Patterns of nucleotide substitution in angiosperm cpDNA trnL (UAA)-trnF (GAA) regions

Patterns of substitution in chloroplast encoded trnL-F regions were compare d between species of Actaea (Ranun-culales), Digitalis (Scrophulariales), D rosera (Caryophyllales), Panicoideae (Poales), the small chromosome species clade of Pelargonium (Geraniales), each representing a different order of flowering plants, and Huperzia (Lyco-podiales). In total, the study include d 265 taxa, each with >900-bp sequences, totaling 0.24 Mb. Both pairwise an d phylogeny-based comparisons were used to assess nucleotide substitution p atterns. In all six groups, we found that transition/transversion ratios, a s estimated by maximum likelihood on most-parsimonious trees, ranged betwee n 0.8 and 1.0 for ingroups. These values occurred both at low sequence dive rgences, where substitutional saturation, i.e., multiple substitutions havi ng occurred at the same (homologous) nucleotide position, was not expected, and at higher levels of divergence. This suggests that the angiosperm trnL -F regions evolve in a pattern different from that generally observed for n uclear and animal mtDNA (transition/transversion ratio greater than or equa l to 2). Transition/transversion ratios in the intron and the spacer region differed in all alignments compared, yet base compositions between the reg ions were highly similar in all six groups. A<->T and G<->C transversions w ere significantly less frequent than the other four substitution types. Thi s correlates with results from studies on fidelity mechanisms in DNA replic ation that predict A<->T and G<->C transversions to be least likely to occu r. It therefore strengthens confidence in the link between mutation bias at the polymerase level and the actual fixation of substitutions as recorded on evolutionary trees and, concomitantly, in the neutrality of nucleotide s ubstitutions as phylogenetic markers.