In
biology
Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary i ...
, taxonomy () is the
scientific
Science is a systematic endeavor that builds and organizes knowledge in the form of testable explanations and predictions about the universe.
Science may be as old as the human species, and some of the earliest archeological evidence for ...
study of naming, defining (
circumscribing) and classifying groups of biological
organism
In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and ...
s based on shared characteristics. Organisms are grouped into
taxa
In biology, a taxon (back-formation from ''taxonomy''; plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular nam ...
(singular: taxon) and these groups are given a
taxonomic rank
In biological classification, taxonomic rank is the relative level of a group of organisms (a taxon) in an ancestral or hereditary hierarchy. A common system consists of species, genus, family (biology), family, order (biology), order, class (b ...
; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are
domain
Domain may refer to:
Mathematics
*Domain of a function, the set of input values for which the (total) function is defined
**Domain of definition of a partial function
**Natural domain of a partial function
**Domain of holomorphy of a function
* Do ...
,
kingdom
Kingdom commonly refers to:
* A monarchy ruled by a king or queen
* Kingdom (biology), a category in biological taxonomy
Kingdom may also refer to:
Arts and media Television
* ''Kingdom'' (British TV series), a 2007 British television drama s ...
,
phylum
In biology, a phylum (; plural: phyla) is a level of classification or taxonomic rank below kingdom and above class. Traditionally, in botany the term division has been used instead of phylum, although the International Code of Nomenclature f ...
(''division'' is sometimes used in botany in place of ''phylum''),
class
Class or The Class may refer to:
Common uses not otherwise categorized
* Class (biology), a taxonomic rank
* Class (knowledge representation), a collection of individuals or objects
* Class (philosophy), an analytical concept used differentl ...
,
order
Order, ORDER or Orders may refer to:
* Categorization, the process in which ideas and objects are recognized, differentiated, and understood
* Heterarchy, a system of organization wherein the elements have the potential to be ranked a number of d ...
,
family
Family (from la, familia) is a Social group, group of people related either by consanguinity (by recognized birth) or Affinity (law), affinity (by marriage or other relationship). The purpose of the family is to maintain the well-being of its ...
,
genus
Genus ( plural genera ) is a taxonomic rank used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In the hierarchy of biological classification, genus com ...
, and
species
In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...
. The Swedish botanist
Carl Linnaeus
Carl Linnaeus (; 23 May 1707 – 10 January 1778), also known after his ennoblement in 1761 as Carl von Linné Blunt (2004), p. 171. (), was a Swedish botanist, zoologist, taxonomist, and physician who formalised binomial nomenclature, the ...
is regarded as the founder of the current system of taxonomy, as he developed a ranked system known as
Linnaean taxonomy
Linnaean taxonomy can mean either of two related concepts:
# The particular form of biological classification (taxonomy) set up by Carl Linnaeus, as set forth in his ''Systema Naturae'' (1735) and subsequent works. In the taxonomy of Linnaeus t ...
for categorizing organisms and
binomial nomenclature
In taxonomy, binomial nomenclature ("two-term naming system"), also called nomenclature ("two-name naming system") or binary nomenclature, is a formal system of naming species of living things by giving each a name composed of two parts, bot ...
for naming organisms.
With advances in the theory, data and analytical technology of biological systematics, the Linnaean system has transformed into a system of modern biological classification intended to reflect the
evolution
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
ary relationships among organisms, both living and extinct.
Definition
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.
As points of reference, recent definitions of taxonomy are presented below:
# Theory and practice of grouping individuals into species, arranging species into larger groups, and giving those groups names, thus producing a classification.
# A field of science (and a major component of
systematics
Biological systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: cladograms, phylogenetic tre ...
) that encompasses description, identification,
nomenclature
Nomenclature (, ) is a system of names or terms, or the rules for forming these terms in a particular field of arts or sciences. The principles of naming vary from the relatively informal naming conventions, conventions of everyday speech to the i ...
, and classification
# The science of classification, in biology the arrangement of organisms into a classification
# "The science of classification as applied to living organisms, including the study of means of formation of species, etc."
# "The analysis of an organism's characteristics for the purpose of classification"
# "Systematics studies
phylogeny
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...
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)
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. There is some disagreement as to whether
biological nomenclature
Nomenclature codes or codes of nomenclature are the various rulebooks that govern biological taxonomic nomenclature, each in their own broad field of organisms. To an end-user who only deals with names of species, with some awareness that species ...
is considered a part of taxonomy (definitions 1 and 2), or a part of systematics outside taxonomy.
For example, definition 6 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".
In 1970, Michener ''et al.'' defined "systematic biology" and "taxonomy" (terms that are often confused and used interchangeably) in relation to one another as follows:
Systematic biology (hereafter called simply systematics) is the field that (a) provides scientific names for organisms, (b) describes them, (c) preserves collections of them, (d) provides classifications for the organisms, keys for their identification, and data on their distributions, (e) investigates their evolutionary histories, and (f) considers their environmental adaptations. This is a field with a long history that in recent years has experienced a notable renaissance, principally with respect to theoretical content. Part of the theoretical material has to do with evolutionary areas (topics e and f above), the rest relates especially to the problem of classification. Taxonomy is that part of Systematics concerned with topics (a) to (d) above.
A whole set of terms including taxonomy, systematic biology,
systematics
Biological systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: cladograms, phylogenetic tre ...
, scientific classification, biological classification, and
phylogenetics
In biology, phylogenetics (; from Greek language, Greek wikt:φυλή, φυλή/wikt:φῦλον, φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary his ...
have at times had overlapping meanings – sometimes the same, sometimes slightly different, but always related and intersecting.
The broadest meaning of "taxonomy" is used here. The term itself was introduced in 1813 by
de Candolle
Augustin Pyramus (or Pyrame) de Candolle (, , ; 4 February 17789 September 1841) was a Swiss botanist. René Louiche Desfontaines launched de Candolle's botanical career by recommending him at a herbarium. Within a couple of years de Candolle ...
, in his ''
Théorie élémentaire de la botanique''.
John Lindley
John Lindley FRS (5 February 1799 – 1 November 1865) was an English botanist, gardener and orchidologist.
Early years
Born in Catton, near Norwich, England, John Lindley was one of four children of George and Mary Lindley. George Lindley w ...
provided an early definition of systematics in 1830, although he wrote of "systematic botany" rather than using the term "systematics". Europeans tend to use the terms "systematics" and "biosystematics" for the study of biodiversity as a whole, whereas North Americans tend to use "taxonomy" more frequently. However, taxonomy, and in particular
alpha taxonomy
In biology, taxonomy () is the science, scientific study of naming, defining (Circumscription (taxonomy), circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxon, taxa (s ...
, is more specifically the identification, description, and naming (i.e., nomenclature) of organisms,
while "classification" focuses on placing organisms within hierarchical groups that show their relationships to other organisms.
