Biological classification

Biological classification, or scientific classification in biology, is a method to group and categorize organisms by biological type, such as genus or species. Biological classification is part of scientific taxonomy.

Modern biological classification has its root in the work of Carolus Linnaeus, who grouped species according to shared physical characteristics. These groupings have since been revised to improve consistency with the Darwinian principle of common descent. Molecular phylogenetics, which uses DNA sequences as data, has driven many recent revisions and is likely to continue to do so. Biological classification belongs to the science of biological systematics.

Definition
Classification has been defined by Mayr as "The arrangement of entities in a hierarchical series of nested classes, in which similar or related classes at one hierarchical level are combined comprehensively into more inclusive classes at the next higher level." A class is defined as "a collection of similar entities", where the similarity consists of the entities having attributes or traits in common.

What makes biological classification different from other classification systems (e.g. classifying books in a library) is evolution: the similarity between organisms placed in the same taxon is not arbitrary, but is instead a result of shared descent from their nearest common ancestor. Accordingly the important attributes or traits for biological classification are those which are 'homologous', i.e. inherited from common ancestors. These must be separated from traits that are analogous. Thus birds and bats both have the power of flight, but this similarity is not used to classify them into a taxon (a "class"), because it is not inherited from a common ancestor. In spite of all the other differences between them, the fact that bats and whales both feed their young on milk is one of the features used to classify both as mammals, since it was inherited from a common ancestor.

Determining whether similarities are homologous or analogous or not can be difficult. Thus until recently, golden moles, found in South Africa, were placed in the same taxon (insectivores) as Northern Hemisphere moles, on the basis of morphological and behavioural similarities. However, molecular analysis has shown that they are not closely related, so that their similarities must be due to convergent evolution and not to shared descent, and so should not be used to place them in the same taxon.

Taxonomic ranks
A classification, as defined above, is necessarily hierarchical. In a biological classification, rank is the level (the relative position) in a hierarchy. (Rarely, the term "taxonomic category" is used instead of "rank".) There are seven main ranks defined by the international nomenclature codes: kingdom, phylum/division, class, order, family, genus, species. "Domain", a level above kingdom, has become popular in recent years, but has not been accepted into the codes.

The most basic rank is that of species, the next higher is genus, and then family. Ranks are somewhat arbitrary, but hope to encapsulate the diversity contained within a group &mdash; a rough measure of the number of diversifications that the group has been through.

The International Code of Zoological Nomenclature defines rank, in the nomenclatural sense, as: "The level, for nomenclatural purposes, of a taxon in a taxonomic hierarchy (e.g. all families are for nomenclatural purposes at the same rank, which lies between superfamily and subfamily). The ranks of the family group, the genus group, and the species group at which nominal taxa may be established are stated in Articles 10.3, 10.4, 35.1, 42.1 and 45.1."

There are slightly different ranks for zoology and for botany, including subdivisions such as tribe.

Ancient through medieval times
Current systems of classifying forms of life descend from the thought presented by the Greek philosopher Aristotle, who published in his metaphysical works the first known classification of everything whatsoever, or "being". This is the scheme that gave such words as 'substance', 'species' and 'genus' and was retained in modified and less general form by Linnaeus.

Aristotle also studied animals and classified them according to method of reproduction, as did Linnaeus later with plants. Aristotle's animal classification was eventually made obsolete by additional knowledge and forgotten.

The philosophical classification is in brief as follows: Primary substance is the individual being; for example, Peter, Paul, etc. Secondary substance is a predicate that can properly or characteristically be said of a class of primary substances; for example, man of Peter, Paul, etc. The characteristic must not be merely in the individual; for example, being skilled in grammar. Grammatical skill leaves most of Peter out and therefore is not characteristic of him. Similarly man (all of mankind) is not in Peter; rather, he is in man.

Species is the secondary substance that is most proper to its individuals. The most characteristic thing that can be said of Peter is that Peter is a man. An identity is being postulated: "man" is equal to all its individuals and only those individuals. Members of a species differ only in number but are totally the same type.

