Group II introns constitute the majority of noncoding sequence in many plant chloroplast genomes and include the commonly sequenced regions trnK/matK, the rps16 intron, and the rpl16 intron. As demand increases for nucleotide characters at lower taxonomic levels, chloroplast introns may come to provide the bulk of plastome sequence data for assessment of evolutionary relationships in intrageneric, intergeneric, and interfamilial studies. Group II introns have many attractive properties for the molecular systematist: they are usually confined to organellar genomes in eukaryotes and the majority are single-copy; they all share a well-defined and empirically tested secondary and tertiary structure; and, they are easily amplified due to highly conserved sequence in flanking exons. Functional importance of structural conformations may be the key to understanding intron sequence evolution and enhancing their phylogenetic utility. A disparity of mutation rates among structural features of a group II intron can be exploited to recover phylogenetic signal at multiple taxonomic levels within a single intron, even between subclasses of flowering plants. Structure-linked mutational phenomena have important implications for the treatment of intron sequence data when aligning nucleotides, assessing mutational biases in the data, and selecting appropriate models of character evolution for phylogenetic analysis. A description of group II intron function and structure will be followed by a discussion of simple strategies to accomodate observed mutational biases and enhance the accuracy of phylogenies derived from intron sequence data.

Key words: group II introns, phylogenetic methods, phylogenetic tools, RNA secondary structure, rpl16 intron, trnK/matK