Monograph and taxonomic revision
A taxonomic revision or taxonomic review is a novel analysis of the variation patterns in a particular
taxon
In biology, a taxon (back-formation from ''taxonomy''; plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular nam ...
. This analysis may be executed on the basis of any combination of the various available kinds of characters, such as morphological,
anatomical
Anatomy () is the branch of biology concerned with the study of the structure of organisms and their parts. Anatomy is a branch of natural science that deals with the structural organization of living things. It is an old science, having it ...
,
palynological
Palynology is the "study of dust" (from grc-gre, παλύνω, palynō, "strew, sprinkle" and ''-logy'') or of "particles that are strewn". A classic palynologist analyses particulate samples collected from the air, from water, or from deposit ...
,
biochemical
Biochemistry or biological chemistry is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology an ...
and
genetic. A
monograph
A monograph is a specialist work of writing (in contrast to reference works) or exhibition on a single subject or an aspect of a subject, often by a single author or artist, and usually on a scholarly subject.
In library cataloging, ''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. 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. A revision results in a conformation of or new insights in the relationships between the subtaxa within the taxon under study, which may lead to a change in the classification of these subtaxa, the identification of new subtaxa, or the merger of previous subtaxa.
Taxonomic characters
Taxonomic characters are the taxonomic attributes that can be used to provide the evidence from which relationships (the
phylogeny
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...
) between taxa are inferred.
Kinds of taxonomic characters include:
*
Morphological characters
** General external
morphology
Morphology, from the Greek and meaning "study of shape", may refer to:
Disciplines
* Morphology (archaeology), study of the shapes or forms of artifacts
* Morphology (astronomy), study of the shape of astronomical objects such as nebulae, galaxies ...
** Special structures (e.g.,
genitalia
A sex organ (or reproductive organ) is any part of an animal or plant that is involved in sexual reproduction. The reproductive organs together constitute the reproductive system. In animals, the testis in the male, and the ovary in the female, a ...
)
** Internal morphology (
anatomy
Anatomy () is the branch of biology concerned with the study of the structure of organisms and their parts. Anatomy is a branch of natural science that deals with the structural organization of living things. It is an old science, having its ...
)
**
Embryology
Embryology (from Greek ἔμβρυον, ''embryon'', "the unborn, embryo"; and -λογία, '' -logia'') is the branch of animal biology that studies the prenatal development of gametes (sex cells), fertilization, and development of embryos and ...
**
Karyology
A karyotype is the general appearance of the complete set of metaphase chromosomes in the cells of a species or in an individual organism, mainly including their sizes, numbers, and shapes. Karyotyping is the process by which a karyotype is disce ...
and other
cytological
Cell biology (also cellular biology or cytology) is a branch of biology that studies the structure, function, and behavior of cells. All living organisms are made of cells. A cell is the basic unit of life that is responsible for the living and ...
factors
*
Physiological
Physiology (; ) is the scientific study of functions and mechanisms in a living system. As a sub-discipline of biology, physiology focuses on how organisms, organ systems, individual organs, cells, and biomolecules carry out the chemical ...
characters
**
Metabolic factors
** Body secretions
** Genic sterility factors
*
Molecular
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioche ...
characters
** Immunological distance
** Electrophoretic differences
** Amino acid sequences of proteins
** DNA hybridization
** DNA and RNA sequences
** Restriction endonuclease analyses
** Other molecular differences
*
Behavioral
Behavior (American English) or behaviour (British English) is the range of actions and mannerisms made by individuals, organisms, systems or artificial entities in some environment. These systems can include other systems or organisms as well ...
characters
** Courtship and other ethological isolating mechanisms
** Other behavior patterns
*
Ecological
Ecology () is the study of the relationships between living organisms, including humans, and their physical environment. Ecology considers organisms at the individual, population, community, ecosystem, and biosphere level. Ecology overlaps wi ...
characters
** Habit and habitats
** Food
** Seasonal variations
** Parasites and hosts
*
Geographic
Geography (from Greek: , ''geographia''. Combination of Greek words ‘Geo’ (The Earth) and ‘Graphien’ (to describe), literally "earth description") is a field of science devoted to the study of the lands, features, inhabitants, and ...
characters
** General
biogeographic distribution patterns
**
Sympatric
In biology, two related species or populations are considered sympatric when they exist in the same geographic area and thus frequently encounter one another. An initially interbreeding population that splits into two or more distinct species sh ...
-
allopatric
Allopatric speciation () – also referred to as geographic speciation, vicariant speciation, or its earlier name the dumbbell model – is a mode of speciation that occurs when biological populations become geographically isolated from ...
relationship of populations
Alpha and beta taxonomy
The term "alpha taxonomy" is primarily used to refer to the discipline of finding, describing, and naming
taxa
In biology, a taxon (back-formation from ''taxonomy''; plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular nam ...
, particularly species.
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.
William Bertram Turrill
William Bertram Turrill FRS OBE FLS (14 June 1890 – 15 December 1961) was an English botanist.
Education
He was born in Woodstock, Oxfordshire to William Banbury and Thirza Mary (née Homan) Turrill and educated at the Woodstock National S ...
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.
... there is an increasing desire amongst taxonomists to consider their problems from wider viewpoints, to investigate the possibilities of closer co-operation with their cytological, ecological and genetics colleagues and to acknowledge that some revision or expansion, perhaps of a drastic nature, of their aims and methods, may be desirable ... Turrill (1935) has suggested that while accepting the older invaluable taxonomy, based on structure, and conveniently designated "alpha", it is possible to glimpse a far-distant taxonomy built upon as wide a basis of morphological and physiological facts as possible, and one in which "place is found for all observational and experimental data relating, even if indirectly, to the constitution, subdivision, origin, and behaviour of species and other taxonomic groups". Ideals can, it may be said, never be completely realized. They have, however, a great value of acting as permanent stimulants, and if we have some, even vague, ideal of an "omega" taxonomy we may progress a little way down the Greek alphabet. Some of us please ourselves by thinking we are now groping in a "beta" taxonomy.
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. He further excludes phylogenetic reconstruction from alpha taxonomy.
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.
Thus,
Ernst Mayr
Ernst Walter Mayr (; 5 July 1904 – 3 February 2005) was one of the 20th century's leading evolutionary biologists. He was also a renowned Taxonomy (biology), taxonomist, tropical explorer, ornithologist, Philosophy of biology, philosopher o ...
in 1968 defined "beta taxonomy" as the classification of ranks higher than species.
An understanding of the biological meaning of variation and of the evolutionary origin of groups of related species is even more important for the second stage of taxonomic activity, the sorting of species into groups of relatives ("taxa") and their arrangement in a hierarchy of higher categories. This activity is what the term classification denotes; it is also referred to as "beta taxonomy".
