XXV.1.1 A natural taxonomic system is now understood to be a system reflecting the progress of the phylogenesis of organisms

The oldest known systems of organisms were, in their nature, basically mostly essentialist. They are based on the assumption that, similarly as it is possible to order geometric shapes or types of crystals in a finite number of predetermined categories, it is also possible to order individual species of organisms. The authors of these systems were of the opinion that some types of traits are, in their nature, more important than other traits; they tried to discover these important, essential traits and to create taxonomic systems on this basis.

Other systems could be termed structuralist. These systems did not assume that there would have to exist only a limited and predetermined number of categories (types) of organisms. However, they were also based on the idea that, for objective reasons following from the properties of the structural elements of organisms, only certain structural plans of bodies exist on the Earth, and that the individual species can always be assigned to these types and subtypes. Some systems assumed that the reason for the existence of basic types of organisms, sometimes called archetypes, lies in the plan of God the Creator.  Later systems looked for the reason for the existence of distinct types in the properties and internal structure of the matter from which living organisms are composed and that forms their surroundings. 

Following the establishment of the theory of evolution, it became apparent that natural relationships actually exist amongst the individual species of organisms and simultaneously that they do not primarily have a structural basis. This basis is historical and specifically consists in the character of phylogenesis, i.e. in the historical process of gradual evolutionary formation of the individual species by branching off from a common ancestor. The main requirement placed on natural taxonomic systems at the present time is that they must respect the history of the phylogenesis of the particular species, i.e. their cladogenesis.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more
Draft translation from: Evoluční biologie, 2. vydání (Evolutionary biology, 2nd edition), J. Flegr, Academia Prague 2009. The translation was not done by biologist, therefore any suggestion concerning proper scientific terminology and language usage are highly welcomed. You can send your comments to flegratcesnet [dot] cz. Thank you.