A physical map constructed for a large part of the Drosophila repleta genome has allowed the most comprehensive study of Drosophila genome evolution to date. The conclusion is that the Drosophila genome evolves faster than any other eukaryotic genome — around two orders of magnitude faster than the mammalian genome.

The study focused on chromosome 2 in D. repleta and the equivalent region in Drosophila melanogaster — the right arm of chromosome 3, which represents about 23% of the euchromatic portion of the D. melanogaster genome. Around 160 markers, known to map to D. melanogaster chromosome 3R, were used for in situ hybridization against D. repleta polytene chromosomes to construct a physical map of chromosome 2. The conservation of synteny between the two species was 100% — all of the markers mapped to chromosome 2 — but strikingly, marker order has been considerably shuffled.

The simplest explanation for the lack of marker order conservation is that many small paracentric inversions have occurred in the Drosophila genome since the divergence of D. melanogaster and D. repleta. Ranz et al. estimate that there have been ∼114 such inversions, and, given the divergence time between the species of 80–124 million years, they estimate that around one inversion has been fixed per million years. This greatly exceeds equivalent estimates in vertebrates, and implies that the Drosophila genome is relatively unconstrained in its ability to shuffle genes.

Ranz et al. speculate that the Drosophila genome has a modular organization, whereby each module is relatively independent and comprises a gene and its immediate flanking region. Recent comparisons of yeast and Candida albicans , and also Hemiascomycete fungi, have led to similar conclusions for these genomes. As well as providing valuable insight into the genome evolution of lower eukaryotes, these results imply that the Drosophila genome will have limited value for comparative mapping in insects of more economic importance.