Taxonomy (biology)

For other uses, see Taxonomy (disambiguation).
This article is about the field of biology. For the practice of stuffing and mounting animals, see Taxidermy.
"Scientific classification" redirects here. For other uses, see Scientific classification (disambiguation).

Taxonomy (from Ancient Greek: τάξις taxis, "arrangement", and -νομία -nomia, "method"[1]) is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. Organisms are grouped together into taxa (singular: taxon) and given a taxonomic rank; groups of a given rank can be aggregated to form a super group of higher rank and thus create a taxonomic hierarchy.[2][3] The Swedish botanist Carl Linnaeus is regarded as the father of taxonomy, as he developed a system known as Linnaean classification for categorization of organisms and binomial nomenclature for naming organisms.

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. An example of a modern classification is the one published in 2009 by the Angiosperm Phylogeny Group for all living flowering plant families (the APG III system).[4]

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. Two other terms are related to taxonomy, namely "systematics" and "classification"; their exact relationship to taxonomy also varies from source to source because the usage of the three terms in biology originated independently.[5] 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[6]
  4. "The science of classification as applied to living organisms, including study of means of formation of species, etc."[7]
  5. "The analysis of an organism's characteristics for the purpose of classification"[8]
  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)[9]

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. For example, definition 6 is paired with the following definition of systematics that places nomenclature outside taxonomy:[8]

The broadest meaning of "taxonomy" is used here. The word taxonomy was introduced in 1813 by Candolle, in his Théorie élémentaire de la botanique.[10]

Alpha and beta taxonomy

Not to be confused with Alpha diversity.

The term "alpha taxonomy" is primarily used today to refer to the discipline of finding, describing, and naming taxa, 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 nineteenth century.

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.[11]

… there is an increasing desire amongst taxonomists to consider their problems from wider view-points, 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 up on 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.[11]

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 (pages 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.[12] Thus, Ernst Mayr in 1968 defined beta taxonomy as the classification of ranks higher than species.[13]

An understanding of the biological meaning of variation and of the evolutionary origin of groups of related speceis 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 causes 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.[14] By extension, macrotaxonomy is the study of groups at higher taxonomic ranks than species.

History of taxonomy

While some descriptions of taxonomic history attempt to date it to ancient civilisations, a truly scientific attempt to classify organisms did not occur till the eighteenth century. Earlier works were primarily descriptive, and focussed on plants that were useful from an agricultural or medicinal perspective. There are a number of stages in this scientific thinking. Up to 1830, 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 that of Bentham and Hooker (1862–1863). These were pre-evolutionary in thinking. The publication of Charles Darwin's 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.[15][16][17]

Pre-Linnaean taxonomy

Early taxonomists

Taxonomy has been called "the world's oldest profession",[18] and naming and classifying our surroundings has likely been taking place as long as mankind has been able to communicate. It would always have been important to know the names of poisonous and edible plants and animals in order to communicate this information to other members of the family or group.

Medicinal plant illustrations show up in Egyptian wall paintings from c. 1500 BC.[19] The paintings clearly show that these societies valued and communicated the uses of different species, and therefore had a basic taxonomy in place.

Aristotle to Pliny the Elder

Historical records show that informally classifying organisms took place at least back to the days of Aristotle (Greece, 384–322 BC),[20] who was the first to begin to classify all living things. Aristotle used a very simple system of classification. He divided all living thing into two groups: plant and animals. Some of the terms he gave to animals, such as "invertebrates" and "vertebrates" are still commonly used today. His student Theophrastus (Greece, 370–285 BC) carried on this tradition, and wrote a classification of some 500 plants called Historia Plantarum. Again, several plant groups currently still recognized can be traced back to Theophrastus, such as Cornus, Crocus, and Narcissus. The next major turn-of-the-millennia era taxonomist came in the form of Pliny the Elder (Rome, 23–79 AD). His elaborate 160-volume work Naturalis Historia described many plants.

Medieval taxonomy

Taxonomy in the Middle Ages was largely based on the Aristotelian system with additions regarding the philosophical and existential order of creatures. This included concepts such as the Great chain of being in the Western scholastic tradition. However, advances were still made in the secular realm by scholars such as Procopius, Timotheos of Gaza, Demetrios Pepagomenos, and Thomas Aquinas.

