The taxonomy is not a straightforward process. As long as it has not been discovered what is the underlying principle the classification is debatable. I hope that this book will contribute to discover this underlying principle, the essence of plants.
The groups at the start are often difficult to establish. For instance, the Eudicots have a beginning with 7 orders of which 5 were only established in the 3rd version of the Apg classification.
This classification is the best that exists at the moment. But it is not definite yet, still under construction. This can be seen from the revisions, going from Apg1, to Apg3. Many aspects are very solid, confirmed over and over by cladistic analysis and confirming chemistry and morphology. But there are also parts that are dubious. Some orders lack morphological confirmation. Others are placed differently according to which DNA is researched. And it can turn out that DNA is not the definite answer. It is also another expression of a deeper essence.
It has been stated that molecular phylogenetics is not a sure-fire, problem-free method of determining systematic relationships. Parasitic plants especially are difficult to place as the most genes for phylogentics are the ones for the chlorophyll, inverting repeat regions of the chloroplast genome.
There is a strong tendency to give names only to monophyletic groups. This works out very well for end branches in the evolutionary tree. But for early development this leads to problems. Many of them can be found in the chapter Phyla.
The first problem is that early evolutionary groups cannot be given an adequate name. For instance the mosses, also called Bryophyta, is not a monophyletic group. The reason for that is that the Tracheophyta, the vascular plants developed out of them. But including the vascular plants into the mosses would give the impression that they are also mosses. This leads to confusion. Bryophta is now a name that sometimes is given to all land plants, sometimes it is a name for all mosses, including the Liverworts and Hornworts and sometimes it is the name for the mosses in a more narrow sense, sensu strictu. In the past the Liverworts and Hornworts were included in one Phylum with the mosses, the Bryophyta.
A second problem is the determination of the level of a clade. For instance the Angiospermae is seen in the past as a phylum, a division. But it is part of the Spermatophyta and thus that should have a higher level, for instance Superphylum. The Spermatophyta are part of the Traceophyta thus Tracheophyta should also have a higher level, for instance Supersuperphylum. The Tracheophyta are part of the Bryophyta thus Bryophyta should have a higher level, for instance Subkingdom.
The latest development in evolution is often the biggest group, like the Angiospermae. But that group has many levels of which it is part. The biggest group then gets the lowest level. And some small clades early in the evolution get a very high level.
In my opinion it is clearer to use the old divisions, even when they are paraphyletic. The mosses and Gymnospermae are clear distinct groups, they can be identified easily and have had a period in the evolution were they were the most prominent group. Later evolutions led to new clades, with special new features. And even when they belong to the old evolutionary group from the point of view of monophyly, it is clearer to see both clades as distinct. The Gymnospermae were once monophyletic in the time they were the main and last evolutionary development.
An example may clarify the situation. Tetradiclis tenella has been described as belonging to the following clades:
Species Tetradiclis tenella
There are 17 Levels in de description, of which 8 are above the level of Angiospermae. These are necessary when one adheres strictly to using only monophyletic clades. The description of the levels become difficult, as one needs Phylum, subphylum, Superphylum, Intraphylum and so on.
The description according to the Plant theory is
Phylum Angiospermae = Magnoliophyta
Species Tetradiclis tenella