Microtaxonomy and macrotaxonomy
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
The species problem is the set of questions that arises when biologists attempt to define what a species is. Such a definition is called a species concept; there are at least 26 recognized species concepts. A species concept that works well for se ...
. The scientific work of deciding how to define species has been called microtaxonomy.
By extension, macrotaxonomy is the study of groups at the higher
taxonomic rank
In biological classification, taxonomic rank is the relative level of a group of organisms (a taxon) in an ancestral or hereditary hierarchy. A common system consists of species, genus, family (biology), family, order (biology), order, class (b ...
s subgenus and above,
or simply in clades that include more than one taxon considered a species, expressed in terms of
phylogenetic nomenclature
Phylogenetic nomenclature is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names as explained below. This contrasts with the traditional approach, in which taxon names are defined by a '' type'', which ...
.
History
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, with the possible exception of Aristotle, whose works hint at a taxonomy.
Earlier works were primarily descriptive and focused on plants that were useful in agriculture or medicine.
There are a number of stages in this scientific thinking. Early taxonomy was based on arbitrary criteria, the so-called "artificial systems", including
Linnaeus
Carl Linnaeus (; 23 May 1707 – 10 January 1778), also known after his ennoblement in 1761 as Carl von Linné Blunt (2004), p. 171. (), was a Swedish botanist, zoologist, taxonomist, and physician who formalised binomial nomenclature, the ...
's system of sexual classification for plants (Linnaeus's 1735 classification of animals was entitled "
Systema Naturae
' (originally in Latin written ' with the ligature æ) is one of the major works of the Swedish botanist, zoologist and physician Carl Linnaeus (1707–1778) and introduced the Linnaean taxonomy. Although the system, now known as binomial nomen ...
" ("the System of Nature"), implying that he, at least, believed that it was more than an "artificial system").
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
De Jussieu, the name of a French family which came into prominence towards the close of the sixteenth century, and was known for a century and a half for the botanists it produced. The following are its more eminent members:
*Antoine de Jussieu ( ...
(1789), de Candolle (1813) and
Bentham and Hooker
A taxonomic system, the Bentham & Hooker system for seed plants, was published in Bentham and Hooker's ''Genera plantarum ad exemplaria imprimis in herbariis kewensibus servata definita'' in three volumes between 1862 and 1883.
George Bentham (18 ...
(1862–1863). These classifications described empirical patterns and were pre-
evolution
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
ary in thinking.
The publication of
Charles Darwin
Charles Robert Darwin ( ; 12 February 1809 – 19 April 1882) was an English naturalist, geologist, and biologist, widely known for his contributions to evolutionary biology. His proposition that all species of life have descended fr ...
's ''
On the Origin of Species
''On the Origin of Species'' (or, more completely, ''On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life''),The book's full original title was ''On the Origin of Species by Me ...
'' (1859) led to a new explanation for classifications, based on evolutionary relationships. This was the concept of
phyletic
In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...
systems, from 1883 onwards. This approach was typified by those of
Eichler (1883) and
Engler (1886–1892).
The advent of
cladistic
Cladistics (; ) is an approach to biological classification in which organisms are categorized in groups (" clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived char ...
methodology in the 1970s led to classifications based on the sole criterion of
monophyly
In cladistics for a group of organisms, monophyly is the condition of being a clade—that is, a group of taxa composed only of a common ancestor (or more precisely an ancestral population) and all of its lineal descendants. Monophyletic grou ...
, supported by the presence of
synapomorphies
In phylogenetics, an apomorphy (or derived trait) is a novel character or character state that has evolved from its ancestral form (or plesiomorphy). A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to have ...
. Since then, the evidentiary basis has been expanded with data from
molecular genetics
Molecular genetics is a sub-field of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms. Molecular genetics often applies an "investigative approach" to determine the ...
that for the most part complements traditional
morphology
Morphology, from the Greek and meaning "study of shape", may refer to:
Disciplines
* Morphology (archaeology), study of the shapes or forms of artifacts
* Morphology (astronomy), study of the shape of astronomical objects such as nebulae, galaxies ...
.
Pre-Linnaean
Early taxonomists
Naming and classifying human surroundings likely began with the onset of language. Distinguishing poisonous plants from edible plants is integral to the survival of human communities. Medicinal plant illustrations show up in Egyptian wall paintings from , indicating that the uses of different species were understood and that a basic taxonomy was in place.
Ancient times
![Huang-Quan-Xie-sheng-zhen-qin-tu](https://upload.wikimedia.org/wikipedia/commons/b/bf/Huang-Quan-Xie-sheng-zhen-qin-tu.jpg)
Organisms were first classified by
Aristotle
Aristotle (; grc-gre, Ἀριστοτέλης ''Aristotélēs'', ; 384–322 BC) was a Greek philosopher and polymath during the Classical period in Ancient Greece. Taught by Plato, he was the founder of the Peripatetic school of phil ...
(
Greece
Greece,, or , romanized: ', officially the Hellenic Republic, is a country in Southeast Europe. It is situated on the southern tip of the Balkans, and is located at the crossroads of Europe, Asia, and Africa. Greece shares land borders with ...
, 384–322 BC) during his stay on the
Island of Lesbos.
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.
He divided all living things into two groups:
plant
Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae exclud ...
s and
animal
Animals are multicellular, eukaryotic organisms in the Kingdom (biology), biological kingdom Animalia. With few exceptions, animals Heterotroph, consume organic material, Cellular respiration#Aerobic respiration, breathe oxygen, are Motilit ...
s.
Some of his groups of animals, such as ''Anhaima'' (animals without blood, translated as
invertebrate
Invertebrates are a paraphyletic group of animals that neither possess nor develop a vertebral column (commonly known as a ''backbone'' or ''spine''), derived from the notochord. This is a grouping including all animals apart from the chordate ...
s) and ''Enhaima'' (animals with blood, roughly the
vertebrate
Vertebrates () comprise all animal taxa within the subphylum Vertebrata () ( chordates with backbones), including all mammals, birds, reptiles, amphibians, and fish. Vertebrates represent the overwhelming majority of the phylum Chordata, ...
s), as well as groups like the
shark
Sharks are a group of elasmobranch fish characterized by a cartilaginous skeleton, five to seven gill slits on the sides of the head, and pectoral fins that are not fused to the head. Modern sharks are classified within the clade Selachimo ...
s and
cetacean
Cetacea (; , ) is an infraorder of aquatic mammals that includes whales, dolphins, and porpoises. Key characteristics are their fully aquatic lifestyle, streamlined body shape, often large size and exclusively carnivorous diet. They propel them ...
s, are commonly used.
His student
Theophrastus
Theophrastus (; grc-gre, Θεόφραστος ; c. 371c. 287 BC), a Greek philosopher and the successor to Aristotle in the Peripatetic school. He was a native of Eresos in Lesbos.Gavin Hardy and Laurence Totelin, ''Ancient Botany'', Routledge ...
