Maximum likelihood genealogy of the <i>D. melanogaster</i> mtDNA in the DGRP and DPGP strains.

<p>Strains infected with <i>Wolbachia</i> are shows in black font and are labelled with asterisks, while uninfected strains are shown in grey font. Strains highlighted with a grey background are from the North American DGRP sample, underlined strains are from the European DPGP sample, and the remainder are from the African DPGP sample. The dm3 and NC_001709 reference sequences are found in clades III and VI, respectively. The numerical suffix after strain names represents the COI haplotype according to Nunes <i>et al. </i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003129#pgen.1003129-Nunes1" target="_blank">[19]</a> with numbering extended to new haplotypes discovered here. The underlying data consist of an ungapped multiple alignment of 292 sequences each of 12,225 bp in length. The unrooted ML tree was midpoint rooted for visualization and branches with >85% RAxML bootstrap values are shown with coloured boxes. Scale bars for branch lengths are in terms of mutations per site.