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Taxonomies

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Hierarchical clustering diagram
Source https://it.wikipedia.org/wiki/File:Hierarchical_clustering_diagram.png

(Phylogenetic trees have the shape of dendrograms, each node of the dendrogram corresponds to a clade. )

Taxonomy (from the Greek: ταξις, taxis, ordering and νομος, nomos, norm or rule) is, in its most general sense, the discipline of classification. Usually, the term is used to designate biological taxonomy, ie the criteria by which organisms are ordered in a classification system composed of a hierarchy of nested taxa.

Definitions

With the term taxonomy, therefore, we can refer both to the hierarchical classification of concepts and to the very principle of classification. Virtually all concepts, animated and non-animated objects, places and events can be classified according to a taxonomic scheme.

  • Taxonomy is the science that generically deals with the modes of classification (of living and non-living beings).
  • Classification means the description and placement in a taxonomic system of an entity.
  • By definition we mean the recognition or identification of a subject. Above all in the scientific field (eg botany, zoology).

Mathematics

According to mathematics, a taxonomy is a tree structure of instances (or categories) belonging to a given group of concepts. At the head of the structure there is a single instance, the root node, whose properties apply to all other instances of the hierarchy (sub-categories). The nodes underlying this root are more specific categories whose properties characterize the subset of the total number of objects classified in the whole taxonomy.

Definitions of taxonomy according to the different schools

According to the Claudist school, taxonomy is the science that must decide which clades of the phylogenetic tree will be converted into taxa, and in which taxonomic category every taxon should be.

The current taxonomy(The current taxonomy: taxonomy (defined according to the Claudist school) decides which nodes of the phylogenetic tree (cladi) will be converted into taxa and into which taxonomic categories should be located.)

There are other classification schools. Perhaps the most important, among the minorities, is that which also considers the paraphyletic groups able to have the possibility of being converted into taxa, if the groups that conform them are sufficiently similar to each other and sufficiently dissimilar from the clade that remains outside (evolutionist school) : Simpson, 1961, Ashlock, 1979, Cronquist, 1987, Mayr & Ashlock, 1991, Stuessy, 1983, Stevens, 1986 and 1988). A classic example of a paraphyletic group that some taxonomists consider a taxon, is that of bacteria, paraphyletic with respect to those eukaryotes. One of the current exponents of this school is the researcher Cavalier-Smith.

Another school that was started by researchers such as Sokal, is that which claimed that it was impossible to know the phylogeny of organisms with the information that was collected, due to the fact that the reasonings tend to become circular (morphology determined kinship relations, and with these the morphology was interpreted) and the information was not complete in order to know the “true” phylogenetic relationships. These researchers opted to make classifications based solely on the amount of similar characters between organisms, without inferring any evolutionary history behind them (Sneath & Sokal, 1973). This school (called the Phoenician school) has perhaps lost its strength with the advent of DNA analysis, and with the greater interpretation of the fossil record that we have today. This is due to the fact that monophyletic groups are more useful in a classification system of groupings based on the similarity of traits (Farris, 1979, Donoghue & Cantino, 1988), and it is currently possible to state more precisely which groups are monophyletic. It must be borne in mind that Systematics owes to this school many methods of numerical analysis (such as Sneath & Sokal, 1973, Abbott et al., 1985), with the difference that they are used as an aid to determine the phylogeny of organisms.

Another school is that which offers a classification free from categories, whose most extreme exponent is perhaps the PhyloCode, although this school never came to be seriously discussed in the scientific environment (Mallet & Willmott, 2003).

Characteristics of classification systems

In addition to the school that defines it, the ultimate goal of taxonomy is to present a classification system that groups all the diversity of organisms into discrete units within a stable system, above which the work of researchers is made possible.

The classification systems are composed of taxa (from the Greek: ταξα, taxa) inserted in their respective taxonomic categories. The decision of which clads should convert into taxa and in which taxonomic categories should be every taxon, is a bit arbitrary, but there are some unwritten rules that researchers use to make the classification system “useful”. In order for a classification system to be useful, it must be manageable, and therefore it must organize the information so that it is easier to remember. Judd and collaborators (2002) agree that:

  1. each taxon must have reliable evidence of the fact that it forms a monophyletic group: to convert a clade into taxon must have many synapomorphisms that justify it, and must have a number of diagnostic characters that allow to differentiate it from the rest of the taxa, facilitating the stability of the classification system;
  2. some systematics support the idea that every taxon should possess obvious morphological characters that allow it to be identified, and this would favor identification for non-systematic ones, as well as helping to infer many aspects of its biology;
  3. the taxa that make up a classification system must have possibly between 3 and 7 subtypes, a number that can easily handle human memory (Stevens, 1998). In the words of Davis & Heywood, 1963-1983: “We must be able to locate taxa in the highest category taxa so that we can meet them again”.
  4. another criterion is the stability of the nomenclature. Groups that have already been nominated in the past should continue with the same name as far as possible.

Once you have decided which clads to convert into taxa, systematics must decide in which taxonomic categories to place them, which is arbitrary. For historical reasons we use the linneana categories of classification: kingdom, phylum or division, class, order, family, genus and species. The same criteria used to know whether to name a taxon can be used to know in which taxonomic category to place it, especially that of stability in the nomenclature.

The classification systems that arise as a result of taxonomy have two uses:

  • They serve as information containers. Scientists around the world use taxa as a unit of work, and publish the results in relation to the studied taxon. Therefore the scientific names of the organisms are the key to access to an immense body of information, dispersed in many languages ​​and coming from many fields of biology.
  • They allow to make predictions about the physiology, ecology and evolution of taxa. For example, it is very common that when a compound of medical interest is found in a plant, it is investigated whether this compound or other similar ones are found in other related species.

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