(Greece, 370–285 BC) carried on this tradition, mentioning some 500 plants and their uses in his ''
Historia Plantarum
Historia may refer to:
* Historia, the local version of the History channel in Spain and Portugal
* Historia (TV channel), a Canadian French language specialty channel
* Historia (newspaper), a French monthly newspaper devoted to History topics
* ...
''. Several plant
genera
Genus ( plural genera ) is a taxonomic rank used in the biological classification of living and fossil organisms as well as viruses. In the hierarchy of biological classification, genus comes above species and below family. In binomial nomenclat ...
can be traced back to Theophrastus, such as ''
Cornus
''Cornus'' is a genus of about 30–60 species of woody plants in the family Cornaceae, commonly known as dogwoods, which can generally be distinguished by their blossoms, berries, and distinctive bark. Most are deciduous trees or shrub ...
'', ''
Crocus
''Crocus'' (; plural: crocuses or croci) is a genus of seasonal flowering plants in the family Iridaceae (iris family) comprising about 100 species of perennials growing from corms. They are low growing plants, whose flower stems remain undergro ...
'', and ''
Narcissus''.
Medieval
Taxonomy in the
Middle Ages
In the history of Europe, the Middle Ages or medieval period lasted approximately from the late 5th to the late 15th centuries, similar to the post-classical period of global history. It began with the fall of the Western Roman Empire a ...
was largely based on the
Aristotelian system
Aristotle's biology is the theory of biology, grounded in systematic observation and collection of data, mainly zoological, embodied in Aristotle's books on the science. Many of his observations were made during his stay on the island of Lesbo ...
,
with additions concerning the philosophical and existential order of creatures. This included concepts such as the
great chain of being
The great chain of being is a hierarchical structure of all matter and life, thought by medieval Christianity to have been decreed by God. The chain begins with God and descends through angels, humans, animals and plants to minerals.
The great c ...
in the Western
scholastic tradition,
again deriving ultimately from Aristotle.
The Aristotelian system did not classify plants or
fungi
A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
, due to the lack of microscopes 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).
This, as well, was taken into consideration in the great chain of being.
Advances were made by scholars such as
Procopius
Procopius of Caesarea ( grc-gre, Προκόπιος ὁ Καισαρεύς ''Prokópios ho Kaisareús''; la, Procopius Caesariensis; – after 565) was a prominent late antique Greek scholar from Caesarea Maritima. Accompanying the Roman gener ...
,
Timotheus of Gaza
Timotheus of Gaza ( el, Τιμόθεος ὁ Γαζαῖος), sometimes referred to as Timothy of Gaza, was a Greek grammarian active during the reign of Anastasius, i.e. 491–518. He is the author of a book on animals which may have been one o ...
,
Demetrios Pepagomenos Demetrios Pepagomenos or Demetrius Pepagomenus ( el, Δημήτριος Πεπαγωμένος, 1200–1300) was a Byzantine Greek savant who resided in Constantinople. He became a physician, a veterinary physician, and a naturalist..
Biography
C ...
, and
Thomas Aquinas
Thomas Aquinas, OP (; it, Tommaso d'Aquino, lit=Thomas of Aquino; 1225 – 7 March 1274) was an Italian Dominican friar and priest who was an influential philosopher, theologian and jurist in the tradition of scholasticism; he is known wi ...
. Medieval thinkers used abstract philosophical and logical categorizations more suited to abstract philosophy than to pragmatic taxonomy.
Renaissance and early modern
During the
Renaissance
The Renaissance ( , ) , from , with the same meanings. is a period in European history marking the transition from the Middle Ages to modernity and covering the 15th and 16th centuries, characterized by an effort to revive and surpass ideas ...
and the
Age of Enlightenment
The Age of Enlightenment or the Enlightenment; german: Aufklärung, "Enlightenment"; it, L'Illuminismo, "Enlightenment"; pl, Oświecenie, "Enlightenment"; pt, Iluminismo, "Enlightenment"; es, La Ilustración, "Enlightenment" was an intel ...
, categorizing organisms became more prevalent,
and taxonomic works became ambitious enough to replace the ancient texts. This is sometimes credited to the development of sophisticated optical lenses, which allowed 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 the Italian physician
Andrea Cesalpino
Andrea Cesalpino ( Latinized as Andreas Cæsalpinus) (6 June 1524 – 23 February 1603) was a Florentine physician, philosopher and botanist.
In his works he Taxonomy (biology), classified plants according to their fruits and seeds, rather th ...
(1519–1603), who has been called "the first taxonomist". His
magnum opus
A masterpiece, ''magnum opus'' (), or ''chef-d’œuvre'' (; ; ) in modern use is a creation that has been given much critical praise, especially one that is considered the greatest work of a person's career or a work of outstanding creativity, ...
''De Plantis'' came out in 1583, and described more than 1500 plant species. Two large plant families that he first recognized are in use: the
Asteraceae
The family Asteraceae, alternatively Compositae, consists of over 32,000 known species of flowering plants in over 1,900 genera within the order Asterales. Commonly referred to as the aster, daisy, composite, or sunflower family, Compositae w ...
and
Brassicaceae
Brassicaceae () or (the older) Cruciferae () is a medium-sized and economically important family of flowering plants commonly known as the mustards, the crucifers, or the cabbage family. Most are herbaceous plants, while some are shrubs. The le ...
.
In the 17th century
John Ray
John Ray FRS (29 November 1627 – 17 January 1705) was a Christian English naturalist widely regarded as one of the earliest of the English parson-naturalists. Until 1670, he wrote his name as John Wray. From then on, he used 'Ray', after ...
(
England
England is a country that is part of the United Kingdom. It shares land borders with Wales to its west and Scotland to its north. The Irish Sea lies northwest and the Celtic Sea to the southwest. It is separated from continental Europe b ...
, 1627–1705) wrote many important taxonomic works.
Arguably his greatest accomplishment was ''Methodus Plantarum Nova'' (1682), in which he published details of 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
Joseph Pitton de Tournefort (5 June 165628 December 1708) was a French botanist, notable as the first to make a clear definition of the concept of genus for plants. Botanist Charles Plumier was his pupil and accompanied him on his voyages.
Lif ...
(France, 1656–1708). 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.
Linnaean era
![Linné-Systema Naturae 1735](https://upload.wikimedia.org/wikipedia/commons/5/54/Linn%C3%A9-Systema_Naturae_1735.jpg)
The Swedish botanist
Carl Linnaeus
Carl Linnaeus (; 23 May 1707 – 10 January 1778), also known after his ennoblement in 1761 as Carl von Linné Blunt (2004), p. 171. (), was a Swedish botanist, zoologist, taxonomist, and physician who formalised binomial nomenclature, the ...
(1707–1778)
ushered in a new era of taxonomy. With his major works ''
Systema Naturae
' (originally in Latin written ' with the ligature æ) is one of the major works of the Swedish botanist, zoologist and physician Carl Linnaeus (1707–1778) and introduced the Linnaean taxonomy. Although the system, now known as binomial nomen ...
