu et al 2001;Zanis et al 2002Zanis et al , 2003Borsch et al 2003;Hilu et al 2003;Lö hne and Borsch 2005).…”

“…Recent molecular analyses have converged on a topology of basal angiosperm relationships in which (1) Amborella, Nymphaeaceae, and Austrobaileyales represent the basal lineages of extant angiosperms; (2) two pairs of traditional magnoliid taxa, Magnoliales-Laurales and Canellales-Piperales, are sister to each other and form the magnoliid clade; and (3) Ceratophyllum, Chloranthaceae, monocots, magnoliids, and eudicots form a polytomy after the initial diversification that led to Amborella, Nymphaeaceae, and Austrobaileyales (Mathews and Donoghue 1999;Qiu et al , 2000Graham and Olmstead 2000b;Soltis et al 2000;Zanis et al 2002Zanis et al , 2003Borsch et al 2003;Hilu et al 2003;Lö hne and Borsch 2005). This set of relationships has been used to formalize a classification system for angiosperms (APG II 2003) and to guide investigation of various aspects of early angiosperm evolution (e.g., Endress and Igersheim 2000;Friis et al 2000;Thien et al 2000;Williams and Friedman 2002;Ronse De Craene et al 2003;Feild et al 2004;Kramer et al 2004).…”

“…The past 20 years have witnessed significant progress in our understanding of the phylogeny of basal angiosperms from analyses of molecular and nonmolecular data (Dahlgren and Bremer 1985;Donoghue and Doyle 1989;Loconte and Stevenson 1991;Martin and Dowd 1991;Hamby and Zimmer 1992;Taylor and Hickey 1992;Chase et al 1993;Qiu et al 1993Qiu et al , 2000Qiu et al , 2001Soltis et al 1997Soltis et al , 2000Nandi et al 1998;Hoot et al 1999;Donoghue 1999, 2000;Parkinson et al 1999;Renner 1999;Soltis et al 1999a;Barkman et al 2000;Doyle and Endress 2000;Graham and Olmstead 2000b;Savolainen et al 2000;Nickrent et al 2002;Zanis et al 2002Zanis et al , 2003Borsch et al 2003;Hilu et al 2003;Lö hne and Borsch 2005). Specifically, it has become increasingly clear that Amborella, Nymphaeaceae, and Austrobaileyales (sensu APG II 2003) represent the earliestdiverging lineages of extant angiosperms.…”

Third-codon transversion rate-based Nymphaea basal angiosperm phylogeny -- concordance with developmental evidence

“…Plant evolutionary biologists have long attempted to reconstruct angiosperm evolutionary history in an effort to determine the root of angiosperms. Since 1999, a series of molecular phylogenetic analyses have identified the monotypic Amborella, followed by Nymphaeales, or Amborella plus Nymphaeales, in the ANITA clade (Amborella, Nymphaeales, Illiciaceae, Trimeniaceae and Austrobaileyaceae) as representative of the most basal taxa (Mathews and Donoghue 1999;Parkinson, Adams, and Palmer 1999;Qiu et al 1999;Soltis, Soltis, and Chase 1999;Graham and Olmstead 2000;Qiu et al 2000;Zanis et al 2002;Borsch et al 2003;Zanis et al 2003;Stefanovic, Rice, and Palmer 2004;Leebens-Mack et al 2005;Chang et al 2006;Qiu et al 2006). In some cases, monocotbasal trees have also been reported (Goremykin et al 2003;Goremykin et al 2004;Chang et al 2006;Goremykin and Hellwig 2006).…”