Taxonomy (biology)

Last updated

In biology, taxonomy (from Ancient Greek τάξις (taxis), meaning 'arrangement',and -νομία (-nomia), meaning ' method ') is the science of defining and naming groups of biological organisms on the basis of shared characteristics. Organisms are grouped together 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. 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. 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.

Biology is the natural science that studies life and living organisms, including their physical structure, chemical processes, molecular interactions, physiological mechanisms, development and evolution. Despite the complexity of the science, there are certain unifying concepts that consolidate it into a single, coherent field. Biology recognizes the cell as the basic unit of life, genes as the basic unit of heredity, and evolution as the engine that propels the creation and extinction of species. Living organisms are open systems that survive by transforming energy and decreasing their local entropy to maintain a stable and vital condition defined as homeostasis.

A taxis is the movement of an organism in response to a stimulus such as light or the presence of food. Taxes are innate behavioural responses. A taxis differs from a tropism in that in the case of taxis, the organism has motility and demonstrates guided movement towards or away from the stimulus source. It is sometimes distinguished from a kinesis, a non-directional change in activity in response to a stimulus.

Scientific method Interplay between observation, experiment and theory in science

The scientific method is an empirical method of acquiring knowledge that has characterized the development of science since at least the 17th century. It involves careful observation, applying rigorous skepticism about what is observed, given that cognitive assumptions can distort how one interprets the observation. It involves formulating hypotheses, via induction, based on such observations; experimental and measurement-based testing of deductions drawn from the hypotheses; and refinement of the hypotheses based on the experimental findings. These are principles of the scientific method, as distinguished from a definitive series of steps applicable to all scientific enterprises.

Contents

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.

Phylogenetics Study of the evolutionary history and relationships among individuals or groups of organisms

In biology, phylogenetics is the study of the evolutionary history and relationships among individuals or groups of organisms. These relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or morphology under a model of evolution of these traits. The result of these analyses is a phylogeny – a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms. The tips of a phylogenetic tree can be living organisms or fossils, and represent the "end", or the present, in an evolutionary lineage. A phylogenetic tree can be rooted or unrooted. A rooted tree indicates the common ancestor, or ancestral lineage, of the tree. An unrooted tree makes no assumption about the ancestral line, and does not show the origin or "root" of the gene or organism in question. Phylogenetic analyses have become central to understanding biodiversity, evolution, ecology, and genomes.

Cladistics A method of biological systematics in evolutionary biology

Cladistics is an approach to biological classification in which organisms are categorized in groups ("clades") based on the most recent common ancestor. Hypothesized relationships are typically based on shared derived characteristics (synapomorphies) that can be traced to the most recent common ancestor and are not present in more distant groups and ancestors. A key feature of a clade is that a common ancestor and all its descendants are part of the clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if within a strict cladistic framework the terms animals, bilateria/worms, fishes/vertebrata, or monkeys/anthropoidea were used, these terms would include humans. Many of these terms are normally used paraphyletically, outside of cladistics, e.g. as a 'grade'. Radiation results in the generation of new subclades by bifurcation.

Systematics The study of the diversification and relationships among living things through time

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. Phylogenies have two components: branching order and branch length. Phylogenetic trees of species and higher taxa are used to study the evolution of traits and the distribution of organisms (biogeography). Systematics, in other words, is used to understand the evolutionary history of life on Earth.

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. [1] As points of reference, recent definitions of taxonomy are presented below:

  1. Theory and practice of grouping individuals into species, arranging species into larger groups, and giving those groups names, thus producing a classification. [2]
  2. A field of science (and major component of systematics) that encompasses description, identification, nomenclature, and classification [3]
  3. The science of classification, in biology the arrangement of organisms into a classification [4]
  4. "The science of classification as applied to living organisms, including study of means of formation of species, etc." [5]
  5. "The analysis of an organism's characteristics for the purpose of classification" [6]
  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) [7]

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 is considered a part of taxonomy (definitions 1 and 2), or a part of systematics outside taxonomy. [8] For example, definition 6 is paired with the following definition of systematics that places nomenclature outside taxonomy: [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. [1] [9] The broadest meaning of "taxonomy" is used here. The term itself was introduced in 1813 by de Candolle, in his Théorie élémentaire de la botanique. [10]

Augustin Pyramus de Candolle 19th-century Swiss botanist

Augustin Pyramus de Candolle also spelled Augustin Pyrame de Candolle was a Swiss botanist. René Louiche Desfontaines launched de Candolle's botanical career by recommending him at an herbarium. Within a couple of years de Candolle had established a new genus, and he went on to document hundreds of plant families and create a new natural plant classification system. Although de Candolle's main focus was botany, he also contributed to related fields such as phytogeography, agronomy, paleontology, medical botany, and economic botany.

