KELCHNER, SCOT A. Australian National Herbarium, CSIRO Plant Industry, G.P.O. Box 1600, Canberra, ACT 2601, AUSTRALIA. - Alignment and analysis of noncoding cpDNA sequences: implications of molecular evolution for phylogeny estimation.
Noncoding chloroplast DNA sequence comparison has become a popular
tool for systematics studies at low taxonomic levels. But earlier
expectations of random, unconstrained, and independent nucleotide
evolution in such regions have not been validated by research results.
Mutation in noncoding cpDNA may be largely dependent on sequence
structure and pattern, resulting in nonindependent and predictable
sequence evolution. Mechanisms of molecular evolution described in
these regions include slipped-strand mispairing, stem-loop secondary
structures, minute and moderate-sized inversions associated with
secondary structures, intramolecular and extra-regional recombination,
and nucleotide substitutions. Detection of mutational mechanisms
contributing to inferred mutations can enhance the alignment of
insertions and deletions and the assessment of nucleotide and indel
homology. The manner of noncoding cpDNA evolution described here has
several important repercussions for phylogenetic analysis, effecting
all levels of methodology by invalidating underlying assumptions.
Unique evolutionary characteristics of noncoding cpDNA may eventually
prove no more difficult to assimilate than related phenomena occuring
in genic DNA; perhaps a reasonable course for now is to identify
probable mutational processes evident in a data set, and carefully
modify existing phylogenetic analysis procedures to more accurately
reflect the underlying mutational model.
Key words: alignment, methodology, models of sequence evolution, molecular evolution, noncoding evolution, phylogeny estimation