Classification

1.2 ClassificationIntroductionClassification is one of the starting points of all sciences. Taxonomy, the classification of living beings, is one of the oldest branches of biology. Taxonomy means the science of classification, originating from the Greek taxis, which means arrangement, and nomia, which means method, rule or law.
Taxonomy comes from the word taxon which means branch. In recent times it is also called cladistics. Cladistics comes from the word clade, meaning a group. The concept of clade is created to have a name for a group without having to refer to the level of that group. A clade can be a tribe, a family, an order, a class or a whole kingdom.
All these words refer to a tree with branches and leaves, symbolic for the growth and evolution in life. Evolution is an important aspect of taxonomy, a good classification reflects the evolution of organisms. In this article I will discuss taxonomy and its problems, especially in reference to the Plant kingdom by comparing the differences between the Apg classifications and the Plant theory. The Plant theory is the classification of the Plant kingdom as developed the last 30 years. It will be presented in the chapter “Plant theory”.MineralsThe classification of the Mineral kingdom is based on the Periodic system, a table in which the elements are arranged in rows and columns. The first step in forming the Periodic system was to find out what are compounds and what are elements, the atoms, the basic building blocks of all minerals. The next step was done by Mendeleev by placing them in the Periodic system, based on their properties. Later it was found that the essence behind it was the atomic number of these elements, which is the number of protons in their nucleus. All elements are arranged according to their atomic number. Quantum mechanics was needed to explain why the elements are arranged in rows, the periodic quality of the Periodic system.QualitiesTaxonomy started with classification by form and behaviour of the living beings. Later, chemical information was additionally used. In the twentieth century many classifications of the whole Plant kingdom were made, like the ones of Cronquist, Stebbins and Takhtajan.
In the last decades DNA information has become an important source for classification. The DNA analyses have added an enormous amount f data and details to the taxonomy of living beings. They have shed more light on the higher clades in the classification, the classes and phyla. The Angiosperm Phylogenetic Group, abbreviated Apg, is a group of botanists who published four versions of their classification, every next one more refined and confirmed. They can be abbreviated as Apg1 to Apg4.EvolutionIn the Plant kingdom and Animal kingdom the classification is connected with the evolution of life. The classification has the form of a tree with stem, branches and leaves. It is also named phylogenetics, originating from the Greek words phylum, meaning leaf, and genesis, meaning origin. A central concept is monophyly: a group is monophyletic if and only if all members of a group have evolved from one ancestor and all descendants of that ancestor are in the group. The opposites of monophyly are named paraphyly or polyphyly. Paraphyly means that a group misses some members. Polyphyly means that the group misses the ancestor. Practically they are the same concept.ConvergenceIt is very interesting that all 3 sources of information usually lead to very similar classifications. The Apg classifications mostly confirmed the old classifications, although there are also differences. Ranunculaceae is still a family; the same applies to most other families.
Other families have been split apart, for instance the Scrophulariaceae has been mostly split into Scrophulariaceae, Orobanchaceae and Plantaginaceae. Some botanists rely mainly or only on DNA analysis for
their classification. Other botanists have their doubts about that approach, especially in cases where a clade has not a single morphological or chemical quality that is common for all members. An example is the order Malpighiales in the Apg4 classification.Plant theoryThe Plant theory is a classification of the Plant kingdom, based on the botanical, mostly Apg, classification. A very important addition is the use of toxicological and healing qualities of the plants, both physical and psychological.
The use of the toxicological and healing qualities has a big advantage, as those qualities are themselves also classified. That classification comes from the Periodic system, with the classification of the rows and columns of the Periodic system. This classification is refined by the themes of the rows and columns. For instance, the 7 rows of the Periodic system are reflected in the 7 phyla in the Plant theory. The Plant theory is based on structure, functionality, use and meaning.DifferencesIn the development of the Plant theory it became necessary to depart from certain aspects of the Apg classification. In some situations older classifications like those of Cronquist, Stebbins and Takhtajan turned out to be better fitting the Plant theory.
