phylogenetic tree of the DNA sequences from the ORF1 region. The reconstruction was performed on the cloned DNA sequences of the ORF1 region from the different populations of D. simulans, and from some sequences detected in the sequenced genome (we eliminated sequences that were too short relative to the global length of the alignment). Colored boxes identify sequences harboring common patterns of deletions and/or insertions. All the positions are given by reference to the complete copy. Green box: sequences display the same deletions of 118 bp (at position 45), 3 bp (at position 839), 6 bp (at position 846), 1 bp (at position 854) and a 1-bp insertion (at position 415). Blue box: sequences display the same 28-bp deletion (at position 1092) – those with a red star also have a 77-bp deletion (at position 508), and a 91-bp deletion (at position 593). Yellow box: sequences display the same deletions of 1 bp (at position 160), 28 bp (at position 165), 19 bp (at position 954), 2 bp (at position 989), and 37 bp (at position 1006), and an insertion of 1 bp (at position 322). Orange box: sequences with no deletion or insertion, very closely related to the complete copy chr3R_1506433. Black asterisks correspond to bootstrap values greater than 50%.