Taxonomy (biology)

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For other uses, see Taxonomy (disambiguation). Taxonomy (biology)_sentence_0

"Scientific classification" redirects here. Taxonomy (biology)_sentence_1

For other uses, see Scientific classification (disambiguation). Taxonomy (biology)_sentence_2

This article is about the field of biology. Taxonomy (biology)_sentence_3

For the practice of stuffing and mounting animals, see Taxidermy. Taxonomy (biology)_sentence_4

In biology, taxonomy (from Ancient Greek (taxis) 'arrangement', and () 'method') is the scientific study of naming, defining (circumscribing) and classifying groups of biological organisms based on shared characteristics. Taxonomy (biology)_sentence_5

Organisms are grouped into taxa (singular: taxon) and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a super-group of higher rank, thus creating a taxonomic hierarchy. Taxonomy (biology)_sentence_6

The principal ranks in modern use are domain, kingdom, phylum (division is sometimes used in botany in place of phylum), class, order, family, genus, and species. Taxonomy (biology)_sentence_7

The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms. Taxonomy (biology)_sentence_8

With the advent of such fields of study as phylogenetics, cladistics, and systematics, the Linnaean system has progressed to a system of modern biological classification based on the evolutionary relationships between organisms, both living and extinct. Taxonomy (biology)_sentence_9

Definition Taxonomy (biology)_section_0

The exact definition of taxonomy varies from source to source, but the core of the discipline remains: the conception, naming, and classification of groups of organisms. Taxonomy (biology)_sentence_10

As points of reference, recent definitions of taxonomy are presented below: Taxonomy (biology)_sentence_11

Taxonomy (biology)_ordered_list_0

  1. Theory and practice of grouping individuals into species, arranging species into larger groups, and giving those groups names, thus producing a classification.Taxonomy (biology)_item_0_0
  2. A field of science (and major component of systematics) that encompasses description, identification, nomenclature, and classificationTaxonomy (biology)_item_0_1
  3. The science of classification, in biology the arrangement of organisms into a classificationTaxonomy (biology)_item_0_2
  4. "The science of classification as applied to living organisms, including study of means of formation of species, etc."Taxonomy (biology)_item_0_3
  5. "The analysis of an organism's characteristics for the purpose of classification"Taxonomy (biology)_item_0_4
  6. "Systematics studies phylogeny to provide a pattern that can be translated into the classification and names of the more inclusive field of taxonomy" (listed as a desirable but unusual definition)Taxonomy (biology)_item_0_5

The varied definitions either place taxonomy as a sub-area of systematics (definition 2), invert that relationship (definition 6), or appear to consider the two terms synonymous. Taxonomy (biology)_sentence_12

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. Taxonomy (biology)_sentence_13

For example, definition 6 is paired with the following definition of systematics that places nomenclature outside taxonomy: Taxonomy (biology)_sentence_14

Taxonomy (biology)_unordered_list_1

  • 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".Taxonomy (biology)_item_1_6

A whole set of terms including taxonomy, systematic biology, systematics, biosystematics, scientific classification, biological classification, and phylogenetics have at times had overlapping meanings – sometimes the same, sometimes slightly different, but always related and intersecting. Taxonomy (biology)_sentence_15

The broadest meaning of "taxonomy" is used here. Taxonomy (biology)_sentence_16

The term itself was introduced in 1813 by de Candolle, in his Théorie élémentaire de la botanique. Taxonomy (biology)_sentence_17

Monograph and taxonomic revision Taxonomy (biology)_section_1

A taxonomic revision or taxonomic review is a novel analysis of the variation patterns in a particular taxon. Taxonomy (biology)_sentence_18

This analysis may be executed on the basis of any combination of the various available kinds of characters, such as morphological, anatomical, palynological, biochemical and genetic. Taxonomy (biology)_sentence_19

A monograph or complete revision is a revision that is comprehensive for a taxon for the information given at a particular time, and for the entire world. Taxonomy (biology)_sentence_20

