Phylogenetic analyses of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes

• Published in: International journal of plant sciences Vol. 166; no. 5; pp. 815 - 842
• Main Authors: Qui, Y.L, Dombrovska, O, Lee, J, Li, L, Whitlock, B.A, Bernasconi-Quadroni, F, Rest, J.S, Davis, C.C, Borsch, T, Hilu, K.W
• Format: Journal Article
• Language: English
• Published: Chicago The University of Chicago Press 01.09.2005; University of Chicago, acting through its Press
• Subjects: 3 genomic compartments; Angiosperms; Bayesian theory; Botany; chloroplast genome; Datasets; Evolutionary biology; flowering plants; Flowers & plants; Genetics; group-ii intron; Gymnosperms; inferring complex phylogenies; land plants; mads-box genes; maximum likelihood analysis; mitochondrial DNA; molecular systematics; molecular-data; Monophyly; Parsimony; parsimony analysis; Phylogenetics; phylogeny; plant genetics; Plant mitochondria; plastid DNA; Plastids; rdna sequences; Ribosomal DNA; ribosomal dna-sequences; Taxa; Topology; magnoliids; basal angiosperms; multigene analysis; phylogeny; synapomorphic substitutions; Amborella
• ISSN: 1058-5893; 1537-5315
• DOI: 10.1086/431800

DNA sequences of nine genes (plastid:atpB,matK, andrbcL; mitochondrial:atp1,matR, mtSSU, and mtLSU; nuclear: 18S and 26S rDNAs) from 100 species of basal angiosperms and gymnosperms were analyzed using parsimony, Bayesian, and maximum likelihood methods. All of these analyses support the following consensus of relationships among basal angiosperms. First,Amborella, Nymphaeaceae, and Austrobaileyales are strongly supported as a basal grade in the angiosperm phylogeny, with eitherAmborellaorAmborellaand Nymphaeales as sister to all other angiosperms. An examination of nucleotide substitution patterns of all nine genes ruled out any possibility of analytical artifacts because of RNA editing and GC‐content bias in placing these taxa at the base of the angiosperm phylogeny. Second, Magnoliales are sister to Laurales and Piperales are sister to Canellales. These four orders together constitute the magnoliid clade. Finally, the relationships amongCeratophyllum, Chloranthaceae, monocots, magnoliids, and eudicots are resolved in different ways in various analyses, mostly with low support. Our study indicates caution in total evidence approaches in that some of the genes employed (e.g., mtSSU, mtLSU, and nuclear 26S rDNA) added signal that conflicted with the other genes in resolving certain parts of the phylogenetic tree.