Taxonomy (biology)

Taxonomy (from τάξις taxis, "arrangement," and -νομία -nomia, "method") is the academic discipline of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. Each group is given a rank and groups of a given rank can be aggregated to form a super group of higher rank and thus create a hierarchical classification. The groups created through this process are referred to as taxa (singular taxon). An example of a modern classification is the one published in 2009 by the Angiosperm Phylogeny Group for all living flowering plant families (the APG III system).

Carolus Linnaeus, the Swedish botanist is regarded as the father of modern taxonomy.

Definition
The exact definition of taxonomy varies from source to source, but the core of the discipline remains: the conception, naming, and classification of organism groups. The exact relationship of systematics and classification to taxonomy also varies because the usage of the terms in biology originated independently. As points of reference, recent definitions of taxonomy are presented below:


 * 1) Theory and practice of grouping individuals into species, arranging species into larger groups, and giving those groups names, thus producing a classification;
 * 2) A field of science (and major component of systematics) that encompasses description, identification, nomenclature, and classification;
 * 3) The science of classification, in biology the arrangement of organisms into a classification.
 * 4) "The science of classification as applied to living organisms, including study of means of formation of species, etc."
 * 5) "The analysis of an organism's characteristics for the purpose of classification"

The varied definitions either place taxonomy as a sub-area of systematics (definition 2), or appear to consider the two terms synonymous. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy (definitions 1 and 2), or a part of systematics outside taxonomy. For example, the last definition is paired with the following definition of systematics that places nomenclature outside taxonomy:
 * Systematics: "The study of the identification, taxonomy and nomenclature of organisms, including the classification of living things with regard to their natural relationships and the study of variation and the evolution of taxa".

Application
Biological taxonomy is a sub-discipline of biology, and is generally practiced by biologists known as "taxonomists", though enthusiastic naturalists are also frequently involved in the publication of new taxa. The work carried out by taxonomists is crucial for the understanding of biology in general. Two fields of applied biology in which taxonomic work is of fundamental importance are the study of biodiversity and conservation. Without a working classification of the organisms in any given area, estimating the amount of diversity present is unrealistic, making informed conservation decisions impossible. As conservation becomes ever more politically important, taxonomic work impacts not only the scientific community, but society as a whole.

Taxonomic descriptions
The 'definition' of a taxon is encapsulated by its description. There are no set rules governing the definition of taxa, but the naming and publication of new taxa is governed by sets of rules. In zoology, the nomenclature for the more commonly used ranks (superfamily to subspecies), is regulated by the International Code of Zoological Nomenclature (ICZN Code). In the fields of botany, phycology, and mycology, the naming of taxa is governed by the International Code of Nomenclature for algae, fungi, and plants (ICN).

The initial description of a taxon involves five main requirements:


 * 1) The taxon must be given a name based on the 26 letters in the Latin alphabet (a binomial for new species, or uninomial for other ranks).
 * 2) The name must be unique (i.e. not a homonym).
 * 3) The description must be based on at least one name-bearing type specimen.
 * 4) It should include reference to enough attributes to differentiate the taxon from other taxa (ICZN Code, Article 13.1.1; ICN, Article 38.2). Both codes deliberately separate defining the content of a taxon (its circumscription) from defining its name.
 * 5) These first four requirements must be published in a work that is obtainable in numerous identical copies, as a permanent scientific record.

However, often much more information is included, like the geographic range of the taxon, ecological notes, chemistry, behavior, etc. How researchers arrive at their taxa varies; depending on the available data, and resources, methods vary from simple quantitative or qualitative comparisons of striking features, to elaborate computer analyses of large amounts of DNA sequence data.

Classifying organisms
Biological classification is a critical step in the taxonomic process, as it informs the user as to what the relatives of the taxon are hypothesized to be. Although the discipline of taxonomy itself does not deal with the investigations of how taxa are related to one another, it does serve to communicate these results to the user. To do this, it uses taxonomic ranks, including, among others (in order from most inclusive to least inclusive): Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species.

Phylogenetics and Cladistics



 * See full articles at Phylogenetics and Cladistics

Today, traditional rank-based biological classifications persist in a structure largely unchanged since the 1700s; however, how the relationships of these taxa are investigated has changed drastically in recent decades. It is now common for biologists to devise a classification based on the results of phylogenetic analysis using DNA sequence data, and taxa are typically required to be clades. Although phylogenetics itself is fundamental to modern-day systematics, its use for the description of new taxa, and for their placement within a classification scheme, is not required.

