Figure 3

Neighbor-net reconstruction based on GBDP distances between whole mitochondrion genomes. The GBDP variant used was derived by scaling and averaging distance matrices based on HSP search with BLASTN and TBLASTX, respectively. Further settings were use of equations (2) and (6) and averaging of asymmetric distance values. With BIONJ as tree reconstruction method, this distance matrix achieved the highest c-score (0.5574), i.e., highest topological accuracy according to the current NCBI taxonomy, of all GBDP trees inferred from mitochondrial genomes. The matrix' δ value was 0.2946, indicative of a relatively high distance quality compared to the other results obtained with mitochondrial genomes. Bacterial outgroup taxa and major eukaryotic groups are indicated. Note the apparently low resolution of the network as compared to the best results obtained with plastid genomes (Figs. 4 and 5). Nevertheless, quite a few subgroups of the major eukaryotic groups are well recovered.