EVOLUTIONARY ANALYSES OF DNA-SEQUENCES SUBJECT TO CONSTRAINTS ON SECONDARY STRUCTURE

Evolutionary models appropriate for analyzing nucleotide sequences tha t are subject to constraints on secondary structure are developed. The models consider the evolution of pairs of nucleotides, and they incor porate the effects of base-pairing constraints on nucleotide substitut ion rates by introducing a new parameter to extensions of standard mod els of sequence evolution. To illustrate some potential uses of the mo dels, a likelihood-ratio test is constructed for the null hypothesis t hat two (prespecified) regions of DNA evolve independently of each oth er. The sampling properties of the test are explored via simulation. T he test is then incorporated into a heuristic method for identifying t he location of unknown stems. The test and related procedures are appl ied to data from ribonuclease P RNA sequences of bacteria.