pone.0027376.g002.png

Maximum likelihood phylogenetic trees of the ftz RCPE (a), ZE (b) and CDS (c), constructed using PHYLIP.

h1, h2…: haplotype 1, haplotype 2…, me: D. melanogaster, si: D. simulans, se: D. sechellia, ma: D. mauritiana, ya: D. yakuba, te: D. teissieri, or: D. orena, er: D. erecta, ps: D. pseudoobscura.*: The D. pseudoobscura sequences that served as outgroup and the ftz CDS sequences are from the database (accession numbers NM_058150.2 for D. melanogaster CDS, XM_002102380.1 for D. simulans CDS, EU670514.1 for D. sechellia CDS, EU310327.1 for D. mauritiana CDS, XM_002096692.1 for D. yakuba CDS, XM_001979089.1 for D. erecta CDS, XM_001359177.2 for D. pseudoobscura CDS, and AY190944 for D. pseudoobscura RCPE and ZE). For better visualization of the species and haplotype branches, the branch length of the outgroup in the ftz RCPE tree is compressed four times, that in the ZE tree eight times and that in the CDS tree compressed ten times. The scales reflect the genetic distance in substitution per site and only bootstrap values higher than 50 are shown.

Done