Other (partial) revisions may be restricted in the sense that they may only use some of the available character sets or have a limited spatial scope. Taxonomy (biology)_sentence_21

A revision results in a conformation of or new insights in the relationships between the subtaxa within the taxon under study, which may result in a change in the classification of these subtaxa, the identification of new subtaxa, or the merger of previous subtaxa. Taxonomy (biology)_sentence_22

Alpha and beta taxonomy Taxonomy (biology)_section_2

Not to be confused with Alpha diversity. Taxonomy (biology)_sentence_23

The term "alpha taxonomy" is primarily used today to refer to the discipline of finding, describing, and naming taxa, particularly species. Taxonomy (biology)_sentence_24

In earlier literature, the term had a different meaning, referring to morphological taxonomy, and the products of research through the end of the 19th century. Taxonomy (biology)_sentence_25

William Bertram Turrill introduced the term "alpha taxonomy" in a series of papers published in 1935 and 1937 in which he discussed the philosophy and possible future directions of the discipline of taxonomy. Taxonomy (biology)_sentence_26

Turrill thus explicitly excludes from alpha taxonomy various areas of study that he includes within taxonomy as a whole, such as ecology, physiology, genetics, and cytology. Taxonomy (biology)_sentence_27

He further excludes phylogenetic reconstruction from alpha taxonomy (pp. 365–366). Taxonomy (biology)_sentence_28

Later authors have used the term in a different sense, to mean the delimitation of species (not subspecies or taxa of other ranks), using whatever investigative techniques are available, and including sophisticated computational or laboratory techniques. Taxonomy (biology)_sentence_29

Thus, Ernst Mayr in 1968 defined "beta taxonomy" as the classification of ranks higher than species. Taxonomy (biology)_sentence_30

Microtaxonomy and macrotaxonomy Taxonomy (biology)_section_3

Main article: Species problem Taxonomy (biology)_sentence_31

How species should be defined in a particular group of organisms gives rise to practical and theoretical problems that are referred to as the species problem. Taxonomy (biology)_sentence_32

The scientific work of deciding how to define species has been called microtaxonomy. Taxonomy (biology)_sentence_33

By extension, macrotaxonomy is the study of groups at the higher taxonomic ranks subgenus and above. Taxonomy (biology)_sentence_34

History Taxonomy (biology)_section_4

While some descriptions of taxonomic history attempt to date taxonomy to ancient civilizations, a truly scientific attempt to classify organisms did not occur until the 18th century. Taxonomy (biology)_sentence_35

Earlier works were primarily descriptive and focused on plants that were useful in agriculture or medicine. Taxonomy (biology)_sentence_36

There are a number of stages in this scientific thinking. Taxonomy (biology)_sentence_37

Early taxonomy was based on arbitrary criteria, the so-called "artificial systems", including Linnaeus's system of sexual classification. Taxonomy (biology)_sentence_38

Later came systems based on a more complete consideration of the characteristics of taxa, referred to as "natural systems", such as those of de Jussieu (1789), de Candolle (1813) and Bentham and Hooker (1862–1863). Taxonomy (biology)_sentence_39

These were pre-evolutionary in thinking. Taxonomy (biology)_sentence_40

The publication of Charles Darwin's On the Origin of Species (1859) led to new ways of thinking about classification based on evolutionary relationships. Taxonomy (biology)_sentence_41

This was the concept of phyletic systems, from 1883 onwards. Taxonomy (biology)_sentence_42

This approach was typified by those of Eichler (1883) and Engler (1886–1892). Taxonomy (biology)_sentence_43

The advent of molecular genetics and statistical methodology allowed the creation of the modern era of "phylogenetic systems" based on cladistics, rather than morphology alone. Taxonomy (biology)_sentence_44