'' 1st Edition in 1735, ''
Species Plantarum
' (Latin for "The Species of Plants") is a book by Carl Linnaeus, originally published in 1753, which lists every species of plant known at the time, classified into genera. It is the first work to consistently apply binomial names and was the ...
'' 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. 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 (known as the
Linnaean system
Linnaean taxonomy can mean either of two related concepts:
# The particular form of biological classification (taxonomy) set up by Carl Linnaeus, as set forth in his '' Systema Naturae'' (1735) and subsequent works. In the taxonomy of Linnaeus ...
).
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
The book ' or ' (Swedish and Latin, respectively, for "Swedish spiders") is one of the major works of the Swedish arachnologist and entomologist Carl Alexander Clerck and was first published in Stockholm in the year 1757. It was the first compre ...
''). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean.
The digital era of taxonomy
Modern taxonomy is heavily influenced by technology such as
DNA sequencing
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. Th ...
,
bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
,
databases
In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases spa ...
, and
imaging
Imaging is the representation or reproduction of an object's form; especially a visual representation (i.e., the formation of an image).
Imaging technology is the application of materials and methods to create, preserve, or duplicate images.
...
.
Modern system of classification
![Spindle diagram](https://upload.wikimedia.org/wikipedia/commons/7/76/Spindle_diagram.jpg)
A pattern of groups nested within groups was specified by Linnaeus' classifications of plants and animals, and these patterns began to be represented as
dendrograms
A dendrogram is a diagram representing a tree. This diagrammatic representation is frequently used in different contexts:
* in hierarchical clustering, it illustrates the arrangement of the clusters produced by the corresponding analyses.
* ...
of the animal and plant
kingdoms
Kingdom commonly refers to:
* A monarchy ruled by a king or queen
* Kingdom (biology), a category in biological taxonomy
Kingdom may also refer to:
Arts and media Television
* ''Kingdom'' (British TV series), a 2007 British television drama s ...
toward the end of the 18th century, well before Charles Darwin's ''On the Origin of Species'' was published.
The pattern of the "Natural System" did not entail a generating process, such as evolution, but may have implied it, inspiring early transmutationist thinkers. Among early works exploring the idea of a
transmutation of species
Transmutation of species and transformism are unproven 18th and 19th-century evolutionary ideas about the change of one species into another that preceded Charles Darwin's theory of natural selection. The French ''Transformisme'' was a term used ...
were ''
Zoonomia
''Zoonomia; or the Laws of Organic Life'' (1794-96) is a two-volume medical work by Erasmus Darwin dealing with pathology, anatomy, psychology, and the functioning of the body. Its primary framework is one of associationist psychophysiology. The ...
'' in 1796 by
Erasmus Darwin
Erasmus Robert Darwin (12 December 173118 April 1802) was an English physician. One of the key thinkers of the Midlands Enlightenment, he was also a natural philosopher, physiologist, slave-trade abolitionist, inventor, and poet.
His poems ...
(Charles Darwin's grandfather), and
Jean-Baptiste Lamarck
Jean-Baptiste Pierre Antoine de Monet, chevalier de Lamarck (1 August 1744 – 18 December 1829), often known simply as Lamarck (; ), was a French naturalist, biologist, academic, and soldier. He was an early proponent of the idea that biologi ...
's ''
Philosophie zoologique
''Philosophie zoologique'' ("Zoological Philosophy, or Exposition with Regard to the Natural History of Animals") is an 1809 book by the French naturalist Jean-Baptiste Lamarck, in which he outlines his pre-Darwinian theory of evolution, part of ...
'' of 1809.
The idea was popularized in the Anglophone world by the speculative but widely read ''
Vestiges of the Natural History of Creation
''Vestiges of the Natural History of Creation'' is an 1844 work of speculative natural history and philosophy by Robert Chambers. Published anonymously in England, it brought together various ideas of stellar evolution with the progressive tra ...
'', published anonymously by
Robert Chambers in 1844.
With Darwin's theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle of
common descent
Common descent is a concept in evolutionary biology applicable when one species is the ancestor of two or more species later in time. All living beings are in fact descendants of a unique ancestor commonly referred to as the last universal comm ...
.
Tree of life
The tree of life is a fundamental archetype in many of the world's mythological, religious, and philosophical traditions. It is closely related to the concept of the sacred tree.Giovino, Mariana (2007). ''The Assyrian Sacred Tree: A History ...
representations became popular in scientific works, with known fossil groups incorporated. One of the first modern groups tied to fossil ancestors was birds. Using the then newly discovered fossils of ''
Archaeopteryx
''Archaeopteryx'' (; ), sometimes referred to by its German name, "" ( ''Primeval Bird''), is a genus of bird-like dinosaurs. The name derives from the ancient Greek (''archaīos''), meaning "ancient", and (''ptéryx''), meaning "feather" ...
'' and ''
Hesperornis
''Hesperornis'' (meaning "western bird") is a genus of cormorant-like bird that spanned the first half of the Campanian age of the Late Cretaceous period (83.5–78 mya). One of the lesser-known discoveries of the paleontologist O. C. Marsh in ...
'',
Thomas Henry Huxley
Thomas Henry Huxley (4 May 1825 – 29 June 1895) was an English biologist and anthropologist specialising in comparative anatomy. He has become known as "Darwin's Bulldog" for his advocacy of Charles Darwin's theory of evolution.
The storie ...
pronounced that they had evolved from dinosaurs, a group formally named by
Richard Owen
Sir Richard Owen (20 July 1804 – 18 December 1892) was an English biologist, comparative anatomist and paleontologist. Owen is generally considered to have been an outstanding naturalist with a remarkable gift for interpreting fossils.
Owe ...
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 centuries,
palaeontologists
Paleontology (), also spelled palaeontology or palæontology, is the scientific study of life that existed prior to, and sometimes including, the start of the Holocene epoch (roughly 11,700 years before present). It includes the study of fossi ...
worked to understand the history of animals through the ages by linking together known groups. With the
modern evolutionary synthesis
Modern synthesis or modern evolutionary synthesis refers to several perspectives on evolutionary biology, namely:
* Modern synthesis (20th century), the term coined by Julian Huxley in 1942 to denote the synthesis between Mendelian genetics and s ...
of the early 1940s, an essentially modern understanding of the evolution of the major groups was in place. As evolutionary taxonomy is based on Linnaean taxonomic ranks, the two terms are largely interchangeable in modern use.
The
cladistic
Cladistics (; ) is an approach to biological classification in which organisms are categorized in groups (" clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived char ...
method has emerged since the 1960s.
In 1958,
Julian Huxley
Sir Julian Sorell Huxley (22 June 1887 – 14 February 1975) was an English evolutionary biologist, eugenicist, and internationalist. He was a proponent of natural selection, and a leading figure in the mid-twentieth century modern synthesis. ...
used the term ''clade''.