Phenetics
In phenetics, also known as taximetrics, organisms are classified based on overall similarity, regardless of their phylogeny or evolutionary relationships. It results in a measure of evolutionary "distance" between taxa. Phenetic methods have become relatively rare in modern times, largely superseded by cladistic analyses, as phenetic methods do not distinguish plesiomorphic from apomorphic traits. However, certain phenetic methods, such as neighbor joining, have found their way into cladistics, as a reasonable approximation of phylogeny when more advanced methods (such as Bayesian inference) are too computationally expensive.

Early taxonomists
Taxonomy has been called "the world's oldest profession", and naming and classifying our surroundings has likely been taking place as long as mankind has been able to communicate. It would always have been important to know the names of poisonous and edible plants and animals in order to communicate this information to other members of the family or group.

In the East, one of the earliest recorded pharmacopoeias was written by Shen Nung, Emperor of China (c. 3000 BC). He wanted to spread information related to agriculture and medicine, and is said to have tasted hundreds of plants with the goal of learning their medicinal value. Records after this are difficult to interpret for some time, but medicinal plant illustrations show up in Egyptian wall paintings from c. 1500 BC. The paintings clearly show that these societies valued and communicated the uses of different species, and therefore had a basic taxonomy in place.

Aristotle to Pliny the Elder
Historical records show that informally classifying organisms took place at least back to the days of Aristotle (Greece, 384-322 BC), who was the first to begin to classify all living things. Some of the terms he gave to animals, such as "invertebrates" and "vertebrates" are still commonly used today. His student Theophrastus (Greece, 370-285 BC) carried on this tradition, and wrote a classification of 480 plants called Historia Plantarum. Again, several plant groups currently still recognized can be traced back to Theophrastus, such as Cornus, Crocus, and Narcissus. The next major turn-of-the-millennia era taxonomist came in the form of Pliny the Elder (Rome, 23-79 AD). His elaborate 160-volume work Naturalis Historia described many plants, and even gave many of them Latin binomial names.

Pre-Linnaean taxonomists
It was not until c. 1500 years later that taxonomic works became ambitious enough to replace the ancient texts. This is often credited to the development of sophisticated optic lenses, which allowed for the morphology of organisms to be studied in much greater detail. One of the earliest authors to take advantage of this leap in technology was Andrea Cesalpino (Italy, 1519–1603), who is often referred to as "the first taxonomist". His magnum opus De Plantis came out in 1583, and described over 1500 plant species. Two large plant families that he first recognized are still in use today: the Asteraceae and Brassicaceae. Then in the seventeenth century John Ray (England, 1627–1705) wrote many important taxonomic works. Arguably his greatest accomplishment was Methodus Plantarum Nova (1682), where he published over 18,000 plant species. At the time his classifications were perhaps the most complex yet produced by any taxonomist, as he based his taxa on many combined characters. The next major taxonomic works were produced by Joseph Pitton de Tournefort (France, 1656–1708). His work from 1700, Institutiones Rei Herbariae, included over 9000 species in 698 genera, and directly influenced Linnaeus as it was the text he used as a young student.

The Linnaean era
The Swedish botanist Carl Linnaeus (1707-1778) ushered in a new era of taxonomy. With his major works Systema Naturae 1st Edition in 1735, Species Plantarum in 1753, and Systema Naturae 10th Edition, he revolutionized modern taxonomy. His works implemented a standardized binomial naming system for animal and plant species, which proved to be an elegant solution to a chaotic and disorganized taxonomic literature. As a result the Linnaean system was born, and is still used in essentially the same way today as it was in the eighteenth century. Currently, plant and animal taxonomists regard Linnaeus' work as the "starting point" for valid names (at 1753 and 1758 respectively). Names published before these dates are referred to as "pre-Linnaean", and not considered valid (with the exception of spiders published in Svenska Spindlar). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean.

The word taxonomy was introduced in 1813 by Candolle, in his Théorie élémentaire de la botanique.

Databases
Modern taxonomy uses database technologies to search and catalog classifications and their documentation. While there is no commonly used database, there are comprehensive databases such as the Catalogue of Life, which attempts to list every documented species. The catalogue listed 1.4 million species for all kingdoms as of May 2012, claiming coverage of more than 74% of the estimated 1.9 million species known to modern science.