The evolution of non-coding chloroplast DNA and its application in plant systematics

This article reviews several proposed mechanisms of molecular evolution operating in non-coding regions of the chloroplast genome and argues that awareness and identification of these mechanisms are essential for improving alignment and phylogenetic analysis of non-coding sequence data. The mechanisms are of five categories: (1) slipped-strand mispairing; (2) insertions and deletions linked with secondary structure formations; (3) inversions associated with hairpins and stem-loop structures; (4) localized or extra-regional intramolecular recombination; and (5) nucleotide substitutions. These mutations seem to be largely a function of sequence structure and pattern and may be highly homoplasious in a parsimony topology; therefore, mutations in non-coding regions of the chloroplast genome are described here as structured, nonrandom, and non-independent events. Established methodologies are based in large part on a collective understanding of genic DNA evolution and may need modification when applied to non-coding sequence data. Here I suggest an approach to the phylogenetic study of non-coding cpDNA that incorporates identification of mutational mechanisms in alignment and homology assessment of indels. I also discuss repercussions of non-coding sequence evolution for such aspects of phylogeny estimation as maximum likelihood, distance, and parsimony analysis, the inclusion of indels as phylogenetic characters, and bootstrapping, jackknifing, and "decay" analysis as measures of clade support.