A chloroplast DNA hairpin structure provides useful phylogenetic data within tribe Senecioneae (Asteraceae)

The distribution of an inversion associated with a small hairpin structure in the psbA-trnH intergenic spacer region of chloroplast DNA was surveyed to determine its phylogenetic utility within the tribe Senecioneae of the Asteraceae. Over 2000 sequences were examined from a wide range of angiosperms. Although the inversion is homoplasious in a number of taxonomic groups, including the Senecioneae, it still provides useful phylogenetic information, especially when point substitutions in both the stem and loop regions are scored along with the inversion. The presence of two nested inversions within the hairpin structure allows it to be treated as a partially ordered multistate character, adding to its potential utility as a phylogenetic marker.