Pre-Linnaean Taxonomy (biology)_section_5

Early taxonomists Taxonomy (biology)_section_6

Naming and classifying our surroundings has probably been taking place as long as mankind has been able to communicate. Taxonomy (biology)_sentence_45

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. Taxonomy (biology)_sentence_46

Medicinal plant illustrations show up in Egyptian wall paintings from c. 1500 BC, indicating that the uses of different species were understood and that a basic taxonomy was in place. Taxonomy (biology)_sentence_47

Ancient times Taxonomy (biology)_section_7

Further information: Aristotle's biology § Classification Taxonomy (biology)_sentence_48

Organisms were first classified by Aristotle (Greece, 384–322 BC) during his stay on the Island of Lesbos. Taxonomy (biology)_sentence_49

He classified beings by their parts, or in modern terms attributes, such as having live birth, having four legs, laying eggs, having blood, or being warm-bodied. Taxonomy (biology)_sentence_50

He divided all living things into two groups: plants and animals. Taxonomy (biology)_sentence_51

Some of his groups of animals, such as Anhaima (animals without blood, translated as invertebrates) and Enhaima (animals with blood, roughly the vertebrates), as well as groups like the sharks and cetaceans, are still commonly used today. Taxonomy (biology)_sentence_52

His student Theophrastus (Greece, 370–285 BC) carried on this tradition, mentioning some 500 plants and their uses in his Historia Plantarum. Taxonomy (biology)_sentence_53

Again, several plant groups currently still recognized can be traced back to Theophrastus, such as Cornus, Crocus, and Narcissus. Taxonomy (biology)_sentence_54

Medieval Taxonomy (biology)_section_8

Taxonomy in the Middle Ages was largely based on the Aristotelian system, with additions concerning the philosophical and existential order of creatures. Taxonomy (biology)_sentence_55

This included concepts such as the Great chain of being in the Western scholastic tradition, again deriving ultimately from Aristotle. Taxonomy (biology)_sentence_56

Aristotelian system did not classify plants or fungi, due to the lack of microscope at the time, as his ideas were based on arranging the complete world in a single continuum, as per the scala naturae (the Natural Ladder). Taxonomy (biology)_sentence_57

This, as well, was taken into consideration in the Great chain of being. Taxonomy (biology)_sentence_58

Advances were made by scholars such as Procopius, Timotheos of Gaza, Demetrios Pepagomenos, and Thomas Aquinas. Taxonomy (biology)_sentence_59

Medieval thinkers used abstract philosophical and logical categorizations more suited to abstract philosophy than to pragmatic taxonomy. Taxonomy (biology)_sentence_60

Renaissance and Early Modern Taxonomy (biology)_section_9

During the Renaissance, the Age of Reason, and the Enlightenment, categorizing organisms became more prevalent, and taxonomic works became ambitious enough to replace the ancient texts. Taxonomy (biology)_sentence_61

This is sometimes credited to the development of sophisticated optical lenses, which allowed the morphology of organisms to be studied in much greater detail. Taxonomy (biology)_sentence_62

One of the earliest authors to take advantage of this leap in technology was the Italian physician Andrea Cesalpino (1519–1603), who has been called "the first taxonomist". Taxonomy (biology)_sentence_63

His magnum opus De Plantis came out in 1583, and described more than 1500 plant species. Taxonomy (biology)_sentence_64

Two large plant families that he first recognized are still in use today: the Asteraceae and Brassicaceae. Taxonomy (biology)_sentence_65

Then in the 17th century John Ray (England, 1627–1705) wrote many important taxonomic works. Taxonomy (biology)_sentence_66

Arguably his greatest accomplishment was Methodus Plantarum Nova (1682), in which he published details of over 18,000 plant species. Taxonomy (biology)_sentence_67

At the time, his classifications were perhaps the most complex yet produced by any taxonomist, as he based his taxa on many combined characters. Taxonomy (biology)_sentence_68