Other pre-Linnaean taxonomists

It was not until c. 1500 years later that taxonomic works became ambitious enough to replace the ancient texts. This is often credited to the development of sophisticated optic lenses, which allowed for the morphology of organisms to be studied in much greater detail. One of the earliest authors to take advantage of this leap in technology was Andrea Cesalpino (Italy, 1519–1603), who is often referred to as "the first taxonomist". His magnum opus De Plantis came out in 1583, and described over 1500 plant species. Two large plant families that he first recognized are still in use today: the Asteraceae and Brassicaceae. Then in the seventeenth century John Ray (England, 1627–1705) wrote many important taxonomic works. Arguably his greatest accomplishment was Methodus Plantarum Nova (1682), where he published over 18,000 plant species. At the time, his classifications were perhaps the most complex yet produced by any taxonomist, as he based his taxa on many combined characters. The next major taxonomic works were produced by Joseph Pitton de Tournefort (France, 1656–1708). His work from 1700, Institutiones Rei Herbariae, included over 9000 species in 698 genera, and directly influenced Linnaeus as it was the text he used as a young student.[19]

The Linnaean era

Main article: Linnaean taxonomy
Title page of Systema Naturae, Leiden, 1735

The Swedish botanist Carl Linnaeus (1707–1778) ushered in a new era of taxonomy. With his major works Systema Naturae 1st Edition in 1735,[21] Species Plantarum in 1753,[22] and Systema Naturae 10th Edition,[23] he revolutionized modern taxonomy. His works implemented a standardized binomial naming system for animal and plant species, which proved to be an elegant solution to a chaotic and disorganized taxonomic literature. As a result, the Linnaean system was born, and is still used in essentially the same way today as it was in the eighteenth century. Currently, plant and animal taxonomists regard Linnaeus' work as the "starting point" for valid names (at 1753 and 1758 respectively).[24] Names published before these dates are referred to as "pre-Linnaean", and not considered valid (with the exception of spiders published in Svenska Spindlar). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean.[19]

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
The same relationship, expressed as a cladogram typical for cladistics

Whereas Linnaeus classified for ease of identification, the idea of the Linnaean taxonomy as translating into a sort of dendrogram of the Animal- and Plant Kingdoms was formulated toward the end of the 18th century, well before On the Origin of Species was published. Among early works exploring the idea of a transmutation of species was Erasmus Darwin's 1796 Zoönomia and Jean-Baptiste Lamarck's Philosophie Zoologique of 1809. The idea was popularised in the Anglophone world by the speculative, but widely read Vestiges of the Natural History of Creation, published anonymously by Robert Chambers in 1844.[25]

With Darwin's theory, a general acceptance that classification should reflect the Darwinian principle of common descent quickly appeared. Tree of Life representations became popular in scientific works, with known fossil groups incorporated. One of the first modern groups tied to fossil ancestors were birds. Using the then newly discovered fossils of Archaeopteryx and Hesperornis, Thomas Henry Huxley pronounced that they had evolved from dinosaurs, a group formally named by Richard Owen in 1842.[26] The resulting description, that of dinosaurs "giving rise to" or being "the ancestors of" birds, is the essential hallmark of evolutionary taxonomic thinking. As more and more fossil groups were found and recognized in the late 19th and early 20th century, palaeontologists worked to understand the history of animals through the ages by linking together known groups[27] With the modern evolutionary synthesis of the early 1940s, an essentially modern understanding of evolution of the major groups was in place. The evolutionary taxonomy being based on Linnaean taxonomic ranks, the two terms are largely interchangeable in modern use.

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

Kingdoms and domains

Main article: Kingdom (biology)

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

Domains are a relatively new grouping. The three-domain system was first proposed in 1990, but not generally accepted until later. One main characteristic of the three-domain method is the separation of Archaea and Bacteria, previously grouped into the single kingdom Bacteria (a kingdom also sometimes called Monera). Consequently, the three domains of life are conceptualized as Archaea, Bacteria, and Eukaryota (comprising the nuclei-bearing eukaryotes).[28] A small minority of scientists add Archaea as a sixth kingdom, but do not accept the domain method.

