This large monophyletic group can be subdivided into two smaller monophyletic clades (Fig. 2C).
Goniacean and tetrabaenacean OTUs were designated as the outgroup because Volvocaceae is monophyletic and sister to the Goniaceae, and these two families and the Tetrabaenaceae form a large monophyletic group [ 3- 5].
Both mimiviruses and mamaviruses have been identified as a new family (mimiviridae) of an apparently large monophyletic group known as the 'Nucleocytoplasmic Large DNA viruses' (NCLDV), which already includes the Poxviridae, Irido/Ascoviridae, Phycodnaviridae, Marseilleviridae, and Asfarviridae[ 10, 11].
A large monophyletic group occurred in cluster IV of Bacteroidales, which comprised symbionts of related protist species in the three families Hoplonymphidae, Staurojoeninidae, and Trichonymphidae of the order Trichonymphida.
Most of the other studied proteins (32 out of 35 remaining sequences) form another large monophyletic group (although of weak support, PP: 0.55) likely corresponding to what may be called a Delta clade since it includes the known Deltas from vertebrates as well as from the main metazoan lineages, including the sponge Amphimedon and the placozoan Trichoplax.
All these trees recover the same set of major lineages as those trees of NT data, clearly indicating that the microlabis and subobscura subgroups are basal to the remainder ingroup species (BP = 53; PP = 0.96 0.99), all of which form a very large monophyletic group.
These sequences clustered into five clades, defined as the largest monophyletic groups containing exclusively sequences from B. neustriaca.
We identified several clades of SRK-related sequences from Biscutella by characterizing the largest monophyletic groups containing exclusively sequences from B. neustriaca.
In order to assign the entire species richness of Magnoliidae to the tips of the phylogeny, it was necessary in several instances to merge tips into a single terminal to represent larger monophyletic groups hereafter referred to as compartments.