The next major taxonomic works were produced by Joseph Pitton de Tournefort (France, 1656–1708). Taxonomy (biology)_sentence_69

His work from 1700, Institutiones Rei Herbariae, included more than 9000 species in 698 genera, which directly influenced Linnaeus, as it was the text he used as a young student. Taxonomy (biology)_sentence_70

The Linnaean era Taxonomy (biology)_section_10

Main article: Linnaean taxonomy Taxonomy (biology)_sentence_71

The Swedish botanist Carl Linnaeus (1707–1778) ushered in a new era of taxonomy. Taxonomy (biology)_sentence_72

With his major works Systema Naturae 1st Edition in 1735, Species Plantarum in 1753, and Systema Naturae 10th Edition, he revolutionized modern taxonomy. Taxonomy (biology)_sentence_73

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. Taxonomy (biology)_sentence_74

He not only introduced the standard of class, order, genus, and species, but also made it possible to identify plants and animals from his book, by using the smaller parts of the flower. Taxonomy (biology)_sentence_75

Thus the Linnaean system was born, and is still used in essentially the same way today as it was in the 18th century. Taxonomy (biology)_sentence_76

Currently, plant and animal taxonomists regard Linnaeus' work as the "starting point" for valid names (at 1753 and 1758 respectively). Taxonomy (biology)_sentence_77

Names published before these dates are referred to as "pre-Linnaean", and not considered valid (with the exception of spiders published in Svenska Spindlar). Taxonomy (biology)_sentence_78

Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean. Taxonomy (biology)_sentence_79

Modern system of classification Taxonomy (biology)_section_11

Main articles: Evolutionary taxonomy and Phylogenetic nomenclature Taxonomy (biology)_sentence_80

Whereas Linnaeus aimed simply to create readily identifiable taxa, 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 On the Origin of Species was published. Taxonomy (biology)_sentence_81

Among early works exploring the idea of a transmutation of species were Erasmus Darwin's 1796 Zoönomia and Jean-Baptiste Lamarck's Philosophie Zoologique of 1809. Taxonomy (biology)_sentence_82

The idea was popularized in the Anglophone world by the speculative but widely read Vestiges of the Natural History of Creation, published anonymously by Robert Chambers in 1844. Taxonomy (biology)_sentence_83

With Darwin's theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle of common descent. Taxonomy (biology)_sentence_84

Tree of life representations became popular in scientific works, with known fossil groups incorporated. Taxonomy (biology)_sentence_85

One of the first modern groups tied to fossil ancestors was birds. Taxonomy (biology)_sentence_86

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. Taxonomy (biology)_sentence_87

The resulting description, that of dinosaurs "giving rise to" or being "the ancestors of" birds, is the essential hallmark of evolutionary taxonomic thinking. Taxonomy (biology)_sentence_88

As more and more fossil groups were found and recognized in the late 19th and early 20th centuries, palaeontologists worked to understand the history of animals through the ages by linking together known groups. Taxonomy (biology)_sentence_89

With the modern evolutionary synthesis of the early 1940s, an essentially modern understanding of the evolution of the major groups was in place. Taxonomy (biology)_sentence_90

As evolutionary taxonomy is based on Linnaean taxonomic ranks, the two terms are largely interchangeable in modern use. Taxonomy (biology)_sentence_91

The cladistic method has emerged since the 1960s. Taxonomy (biology)_sentence_92

In 1958, Julian Huxley used the term clade. Taxonomy (biology)_sentence_93

Later, in 1960, Cain and Harrison introduced the term cladistic. Taxonomy (biology)_sentence_94

The salient feature is arranging taxa in a hierarchical evolutionary tree, ignoring ranks. Taxonomy (biology)_sentence_95

A taxon is called monophyletic, if it includes all the descendants of an ancestral form. Taxonomy (biology)_sentence_96

Groups that have descendant groups removed from them are termed paraphyletic, while groups representing more than one branch from the tree of life are called polyphyletic. Taxonomy (biology)_sentence_97

