— In 1991 de Pinna (Cladistics 7: 367–394) coined the term primary homology as the putative homology statements prior to tree reconstruction. However, some confusion still exists regarding the conjectural nature of homology and to the analysis of DNA sequences. By dividing de Pinna's term primary homology into topographical identity and character state identity, we emphasize the sequential refinement of putative homology statements. We discuss the problem of transformational versus taxic homology and explain the application of our terms to DNA sequence data.

SummaryCuticular structures of insects are often microscopic and intricately complex; among the most complex structures are male genitalia. Genitalic structures are essential in taxonomic and phylogenetic studies of insects. Using well-described species from two disparate dipteran genera, we demonstrate the utility of confocal laser scanning microscopy for studying the morphological characters of fly genitalia by taking advantage of the autofluorescent properties of cuticle material. Reconstructions of confocal data sets obtained from genitalic structures embedded in two commonly used entomological mounting media (euparal and glycerin jelly) are presented. Aberration artefacts often observed in confocal data obtained from thick specimens were analysed and strategies for their minimization are discussed. Our results indicate that confocal laser scanning microscopy and 3D reconstruction are excellent techniques for visualizing small, complex, autofluorescent structures in flies. These techniques could have a profound impact on the quality of information provided by 3D representations of insect structures over more traditional methods of visualization.

Although Drosophila melanogaster is a paradigm eukaryote for biology, relationships of this species and the other 174 species in the melanogaster species group are poorly explored and ambiguous. Gene regions of Cytochrome oxidase II (mt:CoII), Alcohol dehydrogenase (Adh) and hunchback (hb) were sequenced and analysed phylogenetically to test prior hypotheses of relationships for the group based on chromosomes, morphology, and 28S rRNA gene sequences. A simultaneous cladistic analysis of the three newly sequenced gene regions produced a single wellresolved phylogeny for 49 exemplar species representing eight subgroups. Monophyly of each of the ananassae, melanogaster, montium, and takahashii subgroups is supported; the suzukii subgroup is polyphyletic. This phylogeny is consistent with variation in significant morphological structures, such as the male sex comb on the fore tarsus. The broad range of morphological variation among these species is interpreted and the applicability to evolution and developmental investigations is discussed. This phylogeny facilitates comparative investigations, such as gene family evolution, transposable element transmission, and evolution of morphological structures.