This arlic'le reviews several |)r<)p<)st'(] mechanisms of molecular evolution operating in non-coding regions of ihe cliloroplast genome and argues that awareness and identification of tliese mechariisms are essential for improving alignment and phylogcnctic analysis of non-coding sequence data. The mechanisms are of five categories: (1) slippedstrand inispairing; (2) insertions and deletions link

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Minute inversions (4 bp in length), associated with probable hairpin secondary structures, were inferred from comparative analysis of rpl16 intron sequences from the chloroplast genomes of Chusquea species and related bamboos (Poaceae). The inverted sequences, which appear to have arisen independently on several occasions, comprise entire loops of the putative hairpins. The process of inversion seems dependent upon the stem length of the hairpin and its estimated free energy of formation. A similar inversion was uncovered for other plants in a previously published data set for a different non-coding region of the chloroplast genome, suggesting that the inversional process may be a common feature of non-coding DNA evolution. Several implications for phylogenetic analysis are noted.

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