Monograph and taxonomic revision

A taxonomic revision or taxonomic review is a novel analysis of the variation patterns in a particular taxon. 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. 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. 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 result in a change in the classification of these subtaxa, the identification of new subtaxa, or the merger of previous subtaxa. [11]

Taxon Group of one or more populations of an organism or organisms which have distinguishing characteristics in common

In biology, a taxon 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 name and given a particular ranking, especially if and when it is accepted or becomes established. It is not uncommon, however, for taxonomists to remain at odds over what belongs to a taxon and the criteria used for inclusion. If a taxon is given a formal scientific name, its use is then governed by one of the nomenclature codes specifying which scientific name is correct for a particular grouping.

Alpha and beta taxonomy

The term "alpha taxonomy" is primarily used today to refer to the discipline of finding, describing, and naming taxa, particularly species. [12] 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. [13]

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. [14]

… 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 genetical 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. [14]

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 (pp. 365–366).

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. [15] [12] Thus, Ernst Mayr in 1968 defined beta taxonomy as the classification of ranks higher than species. [16]

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 scientific work of deciding how to define species has been called microtaxonomy. [17] [18] [12] By extension, macrotaxonomy is the study of groups at higher taxonomic ranks, from subgenus and above only, than species. [12]

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. 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's system of sexual classification. 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). These were pre-evolutionary in thinking. The publication of Charles Darwin's On the Origin of Species (1859) led to new ways of thinking about classification based on evolutionary relationships. This was the concept of phyletic systems, from 1883 onwards. This approach was typified by those of Eichler (1883) and Engler (1886–1892). 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. [19] [20] [21]

Pre-Linnaean

Early taxonomists

Naming and classifying our surroundings has probably been taking place as long as mankind has been able to communicate. It would always have been important to know the names of poisonous and edible plants and animals in order to communicate this information to other members of the family or group. 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. [22]

Ancient times

Organisms were first classified by Aristotle (Greece, 384–322 BC) during his stay on the Island of Lesbos. [23] [24] [25] 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. [26] He divided all living things into two groups: plants and animals. [24] 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. [27] His student Theophrastus (Greece, 370–285 BC) carried on this tradition, mentioning some 500 plants and their uses in his Historia Plantarum . Again, several plant groups currently still recognized can be traced back to Theophrastus, such as Cornus , Crocus , and Narcissus . [24]

Medieval

Taxonomy in the Middle Ages was largely based on the Aristotelian system, [26] with additions concerning the philosophical and existential order of creatures. This included concepts such as the Great chain of being in the Western scholastic tradition, [26] again deriving ultimately from Aristotle. Aristotelian system did not classify plants or fungi, due to the lack of microscope at the time, [25] as his ideas were based on arranging the complete world in a single continuum, as per the scala naturae (the Natural Ladder). [24] This, as well, was taken into consideration in the Great chain of being. [24] Advances were made by scholars such as Procopius, Timotheos of Gaza, Demetrios Pepagomenos, and Thomas Aquinas. Medieval thinkers used abstract philosophical and logical categorizations more suited to abstract philosophy than to pragmatic taxonomy. [24]

Renaissance and Early Modern

During the Renaissance, the Age of Reason, and the Enlightenment, categorizing organisms became more prevalent, [24] 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 (1519–1603), who has been called "the first taxonomist". [28] His magnum opus De Plantis came out in 1583, and described more than 1500 plant species. [29] [30] Two large plant families that he first recognized are still in use today: the Asteraceae and Brassicaceae. [31] Then in the 17th century John Ray (England, 1627–1705) wrote many important taxonomic works. [25] Arguably his greatest accomplishment was Methodus Plantarum Nova (1682), [32] 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 (France, 1656–1708). [33] 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. [22]

The Linnaean era

Title page of Systema Naturae, Leiden, 1735 Linne-Systema Naturae 1735.jpg
Title page of Systema Naturae , Leiden, 1735

The Swedish botanist Carl Linnaeus (1707–1778) [26] ushered in a new era of taxonomy. With his major works Systema Naturae 1st Edition in 1735, [34] Species Plantarum in 1753, [35] and Systema Naturae 10th Edition, [36] he revolutionized modern taxonomy. His works implemented a standardized binomial naming system for animal and plant species, [37] 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. [37] Thus the Linnaean system was born, and is still used in essentially the same way today as it was in the 18th century. [37] Currently, plant and animal taxonomists regard Linnaeus' work as the "starting point" for valid names (at 1753 and 1758 respectively). [38] Names published before these dates are referred to as "pre-Linnaean", and not considered valid (with the exception of spiders published in Svenska Spindlar [39] ). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean. [22]

