Figure 1

Phylogenetic relationships of the five Drosophila species studied in this paper and the outgroup species, the mosquito Anopheles gambiae. The topology of this tree is based on the accepted relationship of these six species; the divergence times from D. melanogaster are approximately 6-15, 46, 53, 61-65, and 250 million years for D. erecta, D. pseudoobscura, D. willistoni, D. littoralis and A. gambiae, respectively [7,84]. D. melanogaster, D. erecta, D. pseudoobscura and D. willistoni belong to the subgenus Sophophora and D. littoralis belongs to the subgenus Drosophila. Rearrangements are indicated by double-headed arrows below each branch and gene transpositions are indicated by triangles above each branch. Rearrangements are inferred to occur on the lineages leading to (a) the ancestor of the D. melanogaster/D. erecta eve region, (b) the D. pseudoobscura Rh1 region, the D. willistoni (c) eve, (d) Rh1, and (e) Rh3 regions, and (f) the D. littoralis ftz region. Gene transpositions are inferred to occur for the (1) CG13029 and (2) CG12133 genes in the ancestor of the D. melanogaster/D. erecta lineage, (3) the CG5245-like gene in the D. pseudoobscura lineage, (4) the CG8319-like gene in the D. willistoni lineage, (5) the CG2222-like gene in the D. willistoni lineage, and (6) the Rh4 gene in the D. littoralis lineage. We note that the event classified as a rearrangement involving the D. pseudoobscura CG31155 gene at the end of the Rh1 clone may be a gene transposition as this gene is a partial gene spanning the edge of the clone. In addition, we note that rearrangement involving the D. littoralis ftz gene may have occurred on the branch leading to the ancestor of the Sophophoran species since, although the orientation of ftz with respect to Antp is ambiguous in A. gambiae ([85,86] and data not shown), it shares a similar configuration to D. littoralis in the outgroup, Tribolium castaneum [87].