Figure 5

Neighbor-net reconstruction based on GBDP distances between whole plastid genomes. Here, the GBDP variant was derived by scaling and averaging distances based on HSP search with BLASTN and TBLASTX, respectively. Further settings were use of equations (2) and (5) and averaging of asymmetric distance values. The resulting distance matrix achieved the globally lowest δ value (0.1629) and, hence, globally highest distance quality. The highest c-score (topological accuracy) obtained with this matrix was 0.6596 (using BIONJ or STC as phylogenetic reconstruction method). Bacterial outgroup taxa and major eukaryotic groups are indicated. Note the apparently incorrect placement of the highly reduced genome of Epifagus virginiana. Other results are similar to Fig. 4; e.g., most major eukaryotic groups are well recovered.