Modern system of classification

Evolution of the vertebrates at class level, width of spindles indicating number of families. Spindle diagrams are typical for Evolutionary taxonomy Spindle diagram.jpg
Evolution of the vertebrates at class level, width of spindles indicating number of families. Spindle diagrams are typical for Evolutionary taxonomy
The same relationship, expressed as a cladogram typical for cladistics Cladogram vertebrata.jpg
The same relationship, expressed as a cladogram typical for cladistics

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. [25] 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. [12] 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. [40]

With Darwin's theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle of common descent. [41] Tree of life representations became popular in scientific works, with known fossil groups incorporated. One of the first modern groups tied to fossil ancestors was birds. [42] 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. [43] [44] 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 worked to understand the history of animals through the ages by linking together known groups. [45] With the modern evolutionary synthesis 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. [46]

The cladistic method has emerged since the 1960s. [41] In 1958, Julian Huxley used the term clade. [12] Later, in 1960, Cain and Harrison introduced the term cladistic. [12] The salient feature is arranging taxa in a hierarchical evolutionary tree, ignoring ranks. [41] A taxon is called monophyletic, if it includes all the descendants of an ancestral form. [47] [48] Groups that have descendant groups removed from them are termed paraphyletic, [47] while groups representing more than one branch from the tree of life are called polyphyletic. [47] [48] The International Code of Phylogenetic Nomenclature or PhyloCode is intended to regulate the formal naming of clades. [49] [50] Linnaean ranks will be optional under the PhyloCode, which is intended to coexist with the current, rank-based codes. [50]

Kingdoms and domains

The basic scheme of modern classification. Many other levels can be used; domain, the highest level within life, is both new and disputed. Biological classification L Pengo vflip.svg
The basic scheme of modern classification. Many other levels can be used; domain, the highest level within life, is both new and disputed.

Well before Linnaeus, plants and animals were considered separate Kingdoms. [51] Linnaeus used this as the top rank, dividing the physical world into the plant, animal and mineral kingdoms. As advances in microscopy made classification of microorganisms possible, the number of kingdoms increased, five and six-kingdom systems being the most common.

Domains are a relatively new grouping. First proposed in 1977, Carl Woese's three-domain system was not generally accepted until later. [52] 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), [51] with the Eukaryota for all organisms whose cells contain a nucleus. [53] A small number of scientists include a sixth kingdom, Archaea, but do not accept the domain method. [51]

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. His 2004 classification treated the archaeobacteria as part of a subkingdom of the kingdom Bacteria, i.e. he rejected the three-domain system entirely. [54] 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. [55]

Linnaeus
1735 [56]
Haeckel
1866 [57]
Chatton
1925 [58]
Copeland
1938 [59]
Whittaker
1969 [60]
Woese et al.
1990 [61]
Cavalier-Smith
1998 [54]
Cavalier-Smith
2015 [62]
2 kingdoms3 kingdoms 2 empires 4 kingdoms 5 kingdoms 3 domains 2 empires, 6 kingdoms 2 empires, 7 kingdoms
(not treated) Protista Prokaryota Monera Monera Bacteria Bacteria Bacteria
Archaea Archaea
Eukaryota Protoctista Protista Eucarya Protozoa Protozoa
Chromista Chromista
Vegetabilia Plantae Plantae Plantae Plantae Plantae
Fungi Fungi Fungi
Animalia Animalia Animalia Animalia Animalia Animalia

Recent comprehensive classifications

Partial classifications exist for many individual groups of organisms and are revised and replaced as new information becomes available; however, comprehensive treatments of most or all life are rarer; two recent examples are that of Adl et al., 2012, [63] which covers eukaryotes only with an emphasis on protists, and Ruggiero et al., 2015, [64] covering both eukaryotes and prokaryotes to the rank of Order, although both exclude fossil representatives. [64]

Application

Biological taxonomy is a sub-discipline of biology, and is generally practiced by biologists known as "taxonomists", though enthusiastic naturalists are also frequently involved in the publication of new taxa [65] .[ citation needed ] 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. [66] [67]

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, Kingdom, Phylum, Class, Order, Family, Genus, Species, and Strain. [68] [Note 1]

Taxonomic descriptions

Type specimen for Nepenthes smilesii, a tropical pitcher plant. Nepenthes smilesii type specimen.jpg
Type specimen for Nepenthes smilesii , a tropical pitcher plant.