The International Code of Phylogenetic Nomenclature or PhyloCode is intended to regulate the formal naming of clades. Taxonomy (biology)_sentence_98

Linnaean ranks will be optional under the PhyloCode, which is intended to coexist with the current, rank-based codes. Taxonomy (biology)_sentence_99

Kingdoms and domains Taxonomy (biology)_section_12

Main article: Kingdom (biology) Taxonomy (biology)_sentence_100

Well before Linnaeus, plants and animals were considered separate Kingdoms. Taxonomy (biology)_sentence_101

Linnaeus used this as the top rank, dividing the physical world into the plant, animal and mineral kingdoms. Taxonomy (biology)_sentence_102

As advances in microscopy made classification of microorganisms possible, the number of kingdoms increased, five- and six-kingdom systems being the most common. Taxonomy (biology)_sentence_103

Domains are a relatively new grouping. Taxonomy (biology)_sentence_104

First proposed in 1977, Carl Woese's three-domain system was not generally accepted until later. Taxonomy (biology)_sentence_105

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), with the Eukaryota for all organisms whose cells contain a nucleus. Taxonomy (biology)_sentence_106

A small number of scientists include a sixth kingdom, Archaea, but do not accept the domain method. Taxonomy (biology)_sentence_107

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 Eucarya, would have evolved from Bacteria, more precisely from Actinobacteria. Taxonomy (biology)_sentence_108

His 2004 classification treated the archaeobacteria as part of a subkingdom of the kingdom Bacteria, i.e., he rejected the three-domain system entirely. Taxonomy (biology)_sentence_109

Stefan Luketa in 2012 proposed a five "dominion" system, adding Prionobiota (acellular and without nucleic acid) and Virusobiota (acellular but with nucleic acid) to the traditional three domains. Taxonomy (biology)_sentence_110

Recent comprehensive classifications Taxonomy (biology)_section_13

Partial classifications exist for many individual groups of organisms and are revised and replaced as new information becomes available; however, comprehensive, published treatments of most or all life are rarer; recent examples are that of Adl et al., 2012 and 2019, which covers eukaryotes only with an emphasis on protists, and Ruggiero et al., 2015, covering both eukaryotes and prokaryotes to the rank of Order, although both exclude fossil representatives. Taxonomy (biology)_sentence_111

A separate compilation (Ruggiero, 2014) covers extant taxa to the rank of family. Taxonomy (biology)_sentence_112

Other, database-driven treatments include the Encyclopedia of Life, the Global Biodiversity Information Facility, the NCBI taxonomy database, the Interim Register of Marine and Nonmarine Genera, the Open Tree of Life, and the Catalogue of Life. Taxonomy (biology)_sentence_113

The Paleobiology Database is a resource for fossils. Taxonomy (biology)_sentence_114

Application Taxonomy (biology)_section_14

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. Taxonomy (biology)_sentence_115

Because taxonomy aims to describe and organize life, the work conducted by taxonomists is essential for the study of biodiversity and the resulting field of conservation biology. Taxonomy (biology)_sentence_116

Classifying organisms Taxonomy (biology)_section_15

Main article: Taxonomic rank Taxonomy (biology)_sentence_117

Biological classification is a critical component of the taxonomic process. Taxonomy (biology)_sentence_118

As a result, it informs the user as to what the relatives of the taxon are hypothesized to be. Taxonomy (biology)_sentence_119

Biological classification uses taxonomic ranks, including among others (in order from most inclusive to least inclusive): Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species, and Strain. Taxonomy (biology)_sentence_120

Taxonomic descriptions Taxonomy (biology)_section_16

See also: Species description Taxonomy (biology)_sentence_121

The "definition" of a taxon is encapsulated by its description or its diagnosis or by both combined. Taxonomy (biology)_sentence_122

There are no set rules governing the definition of taxa, but the naming and publication of new taxa is governed by sets of rules. Taxonomy (biology)_sentence_123

