Molecular phylogeny of Calyptratae (Diptera : Brachycera): the evolution of 18S and 16S ribosomal rDNAs in higher dipterans and their use in phylogenetic inference

Sequences for nearly complete 18S rRNA and partial 16S rRNA genes were dete rmined for sixteen species representing twelve calyptrate families. Two uni que insertions are present in expansion regions of the 18S rDNA in nycterib iids. Alignments containing other dipteran rRNA genes provided good resolut ion at higher taxonomic level: monophyly of Calyptratae is well supported. While both 16S and 18S rDNA matrices produce unstable topologies within Cal yptratae when analysed separately, their combination results in a tree with several robust and well supported nodes. Of three superfamilies recognized in recent classifications, the Hippoboscoidea is well supported by 16S rDN A and by combined matrices. The representatives of Muscoidea, Musca sp. and Antipoda sp., display a tendency to cluster within Oestroidea. The compari son of secondary structures of two variable regions indicates that Sarcopha gidae are related to Calliphoridae rather than to Tachinidae.