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. [8] In zoology, the nomenclature for the more commonly used ranks (superfamily to subspecies), is regulated by the International Code of Zoological Nomenclature (ICZN Code). [69] In the fields of botany, phycology, and mycology, the naming of taxa is governed by the International Code of Nomenclature for algae, fungi, and plants (ICN). [70]

The initial description of a taxon involves five main requirements: [71]

  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).
  2. The name must be unique (i.e. not a homonym).
  3. The description must be based on at least one name-bearing type specimen.
  4. It should include 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.
  5. These first four requirements must be published in a work that is obtainable in numerous identical copies, as a permanent scientific record.

However, often much more information is included, like the geographic range of the taxon, ecological notes, chemistry, behavior, etc. How researchers arrive at their taxa varies: depending on the available data, and resources, methods vary from simple quantitative or qualitative comparisons of striking features, to elaborate computer analyses of large amounts of DNA sequence data. [72]

Author citation

An "authority" may be placed after a scientific name. [73] The authority is the name of the scientist or scientists who first validly published the name. [73] 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". [74] The names of authors are frequently 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). [75] The system for assigning authorities differs slightly between botany and zoology. [8] However, it is standard that if a species' name or placement has been changed since the original description, the original authority's name is placed in parentheses. [76]

Phenetics

In phenetics, also known as taximetrics, or numerical taxonomy, organisms are classified based on overall similarity, regardless of their phylogeny or evolutionary relationships. [12] It results in a measure of evolutionary "distance" between taxa. Phenetic methods have become relatively rare in modern times, largely superseded by cladistic analyses, as phenetic methods do not distinguish common ancestral (or plesiomorphic) traits from new common (or apomorphic) traits. [77] 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. [78]

Databases

Modern taxonomy uses database technologies to search and catalogue classifications and their documentation. [79] While there is no commonly used database, there are comprehensive databases such as the Catalogue of Life , which attempts to list every documented species. [80] 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. [81]

See also

Notes

  1. This ranking system can be remembered by the mnemonic "Do Kings Play Chess On Fine Glass Sets?"

Related Research Articles

Clade A group of organisms that consists of a common ancestor and all its lineal descendants

A clade, also known as monophyletic group, is a group of organisms that consists of a common ancestor and all its lineal descendants, and represents a single "branch" on the "tree of life".

Linnaean taxonomy A rank based classification system for organisms

Linnaean taxonomy can mean either of two related concepts:

  1. 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 there are three kingdoms, divided into classes, and they, in turn, into orders, genera, and species, with an additional rank lower than species.
  2. a term for rank-based classification of organisms, in general. That is, taxonomy in the traditional sense of the word: rank-based scientific classification. This term is especially used as opposed to cladistic systematics, which groups organisms into clades. It is attributed to Linnaeus, although he neither invented the concept of ranked classification nor gave it its present form. In fact, it does not have an exact present form, as "Linnaean taxonomy" as such does not really exist: it is a collective (abstracting) term for what actually are several separate fields, which use similar approaches.

A genus is a taxonomic rank used in the biological classification of living and fossil organisms, as well as viruses, in biology. In the hierarchy of biological classification, genus comes above species and below family. In binomial nomenclature, the genus name forms the first part of the binomial species name for each species within the genus.

Binomial nomenclature, also called binominal nomenclature or binary nomenclature, is a formal system of naming species of living things by giving each a name composed of two parts, both of which use Latin grammatical forms, although they can be based on words from other languages. Such a name is called a binomial name, a binomen, binominal name or a scientific name; more informally it is also called a Latin name. The first part of the name – the generic name – identifies the genus to which the species belongs, while the second part – the specific name or specific epithet – identifies the species within the genus. For example, humans belong to the genus Homo and within this genus to the species Homo sapiens. Tyrannosaurus rex is probably the most widely known binomial. The formal introduction of this system of naming species is credited to Carl Linnaeus, effectively beginning with his work Species Plantarum in 1753. But Gaspard Bauhin, in as early as 1622, had introduced in his book Pinax theatri botanici many names of genera that were later adopted by Linnaeus.

Family is one of the eight major hierarchical taxonomic ranks in Linnaean taxonomy; it is classified between order and genus. A family may be divided into subfamilies, which are intermediate ranks between the ranks of family and genus. The official family names are Latin in origin; however, popular names are often used: for example, walnut trees and hickory trees belong to the family Juglandaceae, but that family is commonly referred to as being the "walnut family".

In biological classification, class is a taxonomic rank, as well as a taxonomic unit, a taxon, in that rank. Other well-known ranks in descending order of size are life, domain, kingdom, phylum, order, family, genus, and species, with class fitting between phylum and order.

In biological classification, the order is

  1. a taxonomic rank used in the classification of organisms and recognized by the nomenclature codes. Other well-known ranks are life, domain, kingdom, phylum, class, family, genus, and species, with order fitting in between class and family. An immediately higher rank, superorder, may be added directly above order, while suborder would be a lower rank.
  2. a taxonomic unit, a taxon, in that rank. In that case the plural is orders.

Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship, progenitor-descendant relationship, and degree of evolutionary change. This type of taxonomy may consider whole taxa rather than single species, so that groups of species can be inferred as giving rise to new groups. The concept found its most well-known form in the modern evolutionary synthesis of the early 1940s.

<i>Systema Naturae</i> major work by Carolus Linnaeus

Systema Naturae 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 nomenclature, was partially developed by the Bauhin brothers, Gaspard and Johann, 200 years earlier, Linnaeus was first to use it consistently throughout his book. The first edition was published in 1735. The full title of the 10th edition (1758), which was the most important one, was Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis or translated: "System of nature through the three kingdoms of nature, according to classes, orders, genera and species, with characters, differences, synonyms, places".

Botanical nomenclature is the formal, scientific naming of plants. It is related to, but distinct from taxonomy. Plant taxonomy is concerned with grouping and classifying plants; botanical nomenclature then provides names for the results of this process. The starting point for modern botanical nomenclature is Linnaeus' Species Plantarum of 1753. Botanical nomenclature is governed by the International Code of Nomenclature for algae, fungi, and plants (ICN), which replaces the International Code of Botanical Nomenclature (ICBN). Fossil plants are also covered by the code of 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 are assignable to families, it may not be noticeable that there is more than one code, but beyond this basic level these are rather different in the way they work.

Evolutionary grade Non-monophyletic grouping of organisms united by morphological or physiological characteristics

In alpha taxonomy, a grade is a taxon united by a level of morphological or physiological complexity. The term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit.

Phylogenetic nomenclature, often called cladistic 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 can be a specimen or a taxon of lower rank, and a description in words. Phylogenetic nomenclature is currently not regulated, but the International Code of Phylogenetic Nomenclature (PhyloCode) is intended to regulate it once it is ratified.

<i>Philosophia Botanica</i> book by Carolus Linnaeus

Philosophia Botanica was published by the Swedish naturalist and physician Carl Linnaeus (1707–1778) who greatly influenced the development of botanical taxonomy and systematics in the 18th and 19th centuries. It is "the first textbook of descriptive systematic botany and botanical Latin". It also contains Linnaeus's first published description of his binomial nomenclature.

Taxonomic rank Level in a taxonomic hierarchy

In biological classification, taxonomic rank is the relative level of a group of organisms in a taxonomic hierarchy. Examples of taxonomic ranks are species, genus, family, order, class, phylum, kingdom, domain, etc.

Cultivated plant taxonomy study of the theory and practice of the science that identifies, describes, classifies, and names cultigens—those plants whose origin or selection is primarily due to intentional human activity;one part of the study of horticultural botany

Cultivated plant taxonomy is the study of the theory and practice of the science that identifies, describes, classifies, and names cultigens—those plants whose origin or selection is primarily due to intentional human activity. Cultivated plant taxonomists do, however, work with all kinds of plants in cultivation.

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 sexes or mating types can produce fertile offspring, typically by sexual reproduction. Other ways of defining species include their karyotype, DNA sequence, morphology, behaviour or ecological niche. In addition, paleontologists use the concept of the chronospecies since fossil reproduction cannot be examined. While these definitions may seem adequate, when looked at more closely they represent problematic species concepts. For example, the boundaries between closely related species become unclear with hybridisation, in a species complex of hundreds of similar microspecies, and in a ring species. Also, among organisms that reproduce only asexually, the concept of a reproductive species breaks down, and each clone is potentially a microspecies.

Taxonomy (general) is the practice and science of classification of things or concepts, including the principles that underlie such classification.

Outline of evolution Hierarchical outline list of articles related to evolution

The following outline is provided as an overview of and topical guide to evolution:

