Molecular evolution of histone genes within the {\it Sophophoran\/} radiation of {\it Drosophila\/}

This work tests a 250 bp intergenic spacer between the H2A and H2B histone genes in twelve species of Drosophila from the subgenus radiation Sophophora for its phylogenetic resolving power. Like rDNA, histone are repeated in invertebrates and undergo concerted evolution. Histones offer a novel advantage relative to rDNA in that they are translated as well as transcribed. Universal primers anchored in coding regions were used to amplify and sequence the spacer between H2A and H2B. This spacer contains promoters for which we have functional information for both of these divergently transcribed genes. This information aids in alignment of the sequences, which identifies a likely but previously unrecognized regulatory region (subsequently confirmed by other research). Potential for single-stranded DNA stem loops in the spacer which may participate in transcriptional regulation is examined. Parsimony, distance, and maximum likelihood methods, under a variety of assumptions, successfully retrieve the corroborated phylogeny. While the addition of a similar number of bases of flanking coding regions improves support for the corroborated phylogeny, the carefully aligned spacer alone is sufficient under certain assumptions. Given the expense of DNA sequencing, and the amount of information it contains, the 250 bp H2A-H2B intergenic spacer is a good candidate for phylogenetic inference of invertebrate radiations less than fifty million years diverged.