An episodic change of rDNA nucleotide substitution rate has occurred during the emergence of the insect order Diptera.

We have studied the potential reasons for a conspicuous deviation of substitution rates in Dipteran ribosomal genes. Systematic pairwise relative-rate tests reveal that a significant increase in substitution rate is characteristic for Diptera, but not for the other insects analyzed. Estimation of sequence change in specific lineages reveals that most of these substitutions took place during the evolution of the Dipteran stem lineage. When related to the paleontologically documented periods of absolute time, the substitution rate in the stem lineage of the Diptera underwent an at least 20-fold increase compared to other insect groups and subsequently dropped by a factor of 10 before the diversification of the major Dipteran subgroups. Systematic comparisons of nucleotide composition show that this episodic change in substitution rate was accompanied by a significant increase in A+T content of Dipteran rDNA. Our data suggest that the episodic evolution of the Dipteran rDNA has most probably been caused by a change of directional mutation pressure which must have occurred during the evolution of the stem lineage of the Diptera.