Genus is a secondary substance less characteristic of and more general than the species; for example, man is an animal, but not all animals are men. It is clear that a genus contains species. There is no limit to the number of Aristotelian genera that might be found to contain the species. Aristotle does not structure the genera into phylum, class, etc., as the Linnaean classification does.

The secondary substance that distinguishes one species from another within a genus is the specific difference. Man can thus be comprehended as the sum of specific differences (the "differentiae" of biology) in less and less general categories. This sum is the definition; for example, man is an animate, sensate, rational substance. The most characteristic definition contains the species and the next most general genus: man is a rational animal. Definition is thus based on the unity problem: the species is but one yet has many differentiae.

The very top genera are the categories. There are ten: one of substance and nine of "accidents", universals that must be "in" a substance. Substances exist by themselves; accidents are only in them: quantity, quality, etc. There is no higher category, "being", because of the following problem, which was only solved in the Middle Ages by Thomas Aquinas: a specific difference is not characteristic of its genus. If man is a rational animal, then rationality is not a property of animals. Substance therefore cannot be a kind of being because it can have no specific difference, which would have to be non-being.

The problem of "being" occupied the attention of scholastics during the time of the Middle Ages. The solution of St. Thomas, termed the analogy of being, established the field of ontology, which received the better part of the publicity and also drew the line between philosophy and experimental science. The latter rose in the Renaissance from practical technique. Linnaeus, a classical scholar, combined the two on the threshold of the neo-classicist revival now called the Age of Enlightenment.

Renaissance through Age of Reason
An important advance was made by the Swiss professor, Conrad von Gesner (1516–1565). Gesner's work was a critical compilation of life known at the time.

The exploration of parts of the New World by Europeans produced large numbers of new plants and animals that needed descriptions and classification. The old systems made it difficult to study and locate all these new specimens within a collection and often the same plants or animals were given different names simply because there were too many species to keep track of. A system was needed that could group these specimens together so they could be found; the binomial system was developed based on morphology with groups having similar appearances. In the latter part of the 16th century and the beginning of the 17th, careful study of animals commenced, which, directed first to familiar kinds, was gradually extended until it formed a sufficient body of knowledge to serve as an anatomical basis for classification. Advances in using this knowledge to classify living beings bear a debt to the research of medical anatomists, such as Fabricius (1537–1619), Petrus Severinus (1580–1656), William Harvey (1578–1657), and Edward Tyson (1649–1708). Advances in classification due to the work of entomologists and the first microscopists is due to the research of people like Marcello Malpighi (1628–1694), Jan Swammerdam (1637–1680), and Robert Hooke (1635–1702). Lord Monboddo (1714–1799) was one of the early abstract thinkers whose works illustrate knowledge of species relationships and who foreshadowed the theory of evolution.

Early methodists
Since late in the 15th century, a number of authors had become concerned with what they called methodus, (method). By method authors mean an arrangement of minerals, plants, and animals according to the principles of logical division. The term Methodists was coined by Carolus Linnaeus in his Bibliotheca Botanica to denote the authors who care about the principles of classification (in contrast to the mere collectors who are concerned primarily with the description of plants paying little or no attention to their arrangement into genera, etc.). Important early Methodists were Italian philosopher, physician, and botanist Andrea Caesalpino, English naturalist John Ray, German physician and botanist Augustus Quirinus Rivinus, and French physician, botanist, and traveller Joseph Pitton de Tournefort.

Andrea Caesalpino (1519–1603) in his De plantis libri XVI (1583) proposed the first methodical arrangement of plants. On the basis of the structure of trunk and fructification he divided plants into fifteen "higher genera".

John Ray (1627–1705) was an English naturalist who published important works on plants, animals, and natural theology. The approach he took to the classification of plants in his Historia Plantarum was an important step towards modern taxonomy. Ray rejected the system of dichotomous division by which species were classified according to a pre-conceived, either/or type system, and instead classified plants according to similarities and differences that emerged from observation.