References

  1. 1 2 Wilkins, J.S. (5 February 2011). "What is systematics and what is taxonomy?". Archived from the original on 27 August 2016. Retrieved 21 August 2016.
  2. Judd, W.S.; Campbell, C.S.; Kellogg, E.A.; Stevens, P.F.; Donoghue, M.J. (2007). "Taxonomy". Plant Systematics: A Phylogenetic Approach (3rd ed.). Sunderland: Sinauer Associates.
  3. Simpson, Michael G. (2010). "Chapter 1 Plant Systematics: an Overview". Plant Systematics (2nd ed.). Academic Press. ISBN   978-0-12-374380-0.
  4. Kirk, P.M., Cannon, P.F., Minter, D.W., Stalpers, J.A. eds. (2008) "Taxonomy". In Dictionary of the Fungi, 10th edition. CABI, Netherlands.
  5. Walker, P.M.B., ed. (1988). The Wordsworth Dictionary of Science and Technology. W.R. Chambers Ltd. and Cambridge University Press.
  6. 1 2 Lawrence, E. (2005). Henderson's Dictionary Of Biology. Pearson/Prentice Hall. ISBN   978-0-13-127384-9.
  7. Wheeler, Quentin D. (2004). "Taxonomic triage and the poverty of phylogeny". In H.C.J. Godfray & S. Knapp (ed.). Taxonomy for the twenty-first century. Philosophical Transactions of the Royal Society . 359. pp. 571–583. doi:10.1098/rstb.2003.1452. PMC   1693342 . PMID   15253345.
  8. 1 2 3 "Nomenclature, Names, and Taxonomy". 2005. Archived from the original on 23 November 2016.
  9. Small, Ernest (1989). "Systematics of Biological Systematics (Or, Taxonomy of Taxonomy)". Taxon. 38 (3): 335–356. doi:10.2307/1222265. JSTOR   1222265.
  10. Singh, Gurcharan (2004). Plant systematics: An integrated approach. Science Publishers. p. 20. ISBN   978-1-57808-351-0 via Google Books.
  11. Maxted, Nigel (1992). "Towards Defining a Taxonomic Revision Methodology". Taxon. 41 (4): 653–660. doi:10.2307/1222391. JSTOR   1222391.
  12. 1 2 3 4 5 6 7 8 "Taxonomy: Meaning, Levels, Periods and Role". Biology Discussion. 27 May 2016. Archived from the original on 5 April 2017.[ unreliable source? ]
  13. Rosselló-Mora, Ramon; Amann, Rudolf (1 January 2001). "The species concept for prokaryotes". FEMS Microbiology Reviews. 25 (1): 39–67. doi:10.1111/j.1574-6976.2001.tb00571.x. ISSN   1574-6976. PMID   11152940.
  14. 1 2 Turrill, W.B. (1938). "The Expansion Of Taxonomy With Special Reference To Spermatophyta". Biological Reviews. 13 (4): 342–373. doi:10.1111/j.1469-185X.1938.tb00522.x.
  15. Steyskal, G.C. (1965). "Trend curves of the rate of species description in zoology". Science. 149 (3686): 880–882. Bibcode:1965Sci...149..880S. doi:10.1126/science.149.3686.880. PMID   17737388.
  16. Mayr, Ernst (9 February 1968), "The Role of Systematics in Biology: The study of all aspects of the diversity of life is one of the most important concerns in biology", Science, 159 (3815): 595–599, Bibcode:1968Sci...159..595M, doi:10.1126/science.159.3815.595, PMID   4886900, archived from the original on 24 September 2015
  17. Mayr, Ernst (1982). "Chapter 6: Microtaxonomy, the science of species". The Growth of Biological Thought: Diversity, Evolution, and Inheritance. Belknap Press of Harvard University Press. ISBN   978-0-674-36446-2.
  18. "Result of Your Query". www.biological-concepts.com. Archived from the original on 5 April 2017.
  19. Datta 1988.
  20. Stace 1989.
  21. Stuessy 2009.
  22. 1 2 3 Manktelow, M. (2010) History of Taxonomy Archived 29 May 2015 at the Wayback Machine . Lecture from Dept. of Systematic Biology, Uppsala University.
  23. Mayr, E. (1982) The Growth of Biological Thought. Belknap P. of Harvard U.P., Cambridge (Mass.)
  24. 1 2 3 4 5 6 7 "Palaeos : Taxonomy". palaeos.com. Archived from the original on 31 March 2017.
  25. 1 2 3 4 "taxonomy | biology". Encyclopedia Britannica. Archived from the original on 5 April 2017.[ better source needed ]
  26. 1 2 3 4 "Biology 101, Ch 20". www.cbs.dtu.dk. 23 March 1998. Archived from the original on 28 June 2017.
  27. Leroi, Armand Marie (2014). The Lagoon: How Aristotle Invented Science. Bloomsbury. pp. 384–395. ISBN   978-1-4088-3622-4.
  28. "Andrea Cesalpino | Italian physician, philosopher, and botanist". Encyclopedia Britannica. Archived from the original on 5 April 2017.[ better source needed ]
  29. Cesalpino, Andrea; Marescotti, Giorgio (1583). De plantis libri XVI. Florence: Apud Georgium Marescottum via Internet Archive.