Later, in 1960, Cain and Harrison introduced the term ''cladistic''.
The salient feature is arranging taxa in a hierarchical
evolutionary tree
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...
, with the desideratum that all named taxa are monophyletic.
A taxon is called monophyletic if it includes all the descendants of an ancestral form.
Groups that have descendant groups removed from them are termed
paraphyletic
In taxonomy (general), taxonomy, a group is paraphyletic if it consists of the group's most recent common ancestor, last common ancestor and most of its descendants, excluding a few Monophyly, monophyletic subgroups. The group is said to be pa ...
,
while groups representing more than one branch from the tree of life are called
polyphyletic
A polyphyletic group is an assemblage of organisms or other evolving elements that is of mixed evolutionary origin. The term is often applied to groups that share similar features known as homoplasies, which are explained as a result of converg ...
.
Monophyletic groups are recognized and diagnosed on the basis of
synapomorphies
In phylogenetics, an apomorphy (or derived trait) is a novel character or character state that has evolved from its ancestral form (or plesiomorphy). A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to have ...
, shared derived character states.
Cladistic classifications are compatible with traditional Linnean taxonomy and the Codes of
Zoological
Zoology ()The pronunciation of zoology as is usually regarded as nonstandard, though it is not uncommon. is the branch of biology that studies the animal kingdom, including the structure, embryology, evolution, classification, habits, and dis ...
and
Botanical nomenclature
Botanical nomenclature is the formal, scientific naming of plants. It is related to, but distinct from Alpha taxonomy, taxonomy. Plant taxonomy is concerned with grouping and classifying plants; botanical nomenclature then provides names for the ...
, to a certain extent. An alternative system of nomenclature, the ''
International Code of Phylogenetic Nomenclature'' or ''PhyloCode'' has been proposed, which regulates the formal naming of clades.
Linnaean ranks are optional and have no formal standing under the ''PhyloCode'', which is intended to coexist with the current, rank-based codes.
While popularity of phylogenetic nomenclature has grown steadily in the last few decades,
it remains to be seen whether a majority of systematists will eventually adopt the ''PhyloCode'' or continue using the current systems of nomenclature that have been employed (and modified, but arguably not as much as some systematists wish)
for over 250 years.
Kingdoms and domains
![Biological classification L Pengo vflip](https://upload.wikimedia.org/wikipedia/commons/a/a5/Biological_classification_L_Pengo_vflip.svg)
Well before discovery of Carl Linnaeus (Botanist) plants and animals were considered separate Kingdoms.
Linnaeus used this as the top rank, dividing the physical world into the vegetable, animal and mineral kingdoms. As advances in microscopy made the classification of microorganisms possible, the number of kingdoms increased, five- and six-kingdom systems being the most common.
Domains are a relatively new grouping. First proposed in 1977,
Carl Woese
Carl Richard Woese (; July 15, 1928 – December 30, 2012) was an American microbiologist and biophysicist. Woese is famous for defining the Archaea (a new domain of life) in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA, ...
's
three-domain system
The three-domain system is a biological classification introduced by Carl Woese, Otto Kandler, and Mark Wheelis in 1990 that divides cellular life forms into three domains, namely Archaea, Bacteria, and Eukaryota or Eukarya. The key difference fr ...
was not generally accepted until later. One main characteristic of the three-domain method is the separation of
Archaea
Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...
and
Bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
, previously grouped into the single kingdom Bacteria (a kingdom also sometimes called
Monera
Monera (/məˈnɪərə/) (Greek - μονήρης (monḗrēs), "single", "solitary") is a biological kingdom that is made up of prokaryotes. As such, it is composed of single-celled organisms that lack a nucleus.
The taxon Monera was first p ...
),
with the
Eukaryota
Eukaryotes () are organisms whose Cell (biology), cells have a cell nucleus, nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the ...
for all organisms whose cells contain a
nucleus
Nucleus ( : nuclei) is a Latin word for the seed inside a fruit. It most often refers to:
*Atomic nucleus, the very dense central region of an atom
*Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA
Nucle ...
. A small number of scientists include a sixth kingdom, Archaea, but do not accept the domain method.
Thomas Cavalier-Smith
Thomas (Tom) Cavalier-Smith, FRS, FRSC, NERC Professorial Fellow (21 October 1942 – 19 March 2021), was a professor of evolutionary biology in the Department of Zoology, at the University of Oxford.
His research has led to discov ...
, who published extensively on the classification of
protist
A protist () is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor), the exc ...
s, in 2002
proposed that the
Neomura
Neomura is a possible clade composed of the two domains of life of Archaea and Eukaryota. The group was named by Thomas Cavalier-Smith in 2002. Its name means "new walls", reflecting his hypothesis that it evolved from Bacteria, and one of t ...
, the clade that groups together the Archaea and
Eucarya, would have evolved from Bacteria, more precisely from
Actinomycetota
The ''Actinomycetota'' (or ''Actinobacteria'') are a phylum of all gram-positive bacteria. They can be terrestrial or aquatic. They are of great economic importance to humans because agriculture and forests depend on their contributions to soi ...
. His 2004 classification treated the
archaeobacteria
Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebact ...
as part of a subkingdom of the kingdom Bacteria, i.e., he rejected the three-domain system entirely.
Stefan Luketa in 2012 proposed a five "dominion" system, adding
Prion
Prions are misfolded proteins that have the ability to transmit their misfolded shape onto normal variants of the same protein. They characterize several fatal and transmissible neurodegenerative diseases in humans and many other animals. It ...
obiota (
acellular
Non-cellular life, or acellular life is life that exists without a cellular structure for at least part of its life cycle. Historically, most (descriptive) definitions of life postulated that an organism must be composed of one or more cells, ...
and without
nucleic acid
Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main cl ...
) and
Virus
A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea.
Since Dmitri Ivanovsky's 1 ...
obiota (acellular but ''with'' nucleic acid) to the traditional three domains.
Recent comprehensive classifications
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
prokaryote
A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Connec ...
s to the rank of Order, although both exclude fossil representatives.
A separate compilation (Ruggiero, 2014) covers extant taxa to the rank of Family. Other, database-driven treatments include the
Encyclopedia of Life
The ''Encyclopedia of Life'' (''EOL'') is a free, online encyclopedia intended to document all of the 1.9 million living species known to science. It is compiled from existing trusted databases curated by experts and with the assistance of non ...
, the
Global Biodiversity Information Facility
The Global Biodiversity Information Facility (GBIF) is an international organisation that focuses on making scientific data on biodiversity available via the Internet using web services. The data are provided by many institutions from around the ...
, the
NCBI taxonomy database
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...
