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

Yin Long Qiu, Olena Dombrovska, Jungho Lee, Libo Li, Barbara A. Whitlock, Fabiana Bernasconi-Quadroni, Joshua S. Rest, Charles C. Davis, Thomas Borsch, Khidir W. Hilu, Susanne S. Renner, Douglas E. Soltis, Pamela S. Soltis, Michael J. Zanis, Jamie J. Cannone, Robin R. Gutell, Martyn Powell, Vincent Savolainen, Lars W. Chatrou, Mark W. Chase

Research output: Contribution to journalArticlepeer-review

91 Scopus citations


DNA sequences of nine genes (plastid: atpB, matK, and rbcL; mitochondrial: atp1, matR, mtSSU, and mtLSU; nuclear: 18S and 26S rDNAs) from 100 species of basal angiosperme and gymnosperms were analyzed using parsimony, Bayesian, and maximum likelihood methods. All of these analyses support the following consensus of relationships among basal angiosperme. First, Amborella, Nymphaeaceae, and Austrobaileyales are strongly supported as a basal grade in the angiosperm phylogeny, with either Amborella or Amborella and 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 among Ceratophyllum, 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.

Original languageEnglish
Pages (from-to)815-842
Number of pages28
JournalInternational Journal of Plant Sciences
Issue number5
StatePublished - Sep 2005


  • Amborella
  • Basal angiosperms
  • Magnoliids
  • Multigene analysis
  • Phylogeny
  • Synapomorphic substitutions


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