Microstructural changes in noncoding chloroplast DNA: Interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference

Microstructural changes in several very slowly evolving chloroplast introns and intergenic spacers were characterized across a broad range of angiospe rms, including most of the major basal lineages. Insertion/deletion events (indels) in the surveyed noncoding regions of the large inverted repeat (IR ) region were shown to be rarer than nucleotide substitutions and thus cons titute one of the slowest and least homoplastic types of data available to plant systematists. In our study we scored 180 indels in noncoding regions, of which 36 were parsimony informative within the angiosperms. Because the y are relatively few in number, their general utility is currently limited. However, they provide support for specific major taxa, including the angio sperms as a whole, the water lilies, and Illiciaceae and relatives. Support for the basalmost angiosperm split is largely inconclusive, but a single i ndel supported a basal placement of the water lilies, not Amborella. We est imate that roughly double or triple the current amount (ca. 2.2 kb) of nonc oding IR DNA would be required to obtain indel support for most of the deep est branches at the base of the angiosperms. A variety of molecular process es appear to be responsible for the observed indels. Indels are more freque ntly associated with tandem repeat sequences than not. Insertions are signi ficantly more frequently associated with tandem repeats than are deletions. The latter finding may be, in part, a function of an ascertainment bias fo r insertions versus deletions. Single-base indels were the most common size class, but there was an unexplained deficit of some other small indel size classes. Coding indels can be problematical, particularly when they overla p among taxa in an alignment. We favor one simple scheme for coding overlap ping indels but argue that no existing scheme for coding overlapping indels for phylogenetic analysis, or dealing with them in alignment, is ideal. Se veral small inversions were observed. These included the most homoplastic m icrostructural character in the current study. Each inversion was associate d with short flanking inverted repeats.