Figure 4

Neighbor-net reconstruction based on GBDP distances between whole plastid genomes. The GBDP variant used was based on equations (2) and (6) as well as BLASTN HSP search. In case of asymmetric distances, the minimum value was taken. This distance matrix achieved the globally highest c-score (0.8298), i.e., highest phylogenetic accuracy according to our reference topology, with BIONJ as tree reconstruction method. The matrix' δ value was 0.2013, pointing to fairly high distance quality. Bacterial outgroup taxa and major eukaryotic groups are indicated. Resolution is much higher than in best results obtained with mitochondrial genomes (Fig. 3), and most major eukaryotic groups are recovered.