  30. "Andrea Cesalpino | Italian physician, philosopher, and botanist". Encyclopedia Britannica. Archived from the original on 5 April 2017.[ better source needed ]
  31. Jaime, Prohens (2010). International Edition Vegetables I: Asteraceae, Brassicaceae, Chenopodicaceae, and Cucurbitaceae (Handbook of Plant Breeding). ISBN   978-1-4419-2474-2.
  32. John, Ray (1682). "Methodus plantarum nova". impensis Henrici Faithorne & Joannis Kersey, ad insigne Rofæ Coemeterio D. Pauli. Archived from the original on 29 September 2017.
  33. "Joseph Pitton de Tournefort | French botanist and physician". Encyclopedia Britannica. Archived from the original on 5 April 2017.[ better source needed ]
  34. Linnaeus, C. (1735) Systema naturae, sive regna tria naturae systematice proposita per classes, ordines, genera, & species. Haak, Leiden
  35. Linnaeus, C. (1753) Species Plantarum. Stockholm, Sweden.
  36. Linnaeus, C. (1758) Systema naturae, sive regna tria naturae systematice proposita per classes, ordines, genera, & species, 10th Edition. Haak, Leiden
  37. 1 2 3 "taxonomy – The Linnaean system | biology". Encyclopedia Britannica. Archived from the original on 5 April 2017.[ better source needed ]
  38. Donk, M.A. (December 1957). "Typification and later starting-points" (PDF). Taxon. 6 (9): 245–256. doi:10.2307/1217493. JSTOR   1217493. Archived (PDF) from the original on 18 May 2015.
  39. Carl, Clerck; Carl, Bergquist; Eric, Borg; L., Gottman; Lars, Salvius (1757). "Svenska spindlar". Literis Laur. Salvii. Archived from the original on 1 December 2017.
  40. Secord, James A. (2000). Victorian Sensation: The Extraordinary Publication, Reception, and Secret Authorship of Vestiges of the Natural History of Creation. University of Chicago Press. ISBN   978-0-226-74410-0. Archived from the original on 16 May 2008.
  41. 1 2 3 "taxonomy – Classification since Linnaeus | biology". Encyclopedia Britannica. Archived from the original on 5 April 2017.[ better source needed ]
  42. "Fossil of world's earliest modern bird could help us understand the extinction of dinosaurs". Archived from the original on 5 April 2017.[ better source needed ]
  43. Huxley, T.H. (1876): Lectures on Evolution. New York Tribune. Extra. no. 36. In Collected Essays IV: pp. 46–138 original text w/ figures Archived 28 June 2011 at the Wayback Machine
  44. "Thomas Henry Huxley | British biologist". Encyclopedia Britannica. Archived from the original on 6 February 2018.[ better source needed ]
  45. Rudwick, M.J.S. (1985). The Meaning of Fossils: Episodes in the History of Palaeontology. University of Chicago Press. p. 24. ISBN   978-0-226-73103-2.
  46. Paterlini, Marta (September 2007). "There shall be order. The legacy of Linnaeus in the age of molecular biology". EMBO Reports. 8 (9): 814–816. doi:10.1038/sj.embor.7401061. PMC   1973966 . PMID   17767191.
  47. 1 2 3 Taylor, Mike. "What do terms like monophyletic, paraphyletic and polyphyletic mean?". www.miketaylor.org.uk. Archived from the original on 1 August 2010.
  48. 1 2 "Polyphyletic vs. Monophyletic". ncse.com. Archived from the original on 5 April 2017.
  49. Queiroz, Philip D. Cantino, Kevin de. "The PhyloCode". www.ohio.edu. Archived from the original on 10 May 2016.
  50. 1 2 "PhyloCode: Concept, History and Advantages | Taxonomy". Biology Discussion. 12 July 2016. Archived from the original on 5 April 2017.[ unreliable source? ]
  51. 1 2 3 "Kingdom Classification of Living Organism". Biology Discussion. 2 December 2014. Archived from the original on 5 April 2017.[ unreliable source? ]
  52. "Carl Woese | Carl R. Woese Institute for Genomic Biology". www.igb.illinois.edu. Archived from the original on 28 April 2017.
  53. Cracraft, Joel and Donaghue, Michael J. (eds.) (2004). Assembling the Tree of Life. Oxford, England: Oxford University Press. ISBN   0-19-517234-5. pp. 45, 78, 555
  54. 1 2 Cavalier-Smith, T. (1998). "A revised six-kingdom system of life". Biological Reviews. 73 (03): 203–66. doi:10.1111/j.1469-185X.1998.tb00030.x. PMID   9809012.
  55. Luketa, S. (2012). "New views on the megaclassification of life" (PDF). Protistology. 7 (4): 218–237. Archived (PDF) from the original on 2 April 2015.
  56. Linnaeus, C. (1735). Systemae Naturae, sive regna tria naturae, systematics proposita per classes, ordines, genera & species.