Many differences do not affect the monophyly of the clades. The Plant theory has split some clades in subclades that are also monophyletic. Monophyly is a good and strong requirement for classification. But it is questionable if DNA can be decisive in determining the monophyly.Fusing cladesThe Plant theory has fused many clades, especially very small ones. For example, in the order Brassicales the small families Emblingiaceae, Resedaceae, Grystemonaceae, Tovariaceae, Capparaceae and Cleomaceae are fused into one family Capparaceae. This fusion is not fully monophyletic.
In the development of the Plant theory it has become clear that in an order, or any other clade, the families at the start and end are very small, often containing only one genus. The central families of an order are often very large, like Brassicaceae in the Brassicales. This might come from the development of the theme of the order: in the beginning the theme is still not crystallised and goes into all kinds of directions, like in the Cambrian explosion. When the theme comes to full development the forms converge more and the clades get fused together. At the end the theme diverges again, leading to many different, small families in taxonomy.Fusing oversplit cladesThe Gymnospermae clade of pine trees is not monophyletic and is split accordingly into subclades in the Apg classification. The reason is that the Angiospermae are descendants of some member of the Gymnospermae. The result is that Gymnospermae cannot be used as clade anymore. This is in contrast with the fact that they have very similar qualities, and have evolved in the same time.
The same can be said of the mosses, the Bryophyta, the Ferns and basically of all clades from the same evolutionary situation. Every new development in evolution had to arise from an older level. The new group violates the monophyly of the old group. But from a structural point of view it is still justified to use them as clades. This controversy is obvious from the Pteridophyte Phylogeny Group, abbreviated Ppg, which classified the Ferns, the Pteridophyta, which is not monophyletic anymore.Splitting cladesThe Plant theory has split many clades. For example, the family Brassicaceae is split into 5 subfamilies. This does not affect the monophyly.LevelsThis stress on monophyly and oversplitting of clades also has another awkward aspect: it increases the amount of levels in the taxonomy enormously. For example it is not uncommon to find 35 levels of clades that a species belongs to on Wikispecies. One can name those clades subregnum, infraregnum, superregnum and so on. But at a certain moment there are no concepts, names for those levels anymore. They are described as unranked. That is where the concept of clade came from: one can describe groups without having to ascertain the level.
In the Plant theory there are 7 levels, with similar ranks for all the plants.RegionalIn the Plant theory, Pedaliaceae and Martyniaceae are fused into one family. They have very similar qualities in form, but are treated as separate families in the Apg classifications, based on their DNA. The toxocological and healing qualities are very similar though.
The difference probably arises from the evolution of Pedaliaceae and Martyniaceae in different parts of the world, but evolving to the same theme. It can be compared to arriving at the same city via different routes. The DNA can be seen as an expression of the route of their evolution, and of the theme, the point of arrival.FractalsAnother aspect of the Plant theory is the idea of fractals. For instance, parasitic plants can be found in different places in the Plant kingdom. In the past they were grouped into one family. DNA analyses have shown them to be in different orders and classes. In the Plant theory, the theme of parasitism is classified in Phase 7; both parasitism and Phase 7 return at many levels.DNAMany researchers have the idea that the DNA is the best or even the only reliable source for classifications. This comes from the idea that the DNA is the essence of life, directing and regulating life and the differences in species. This idea is used as an axiom, but it is incorrect. We can see that already from the human genome which has about 20,000 genes, but should have 100,000 genes to be able to explain human existence. We can see it also in the experimental fact that different phylogenetic studies, DNA analyses lead to different classifications, depending on which parts of the DNA are analysed.
I think it is much more accurate to see DNA as a library: life uses the DNA information to create what it needs, instead of seeing DNA as the creator of life.
Further information can be found in the chapters “Element theory”, “Plant theory” and “Animal theory”.