Both Caesalpino and Ray used traditional plant names and thus, the name of a plant did not reflect its taxonomic position (e.g. even though the apple and the peach belonged to different "higher genera" of John Ray's methodus, both retained their traditional names Malus and Malus Persica respectively). A further step was taken by Rivinus and Pitton de Tournefort who made genus a distinct rank within taxonomic hierarchy and introduced the practice of naming the plants according to their genera.

Augustus Quirinus Rivinus (1652–1723), in his classification of plants based on the characters of the flower, introduced the category of order (corresponding to the "higher" genera of John Ray and Andrea Caesalpino). He was the first to abolish the ancient division of plants into herbs and trees and insisted that the true method of division should be based on the parts of the fructification alone. Rivinus extensively used dichotomous keys to define both orders and genera. His method of naming plant species resembled that of Joseph Pitton de Tournefort. The names of all plants belonging to the same genus should begin with the same word (generic name). In the genera containing more than one species the first species was named with generic name only, while the second, etc. were named with a combination of the generic name and a modifier (differentia specifica).

Joseph Pitton de Tournefort (1656–1708) introduced an even more sophisticated hierarchy of class, section, genus, and species. He was the first to use consistently the uniformly composed species names that consisted of a generic name and a many-worded diagnostic phrase differentia specifica. Unlike Rivinus, he used differentiae with all species of polytypic genera.

Linnaean taxonomy
Carolus Linnaeus' great work, the Systema Naturæ (1st ed. 1735), ran through twelve editions during his lifetime. In this work, nature was divided into three kingdoms: mineral, vegetable and animal. Linnaeus used five ranks: class, order, genus, species, and variety.

He abandoned long descriptive names of classes and orders still used by his immediate predecessors (Rivinus and Pitton de Tournefort) and replaced them with single-word names, provided genera with detailed diagnoses (characteres naturales), and combined numerous varieties into their species, thus saving botany from the chaos of new forms produced by horticulturalists.

Linnaeus is best known for his introduction of the method still used to formulate the scientific name of every species. Before Linnaeus, long many-worded names (composed of a generic name and a differentia specifica) had been used, but as these names gave a description of the species, they were not fixed. In his Philosophia Botanica (1751) Linnaeus took every effort to improve the composition and reduce the length of the many-worded names by abolishing unnecessary rhetorics, introducing new descriptive terms and defining their meaning with an unprecedented precision. In the late 1740s Linnaeus began to use a parallel system of naming species with nomina trivialia. Nomen triviale, a trivial name, was a single- or two-word epithet placed on the margin of the page next to the many-worded "scientific" name. The only rules Linnaeus applied to them was that the trivial names should be short, unique within a given genus, and that they should not be changed. Linnaeus consistently applied nomina trivialia to the species of plants in Species Plantarum (1st edn. 1753) and to the species of animals in the 10th edition of Systema Naturæ (1758).

By consistently using these specific epithets, Linnaeus separated nomenclature from description. Even though the parallel use of nomina trivialia and many-worded descriptive names continued until late in the eighteenth century, it was gradually replaced by the practice of using shorter proper names consisting of the generic name and the trivial name of the species. In the nineteenth century, this new practice was codified in the first Rules and Laws of Nomenclature, and the 1st edn. of Species Plantarum and the 10th edn. of Systema Naturae were chosen as starting points for the Botanical and Zoological Nomenclature respectively. This convention for naming species is referred to as binomial nomenclature.

Today, nomenclature is regulated by Nomenclature Codes, which allows names divided into taxonomic ranks.

Modern system


Whereas Linnaeus classified for ease of identification, the idea of the Linnaean taxonomy as translating into a sort of dendrogram of the Animal- and Plant Kingdoms was formulated toward the end of the 18th century, well before the On the Origin of Species was published. Among early works exploring the idea of a transmutation of species was Erasmus Darwin's 1796 Zoönomia and Jean-Baptiste Lamarck's Philosophie Zoologique of 1809. The idea was popularised in the Anglophone world by the speculative, but widely read Vestiges of the Natural History of Creation, published anonymously by Robert Chambers in 1844.

