A highly resolved phylogeny of basal angiosperms was inferred from sequences of the trnT-L- and trnL-F-spacers and the trnL-intron. A robust alignment was obtained, although it was complicated by the recognition of a large number of indels, mostly simple direct repeats ranging from 3-10 bp. About 30% of the aligned positions had to be excluded from analysis because of too high variability. Conifers and Ginkgo were used as outgroups. Gnetum shows such a high sequence divergence that no part of the trnT-F-region could be aligned with conifers, Ginkgo, or angiosperms. The ingroup comprises 35 taxa to represent all major lineages of basal angiosperms. In parsimony analysis, Amborella appears as sister to all other angiosperms examined. A Nymphaeales-clade (Nymphaeaceae plus Cabombaceae) and an Austrobaileya-Illicium-Schisandra-clade diverge next. These results are in agreement with recent phylogenies based on multiple coding regions. Bootstrap and decay support for the majority of nodes in the trees of the trnT-trnF-analysis was found to be high, and phylogenies obtained from separate versus combined analyses of the two spacers and the intron were largely congruent. Patterns of molecular evolution in the trnT-F-region are analyzed in order to elucidate these unexpected findings.

Key words: Amborella, basal angiosperms, noncoding chloroplast DNA, phylogeny, trnT-trnF