, the
Interim Register of Marine and Nonmarine Genera
The Interim Register of Marine and Nonmarine Genera (IRMNG) is a taxonomic database which attempts to cover published genus names for all domains of life from 1758 in zoology (1753 in botany) up to the present, arranged in a single, internally c ...
, the
Open Tree of Life
The Open Tree of Life is an online phylogenetic tree of life – a collaborative effort, funded by the National Science Foundation. The first draft, including 2.3 million species, was released in September 2015. The Interactive graph allows the u ...
, and the
Catalogue of Life
The Catalogue of Life is an online database that provides an index of known species of animals, plants, fungi, and microorganisms. It was created in 2001 as a partnership between the global Species 2000 and the American Integrated Taxonomic Info ...
. The
Paleobiology Database
The Paleobiology Database is an online resource for information on the distribution and classification of fossil animals, plants, and microorganisms.
History
The Paleobiology Database (PBDB) originated in the NCEAS-funded Phanerozoic Marine Pale ...
is a resource for fossils.
Application
Biological taxonomy is a sub-discipline of
biology
Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary i ...
, and is generally practiced by biologists known as "taxonomists", though enthusiastic
naturalists are also frequently involved in the publication of new taxa. Because taxonomy aims to describe and organize
life
Life is a quality that distinguishes matter that has biological processes, such as signaling and self-sustaining processes, from that which does not, and is defined by the capacity for growth, reaction to stimuli, metabolism, energ ...
, the work conducted by taxonomists is essential for the study of
biodiversity
Biodiversity or biological diversity is the variety and variability of life on Earth. Biodiversity is a measure of variation at the genetic (''genetic variability''), species (''species diversity''), and ecosystem (''ecosystem diversity'') l ...
and the resulting field of
conservation biology
Conservation biology is the study of the conservation of nature and of Earth's biodiversity with the aim of protecting species, their habitats, and ecosystems from excessive rates of extinction and the erosion of biotic interactions. It is an int ...
.
Classifying organisms
Biological classification is a critical component of the taxonomic process. As a result, it informs the user as to what the relatives of the taxon are hypothesized to be. Biological classification uses taxonomic ranks, including among others (in order from most inclusive to least inclusive):
Domain
Domain may refer to:
Mathematics
*Domain of a function, the set of input values for which the (total) function is defined
**Domain of definition of a partial function
**Natural domain of a partial function
**Domain of holomorphy of a function
* Do ...
,
Kingdom
Kingdom commonly refers to:
* A monarchy ruled by a king or queen
* Kingdom (biology), a category in biological taxonomy
Kingdom may also refer to:
Arts and media Television
* ''Kingdom'' (British TV series), a 2007 British television drama s ...
,
Phylum
In biology, a phylum (; plural: phyla) is a level of classification or taxonomic rank below kingdom and above class. Traditionally, in botany the term division has been used instead of phylum, although the International Code of Nomenclature f ...
,
Class
Class or The Class may refer to:
Common uses not otherwise categorized
* Class (biology), a taxonomic rank
* Class (knowledge representation), a collection of individuals or objects
* Class (philosophy), an analytical concept used differentl ...
,
Order
Order, ORDER or Orders may refer to:
* Categorization, the process in which ideas and objects are recognized, differentiated, and understood
* Heterarchy, a system of organization wherein the elements have the potential to be ranked a number of d ...
,
Family
Family (from la, familia) is a Social group, group of people related either by consanguinity (by recognized birth) or Affinity (law), affinity (by marriage or other relationship). The purpose of the family is to maintain the well-being of its ...
,
Genus
Genus ( plural genera ) is a taxonomic rank used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In the hierarchy of biological classification, genus com ...
,
Species
In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...
, and
Strain
Strain may refer to:
Science and technology
* Strain (biology), variants of plants, viruses or bacteria; or an inbred animal used for experimental purposes
* Strain (chemistry), a chemical stress of a molecule
* Strain (injury), an injury to a mu ...
.
Taxonomic descriptions
![Nepenthes smilesii type specimen](https://upload.wikimedia.org/wikipedia/commons/d/da/Nepenthes_smilesii_type_specimen.jpg)
The "definition" of a taxon is encapsulated by its description or its diagnosis or by both combined. 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
Zoology ()The pronunciation of zoology as is usually regarded as nonstandard, though it is not uncommon. is the branch of biology that studies the Animal, animal kingdom, including the anatomy, structure, embryology, evolution, Biological clas ...
, the
nomenclature
Nomenclature (, ) is a system of names or terms, or the rules for forming these terms in a particular field of arts or sciences. The principles of naming vary from the relatively informal naming conventions, conventions of everyday speech to the i ...
for the more commonly used ranks (
superfamily
SUPERFAMILY is a database and search platform of structural and functional annotation for all proteins and genomes. It classifies amino acid sequences into known structural domains, especially into SCOP superfamilies. Domains are functional, str ...
to
subspecies
In biological classification, subspecies is a rank below species, used for populations that live in different areas and vary in size, shape, or other physical characteristics (morphology), but that can successfully interbreed. Not all species ...
), is regulated by the ''
International Code of Zoological Nomenclature
The International Code of Zoological Nomenclature (ICZN) is a widely accepted convention in zoology that rules the formal scientific naming of organisms treated as animals. It is also informally known as the ICZN Code, for its publisher, the ...
'' (''ICZN Code''). In the fields of
phycology
Phycology () is the scientific study of algae. Also known as algology, phycology is a branch of life science.
Algae are important as primary producers in aquatic ecosystems. Most algae are eukaryotic, photosynthetic organisms that live in a w ...
,
mycology
Mycology is the branch of biology concerned with the study of fungi, including their genetic and biochemical properties, their taxonomy and their use to humans, including as a source for tinder, traditional medicine, food, and entheogens, as ...
, and
botany
Botany, also called , plant biology or phytology, is the science of plant life and a branch of biology. A botanist, plant scientist or phytologist is a scientist who specialises in this field. The term "botany" comes from the Ancient Greek w ...
, the naming of taxa is governed by the ''
'' (''ICN'').
The initial description of a taxon involves five main requirements:
# The taxon must be given a name based on the 26 letters of the Latin alphabet (a
binomial
Binomial may refer to:
In mathematics
*Binomial (polynomial), a polynomial with two terms
* Binomial coefficient, numbers appearing in the expansions of powers of binomials
*Binomial QMF, a perfect-reconstruction orthogonal wavelet decomposition
...
for new species, or uninomial for other ranks).
# The name must be unique (i.e. not a
homonym
In linguistics, homonyms are words which are homographs (words that share the same spelling, regardless of pronunciation), or homophones (equivocal words, that share the same pronunciation, regardless of spelling), or both. Using this definition, ...
).
# The description must be based on at least one name-bearing
type specimen
In biology, a type is a particular wiktionary:en:specimen, specimen (or in some cases a group of specimens) of an organism to which the scientific name of that organism is formally attached. In other words, a type is an example that serves to a ...
.