In zoology, the nomenclature for the more commonly used ranks (superfamily to subspecies), is regulated by the International Code of Zoological Nomenclature (ICZN Code). Taxonomy (biology)_sentence_124

In the fields of phycology, mycology, and botany, the naming of taxa is governed by the International Code of Nomenclature for algae, fungi, and plants (ICN). Taxonomy (biology)_sentence_125

The initial description of a taxon involves five main requirements: Taxonomy (biology)_sentence_126

Taxonomy (biology)_ordered_list_2

  1. The taxon must be given a name based on the 26 letters of the Latin alphabet (a binomial for new species, or uninomial for other ranks).Taxonomy (biology)_item_2_7
  2. The name must be unique (i.e. not a homonym).Taxonomy (biology)_item_2_8
  3. The description must be based on at least one name-bearing type specimen.Taxonomy (biology)_item_2_9
  4. It should include statements about appropriate attributes either to describe (define) the taxon or to differentiate it from other taxa (the diagnosis, ICZN Code, Article 13.1.1, ICN, Article 38). Both codes deliberately separate defining the content of a taxon (its circumscription) from defining its name.Taxonomy (biology)_item_2_10
  5. These first four requirements must be published in a work that is obtainable in numerous identical copies, as a permanent scientific record.Taxonomy (biology)_item_2_11

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. Taxonomy (biology)_sentence_127

Author citation Taxonomy (biology)_section_17

Main articles: Author citation (botany) and Author citation (zoology) Taxonomy (biology)_sentence_128

An "authority" may be placed after a scientific name. Taxonomy (biology)_sentence_129

The authority is the name of the scientist or scientists who first validly published the name. Taxonomy (biology)_sentence_130

For example, in 1758 Linnaeus gave the Asian elephant the scientific name Elephas maximus, so the name is sometimes written as "Elephas maximus Linnaeus, 1758". Taxonomy (biology)_sentence_131

The names of authors are frequently abbreviated: the abbreviation L., for Linnaeus, is commonly used. Taxonomy (biology)_sentence_132

In botany, there is, in fact, a regulated list of standard abbreviations (see list of botanists by author abbreviation). Taxonomy (biology)_sentence_133

The system for assigning authorities differs slightly between botany and zoology. Taxonomy (biology)_sentence_134

However, it is standard that if the genus of a species has been changed since the original description, the original authority's name is placed in parentheses. Taxonomy (biology)_sentence_135

Phenetics Taxonomy (biology)_section_18

Main article: Phenetics Taxonomy (biology)_sentence_136

In phenetics, also known as taximetrics, or numerical taxonomy, organisms are classified based on overall similarity, regardless of their phylogeny or evolutionary relationships. Taxonomy (biology)_sentence_137

It results in a measure of evolutionary "distance" between taxa. Taxonomy (biology)_sentence_138

Phenetic methods have become relatively rare in modern times, largely superseded by cladistic analyses, as phenetic methods do not distinguish common ancestral (or plesiomorphic) traits from new common (or apomorphic) traits. Taxonomy (biology)_sentence_139

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. Taxonomy (biology)_sentence_140

Databases Taxonomy (biology)_section_19

Main article: Taxonomic database Taxonomy (biology)_sentence_141

Modern taxonomy uses database technologies to search and catalogue classifications and their documentation. Taxonomy (biology)_sentence_142

While there is no commonly used database, there are comprehensive databases such as the Catalogue of Life, which attempts to list every documented species. Taxonomy (biology)_sentence_143

The catalogue listed 1.64 million species for all kingdoms as of April 2016, claiming coverage of more than three quarters of the estimated species known to modern science. Taxonomy (biology)_sentence_144

See also Taxonomy (biology)_section_20

Credits to the contents of this page go to the authors of the corresponding Wikipedia page: en.wikipedia.org/wiki/Taxonomy (biology).