  57. Haeckel, E. (1866). Generelle Morphologie der Organismen. Reimer, Berlin.
  58. Chatton, É. (1925). "Pansporella perplexa. Réflexions sur la biologie et la phylogénie des protozoaires". Annales des Sciences Naturelles - Zoologie et Biologie Animale. 10-VII: 1–84.
  59. Copeland, H. (1938). "The kingdoms of organisms". Quarterly Review of Biology. 13: 383–420. doi:10.1086/394568.
  60. Whittaker, R. H. (January 1969). "New concepts of kingdoms of organisms". Science. 163 (3863): 150–60. Bibcode:1969Sci...163..150W. doi:10.1126/science.163.3863.150. PMID   5762760.
  61. Woese, C.; Kandler, O.; Wheelis, M. (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America. 87 (12): 4576–9. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC   54159 . PMID   2112744.
  62. Ruggiero, Michael A.; Gordon, Dennis P.; Orrell, Thomas M.; Bailly, Nicolas; Bourgoin, Thierry; Brusca, Richard C.; Cavalier-Smith, Thomas; Guiry, Michael D.; Kirk, Paul M.; Thuesen, Erik V. (2015). "A higher level classification of all living organisms". PLOS ONE. 10 (4): e0119248. Bibcode:2015PLoSO..1019248R. doi:10.1371/journal.pone.0119248. PMC   4418965 . PMID   25923521.
  63. Adl, S.M.; Simpson, A.G.B.; Lane, C.E.; Lukeš, J.; Bass, D.; Bowser, S.S.; et al. (December 2015). "The revised classification of eukaryotes". Journal of Eukaryotic Microbiology. 59 (5): 429–493. doi:10.1111/j.1550-7408.2012.00644.x. PMC   3483872 . PMID   23020233.
  64. 1 2 Ruggiero, M.A.; Gordon, D.P.; Orrell, T.M.; Bailly, N.; Bourgoin, T.; Brusca, R.C.; et al. (2015). "A higher level classification of all living organisms". PLOS One. 10 (4): e0119248. Bibcode:2015PLoSO..1019248R. doi:10.1371/journal.pone.0119248. PMC   4418965 . PMID   25923521.
  65. "A Few Bad Scientists Are Threatening to Topple Taxonomy". Smithsonian. Retrieved 24 February 2019.
  66. "What is taxonomy?". London: Natural History Museum. Archived from the original on 1 October 2013. Retrieved 23 December 2017.
  67. McNeely, Jeffrey A. (2002). "The role of taxonomy in conserving biodiversity" (PDF). J. Nat. Conserv. 10 (3): 145–153. doi:10.1078/1617-1381-00015. Archived (PDF) from the original on 24 December 2017 via Semantic Scholar.
  68. "Mnemonic taxonomy / biology: Kingdom Phylum Class Order..." Archived from the original on 6 June 2017.
  69. "ICZN Code". www.animalbase.uni-goettingen.de.
  70. "International Code of Nomenclature for algae, fungi, and plants". www.iapt-taxon.org. Archived from the original on 11 January 2013.
  71. "How can I describe new species?". International Commission on Zoological Nomenclature. Archived from the original on 6 March 2012.
  72. "taxonomy – Evaluating taxonomic characters | biology". Encyclopedia Britannica. Archived from the original on 5 April 2017.
  73. 1 2 "Editing Tip: Scientific Names of Species | AJE | American Journal Experts". www.aje.com. Archived from the original on 9 April 2017.
  74. "Carolus Linnaeus: Classification, Taxonomy & Contributions to Biology – Video & Lesson Transcript | Study.com". Study.com. Archived from the original on 9 April 2017.
  75. Biocyclopedia.com. "Biological Classification". www.biocyclopedia.com. Archived from the original on 14 May 2017.
  76. "Zoological nomenclature: a basic guide for non-taxonomist authors". Annelida.net. Archived from the original on 16 March 2017.
  77. "Classification". North Carolina State University. Archived from the original on 14 April 2017. Retrieved 27 April 2017.
  78. "Molecular Marker Glossary". University of Wyoming. Archived from the original on 10 June 2007.
  79. Wood, Dylan; King, Margaret; Landis, Drew; Courtney, William; Wang, Runtang; Kelly, Ross; Turner, Jessica A.; Calhoun, Vince D. (26 August 2014). "Harnessing modern web application technology to create intuitive and efficient data visualization and sharing tools". Frontiers in Neuroinformatics. 8: 71. doi:10.3389/fninf.2014.00071. ISSN   1662-5196. PMC   4144441 . PMID   25206330.
  80. "About – The Plant List". www.theplantlist.org.
  81. "About the Catalogue of Life: 2016 Annual Checklist". Catalogue of Life. Integrated Taxonomic Information System (ITIS). Archived from the original on 15 May 2016. Retrieved 22 May 2016.

Bibliography