# 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, which may or may not be based on morphology). Both codes deliberately separate defining the content of a taxon (its
circumscription
Circumscription may refer to:
*Circumscribed circle
*Circumscription (logic)
*Circumscription (taxonomy)
* Circumscription theory, a theory about the origins of the political state in the history of human evolution proposed by the American anthrop ...
) from defining its name.
# 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
Quantitative may refer to:
* Quantitative research, scientific investigation of quantitative properties
* Quantitative analysis (disambiguation)
* Quantitative verse, a metrical system in poetry
* Statistics, also known as quantitative analysis ...
or
qualitative comparisons of striking features, to elaborate computer analyses of large amounts of
DNA sequence
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. Th ...
data.
Author citation
An "authority" may be placed after a scientific name.
The authority is the name of the scientist or scientists who first validly published the name.
For example, in 1758 Linnaeus gave the
Asian elephant
The Asian elephant (''Elephas maximus''), also known as the Asiatic elephant, is the only living species of the genus ''Elephas'' and is distributed throughout the Indian subcontinent and Southeast Asia, from India in the west, Nepal in the no ...
the scientific name ''Elephas maximus'', so the name is sometimes written as "''Elephas maximus'' Linnaeus, 1758". The names of authors are often abbreviated: the abbreviation ''L.'', for ''Linnaeus,'' is commonly used. In botany, there is, in fact, a regulated list of standard abbreviations (see
list of botanists by author abbreviation
__NOTOC__
A
* Aa – Hubertus Antonius van der Aa (1935–2017)
* A.A.Cocucci – (born 1959)
* A.A.Eaton – Alvah Augustus Eaton (1865–1908)
* A.A.Fisch.Waldh. – Alexandr Alexandrovich Fischer von Waldheim (1839–1920)
* A.Agostini ...
). The system for assigning authorities differs slightly between
botany
Botany, also called , plant biology or phytology, is the science of plant life and a branch of biology. A botanist, plant scientist or phytologist is a scientist who specialises in this field. The term "botany" comes from the Ancient Greek w ...
and
zoology
Zoology ()The pronunciation of zoology as is usually regarded as nonstandard, though it is not uncommon. is the branch of biology that studies the Animal, animal kingdom, including the anatomy, structure, embryology, evolution, Biological clas ...
.
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.
Phenetics
![Phylogenetics](https://upload.wikimedia.org/wikipedia/commons/6/69/Phylogenetics.svg)
In phenetics, also known as taximetrics, or numerical taxonomy, organisms are classified based on overall similarity, regardless of their phylogeny or evolutionary relationships.
It results in a measure of hypergeometric "distance" between taxa. Phenetic methods have become relatively rare in modern times, largely superseded by
cladistic
Cladistics (; ) is an approach to biological classification in which organisms are categorized in groups (" clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived char ...
analyses, as phenetic methods do not distinguish shared ancestral (or
plesiomorph
In phylogenetics, a plesiomorphy ("near form") and symplesiomorphy are synonyms for an ancestral character shared by all members of a clade, which does not distinguish the clade from other clades.
Plesiomorphy, symplesiomorphy, apomorphy, and ...
ic) traits from shared derived (or
apomorphic
In phylogenetics, an apomorphy (or derived trait) is a novel character or character state that has evolved from its ancestral form (or plesiomorphy). A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to have ...
) traits. However, certain phenetic methods, such as
neighbor joining
In bioinformatics, neighbor joining is a bottom-up (agglomerative) clustering method for the creation of phylogenetic trees, created by Naruya Saitou and Masatoshi Nei in 1987. Usually based on DNA or protein sequence data, the algorithm require ...
, have persisted, as rapid estimators of relationships when more advanced methods (such as
Bayesian inference
Bayesian inference is a method of statistical inference in which Bayes' theorem is used to update the probability for a hypothesis as more evidence or information becomes available. Bayesian inference is an important technique in statistics, a ...
) are too computationally expensive.
Databases
Modern taxonomy uses
database
In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases sp ...
technologies to search and catalogue classifications and their documentation. While there is no commonly used database, there are comprehensive databases such as the ''
Catalogue of Life
The Catalogue of Life is an online database that provides an index of known species of animals, plants, fungi, and microorganisms. It was created in 2001 as a partnership between the global Species 2000 and the American Integrated Taxonomic Info ...
'', which attempts to list every documented species.
The catalogue listed 1.64 million species for all kingdoms , claiming coverage of more than three-quarters of the estimated species known to modern science.
See also
*
Automated species identification
Automated species identification is a method of making the expertise of Taxonomy (biology), taxonomists available to ecologists, parataxonomy, parataxonomists and others via digital technology and artificial intelligence. Today, most automated ide ...
*
Bacterial taxonomy
Bacterial taxonomy is the taxonomy, i.e. the rank-based classification, of bacteria.
In the scientific classification established by Carl Linnaeus, each species has to be assigned to a genus ( binary nomenclature), which in turn is a lower level ...
*
Cluster analysis
Cluster analysis or clustering is the task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense) to each other than to those in other groups (clusters). It is a main task of ...
*
Consortium for the Barcode of Life
The Consortium for the Barcode of Life (CBOL) was an international initiative dedicated to supporting the development of DNA barcoding as a global standard for species identification. CBOL's Secretariat Office is hosted by the National Museum of ...
*
Consortium of European Taxonomic Facilities
The Consortium of European Taxonomic Facilities (CETAF) is a taxonomic research network formed by scientific institutions in Europe. It was formed in December 1996 by ten of the largest European natural history museums and botanical gardens to be ...
*
Genetypes
Genetypes is a taxonomic concept proposed in 2010 to describe any genetic sequences from type specimens. This nomenclature integrates molecular systematics and terms used in biological taxonomy. This nomenclature is designed to label, or flag, ge ...
*
Glossary of scientific naming
This is a list of terms and symbols used in scientific names for organisms, and in describing the names. For proper parts of the names themselves, see List of Latin and Greek words commonly used in systematic names. Note that many of the abbreviat ...
*
Identification (biology)
Identification in biology is the process of assigning a pre-existing taxon name to an individual organism. Identification of organisms to individual scientific names (or codes) may be based on individualistic natural body features, experimentally ...
* ''
Incertae sedis
' () or ''problematica'' is a term used for a taxonomic group where its broader relationships are unknown or undefined. Alternatively, such groups are frequently referred to as "enigmatic taxa". In the system of open nomenclature, uncertainty ...
''
*
Open Tree of Life
The Open Tree of Life is an online phylogenetic tree of life – a collaborative effort, funded by the National Science Foundation. The first draft, including 2.3 million species, was released in September 2015. The Interactive graph allows the u ...
*
Parataxonomy
Parataxonomy is a system of labor division for use in biodiversity research, in which the rough sorting tasks of specimen collection, field identification, documentation and preservation are conducted by primarily local, less specialized individu ...
*