Hierarchical analysis of variation in the mitochondrial 16S rRNA gene among Hymenoptera

Nucleotide sequences from a 434-bp region of the 16S rRNA gene wereanalyzed for 65 taxa of Hymenoptera (ants, bees, wasps, parasitoid wasps,sawflies) to examine the patterns of variation within the gene fragment andthe taxonomic levels for which it shows maximum utility in phylogenyestimation. A hierarchical approach was adopted in the study throughcomparison of levels of sequence variation among taxa at differenttaxonomic levels. As previously reported for many holometabolous insects,the 16S data reported here for Hymenoptera are highly AT-rich and exhibitstrong site-to-site variation in substitution rate. More precise estimatesof the shape parameter (alpha) of the gamma distribution and the proportionof invariant sites were obtained in this study by employing a referencephylogeny and utilizing maximum-likelihood estimation. The effectiveness ofthis approach to recovering expected phylogenies of selected hymenopterantaxa has been tested against the use of maximum parsimony. This study findsthat the 16S gene is most informative for phylogenetic analysis at twodifferent levels: among closely related species or populations, and amongtribes, subfamilies, and families. Maximization of the phylogenetic signalextracted from the 16S gene at higher taxonomic levels may requireconsideration of the base composition bias and the site-to-site ratevariation in a maximum-likelihood framework.