Substitution bias and evolutionary rate of mitochondrial protein-encoding genes in four species of Cecidomyiidae

Five mitochondrial protein-encoding genes (COX1, COX2, CytB, ND4 and ND5) from the wheat midge, Sitodiplosis mosellana (Diptera: Cecidomyiidae), were sequenced and compared with those of 3 other Cecidoidae species, Mayetiola destructor, Rhopalomyia pomum and Asphondylia rosetta. These genes shared similar AT content (74.0-80.1%) and base substitution bias in favour of transversions (68.87-79.72%) over transitions (20.28-37.04%). Substitution saturation analyses indicated fast saturation of transitional substitutions in COX2, CytB, ND4 and ND5, especially at the 3rd codon positions. Analysis of interspecific divergence among the 4 species showed that the sequence divergence rates (evolutionary rates) were in the order of ND4 = CytB > COX2 = ND5 > COX1. Intraspecific genetic polymorphism analysis within the field populations of S. mosellana indicated that ND4 had the highest genetic polymorphism and COX1 the lowest. Genetic variation patterns suggested that COX1 could be used as a molecular marker for phylogenetic analysis across a relatively wide taxonomic range in Cecidomyiidae, while COX2 and ND5 may be useful for estimating relationships at a subgenus level or among closely related species. With its high genetic polymorphism, ND4 was the molecular market most suitable for population genetics studies. These findings will be valuable for our further understanding and studies in evolutionary biology and population genetics for S. mosellana and other Cecidomyiidae insects.