Studies of Angiosperm Phylogeny using Protein Sequences

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

“…Abbreviations: GYM ¼ gymnosperms; AMB ¼ Amborella; NYM ¼ Nymphaeaceae; AUS ¼ Austrobaileyales; CHL ¼ Chloranthaceae; CER ¼ Ceratophyllum; MON ¼ monocots; EUD ¼ eudicots; CAN ¼ Canellales; PIP ¼ Piperales; MAG ¼ Magnoliales; LAU ¼ Laurales; Acorus cal ¼ Acorus calamus; Acorus gra ¼ Acorus gramineus; Ceratophyllum dem ¼ Ceratophyllum demersum; Ceratophyllum sub ¼ Ceratophyllum submersum. Several early studies hinted at the possibility that one or more of the three lineages now placed at the base of the angiosperm phylogenetic tree, Amborella, Nymphaeaceae, and Austrobaileyales, could represent the earliest-diverging lineages of extant angiosperms (Donoghue and Doyle 1989;Martin and Dowd 1991;Hamby and Zimmer 1992;Qiu et al 1993;Soltis et al 1997). However, lack of strong internal support and poor resolution in parts of the topologies prevented general acceptance of those results.…”

“…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.…”

Duplicate Genes and the Root of Angiosperms, with an Example Using Phytochrome Sequences

“…Studies based on rbcL sequences Rice et al, 1997), on rbcS amino acid sequences (Martin and Dowd, 1991), and on ribosomal sequences (Hamby and Zimmer, 1992;Doyle et al, 1994;Chaw et al, 1997;Soltis et al, 1997) have produced quite varied results (also see Goremykin et al, 1996, on cpITS sequences; Martin et al, 1993, on the nuclear gene gapC). In each of these cases support for the position of the root has been rather weak (with bootstrap values generally well under 50% for major clades near the base of the tree), and many alternatives can be found among trees that are almost as parsimonious.…”

Progress and Prospects in Reconstructing Plant Phylogeny

“…For example, there is little evidence that the root of angiosperms is among monocots, and I find it interesting that molecular data in particular do not support rooting the tree in the vicinity of Chloranthaceae. Furthermore, it is worth noting that conflicts appear to be as significant among different molecular trees (contrast Martin & Dowd, 1991;Hamby & Zimmer, 1992;Chase et al, 1993), and among different morphological results (contrast Dahlgren & Bremer, 1985;Donoghue & Doyle, 1989;Loconte & Stevenson, 1991;Taylor & Hickey, 1992;Nixon et al, 1994), as they are between molecular and morphological results.…”