Phylogeny of Basal Angiosperms: Analyses of Five Genes from Three Genomes

Abstract

DNA sequences of five mitochondrial, plastid, and nuclear genes from 105 species (103 genera and 63 families) representing all major lineages of gymnosperms and basal angiosperms were analyzed using parsimony methods to reconstruct the phylogeny of basal angiosperms. The standard most parsimonious trees search, taxon deletion analyses, and constraint analyses in combination with Kishino‐Hasegawa tests provided a rigorous analytical perspective for identifying Amborella, Nymphaeales, and Illiciales‐Trimeniaceae‐Austrobaileya (ANITA) as the basalmost lineages of extant angiosperms. The parsimony criterion (equal weighting) favored the trees in which Amborella was sister to all other angiosperms, whereas the likelihood measure favored the trees in which the Amborella‐Nymphaeales clade represented the first diverging lineage of angiosperms. However, the Kishino‐Hasegawa test showed that these trees, as well as those in which Nymphaeales were sister to all other angiosperms, were not significantly different from each other. The clade of eumagnoliids, consisting of Winterales, Piperales, Magnoliales, and Laurales, was also consistently recovered in all of the analyses, albeit with low bootstrap support. Two genera of Gnetales, Gnetum and Welwitschia, did not form a sister group to angiosperms but fell into conifers with strong support. This result refutes the anthophyte hypothesis.