Figure 3. Reconstructed phylogenetic trees of the Chlorophyceae group.

Three different methods were compared: FST distance (left) using the full kernel score, F84 distance estimation on a Muscle alignment (top right) and maximum-likelihood tree on the same Muscle alignment (bottom right). Only the FST tree reveals the same grouping of the major clades as discussed in [38], which we use as a ‘gold standard’. The distance tree erroneously places the Sphaeroplea clade between the Hydrodictyon and Scenedesmus clades, while the ML tree places them within the reinhardtii-subgroup.