With Darwin's theory, a general acceptance that classification should reflect the Darwinian principle of common descent quickly appeared. Tree of Life representations became popular in scientific works, with known fossil groups incorporated. One of the first modern groups to be tied to fossil ancestors were birds. Using the then newly discovered fossils of Archaeopteryx and Hesperornis, Thomas Henry Huxley pronounced that they had evolved from dinosaurs, a group formally named by Richard Owen in 1842. The resulting description, that of dinosaurs "giving rise to" or being "the ancestors of" birds, is the essential hallmark of evolutionary taxonomic thinking. As more and more fossil groups were found and recognized in the late 19th and early 20th century, palaeontologists worked to understand the history of animals through the ages by linking together known groups With the modern evolutionary synthesis of the early 1940s, an essentially modern understanding of evolution of the major groups was in place. The evolutionary taxonomy being based on Linnaean taxonomic ranks, the two terms are largely interchangeable in modern use.

Since the 1960s a trend called cladistic taxonomy (or cladistics or cladism) has emerged, arranging taxa in a hierarchical evolutionary tree, ignoring ranks. If a taxon includes all the descendants of some ancestral form, it is called monophyletic. Groups that have descendant groups removed from them (e.g. dinosaurs, with birds as offspring group) are termed paraphyletic, while groups representing more than one branch from the tree of life are called polyphyletic. A formal code of nomenclature, the International Code of Phylogenetic Nomenclature, or PhyloCode for short, is currently under development, intended to deal with names of clades. Linnaean ranks will be optional under the PhyloCode, which is intended to coexist with the current, rank-based codes.

Kingdoms and domains
From well before Linnaeus, plants and animals were considered separate Kingdoms. Linnaeus used this as the top rank, dividing the physical world into the plant, animal and mineral kingdoms. As advances in microscopy made classification of microorganisms possible, the number of kingdoms increased, five and six-kingdom systems being the most common.

Domains are a relatively new grouping. The three-domain system was first invented in 1990, but not generally accepted until later. One main characteristic of the three-domain method is the separation of Archaea and Bacteria, previously grouped into the single kingdom Bacteria (a kingdom also sometimes called Monera). Consequently, the three domains of life are conceptualized as Archaea, Bacteria, and Eukaryota (comprising the nuclei-bearing eukaryotes). A small minority of scientists add Archaea as a sixth kingdom, but do not accept the domain method.

Thomas Cavalier-Smith, who has published extensively on the classification of protists, has recently proposed that the Neomura, the clade that groups together the Archaea and Eukarya, would have evolved from Bacteria, more precisely from Actinobacteria. His classification of 2004 treats the archaebacteria as part of a subkingdom of the Kingdom Bacteria, i.e. he rejects the three-domain system entirely.

Authorities (author citation)
The name of any taxon may be followed by the "authority" for the name, that is, the name of the author who first published a valid description of it. These names are frequently abbreviated: the abbreviation "L." is universally accepted for Linnaeus, and in botany there is a regulated list of standard abbreviations (see list of botanists by author abbreviation). The system for assigning authorities is slightly different in different branches of biology: see author citation (botany) and author citation (zoology). However, it is standard that if a name or placement has been changed since the original description, the first authority's name is placed in parentheses and the authority for the new name or placement may be placed after it (usually only in botany and zoology ).

Globally Unique Identifiers for names
There is a movement within the biodiversity informatics community to provide Globally Unique Identifiers in the form of Life Science Identifiers (LSID) for all biological names. This would allow authors to cite names unambiguously in electronic media and reduce the significance of errors in the spelling of names or the abbreviation of authority names. Three large nomenclatural databases (referred to as nomenclators) have already begun this process, these are Index Fungorum, International Plant Names Index and ZooBank. Other databases, that publish taxonomic rather than nomenclatural data, have also started using LSIDs to identify taxa. The key example of this is Catalogue of Life. The next step in integration will be when these taxonomic databases include references to the nomenclatural databases using LSIDs.