Thomas Cavalier-Smith, who has published extensively on the classification of protists, has recently proposed that the Neomura, the clade that groups together the Archaea and Eukarya, would have evolved from Bacteria, more precisely from Actinobacteria. His classification of 2004 treats the archaebacteria as part of a subkingdom of the Kingdom Bacteria, i.e., he rejects the three-domain system entirely.[29] 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.[30]

Linnaeus
1735[31]		 Haeckel
1866[32]		 Chatton
1925[33]		 Copeland
1938[34]		 Whittaker
1969[35]		 Woese et al.
1990[36]		 Cavalier-Smith
1998[29]
2 kingdoms 3 kingdoms 2 empires 4 kingdoms 5 kingdoms 3 domains 6 kingdoms
(not treated) Protista Prokaryota Monera Monera Bacteria Bacteria
Archaea
Eukaryota Protoctista Protista Eucarya Protozoa
Chromista
Vegetabilia Plantae Plantae Plantae Plantae
Fungi Fungi
Animalia Animalia Animalia Animalia Animalia

Application

Biological taxonomy is a sub-discipline of biology, and is generally practiced by biologists known as "taxonomists", though enthusiastic naturalists are also frequently involved in the publication of new taxa. The work carried out by taxonomists is crucial for the understanding of biology in general. Two fields of applied biology in which taxonomic work is of fundamental importance are the study of biodiversity and conservation.[37] Without a working classification of the organisms in any given area, estimating the amount of diversity present is unrealistic, making informed conservation decisions impossible. As conservation becomes ever more politically important, taxonomic work impacts not only the scientific community, but society as a whole.[18]

Classifying organisms

Main article: Taxonomic rank

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, and Species.[Note 1]

Taxonomic descriptions

Type specimen for Nepenthes smilesii, a tropical pitcher plant.

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

The initial description of a taxon involves five main requirements:[38]

  1. The taxon must be given a name based on the 26 letters in the Latin alphabet (a binomial for new species, or uninomial for other ranks).
  2. The name must be unique (i.e. not a homonym).
  3. The description must be based on at least one name-bearing type specimen.
  4. It should include statements about appropriate attributes to either describe (define) the taxon, and/or 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.

Authorities (author citation)

An "authority" may be placed after a scientific name. The authority is the name of the scientist who first validly published the name. 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". The names of authors are frequently abbreviated: the abbreviation L. is universally accepted for Linnaeus, and in botany there is a regulated list of standard abbreviations (see list of botanists by author abbreviation). The system for assigning authorities differs slightly between botany and zoology. 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.

Phenetics

Main article: Phenetics

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

Databases

Modern taxonomy uses database technologies to search and catalog classifications and their documentation. While there is no commonly used database, there are comprehensive databases such as the Catalogue of Life, which attempts to list every documented species. The catalogue listed 1.4 million species for all kingdoms as of May 2012, claiming coverage of more than 74% of the estimated 1.9 million species known to modern science.[39]

See also

Notes

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

References

  1. ↑ Harper, Douglas. "Taxonomy". Online Etymology Dictionary. Retrieved April 18, 2011.
  2. 1 2 Judd, W.S., Campbell, C.S., Kellogg, E.A., Stevens, P.F., Donoghue, M.J. (2007) Taxonomy. In Plant Systematics – A Phylogenetic Approach, Third Edition. Sinauer Associates, Sunderland.
  3. 1 2 Simpson, Michael G. (2010). "Chapter 1 Plant Systematics: an Overview". Plant Systematics (2nd ed.). Academic Press. ISBN 978-0-12-374380-0.
  4. ↑ Angiosperm Phylogeny Group (2009), "An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III", Botanical Journal of the Linnean Society 161 (2): 105–121, doi:10.1111/j.1095-8339.2009.00996.x
  5. ↑ Wilkins, J. S. What is systematics and what is taxonomy?.
  6. ↑ Kirk, P.M., Cannon, P.F., Minter, D.W., Stalpers, J.A. eds. (2008) "Taxonomy". In Dictionary of the Fungi, 10th edition. CABI, Netherlands.
  7. ↑ Walker, P.M.B., ed. (1988). The Wordsworth Dictionary of Science and Technology. W. R. Chambers Ltd. and Cambridge University Press.
  8. 1 2 Lawrence, E. (2005). Henderson's Dictionary Of Biology. Pearson/Prentice Hall. ISBN 9780131273849.
  9. ↑ Wheeler, Quentin D. (2004). "Taxonomic triage and the poverty of phylogeny". In H. C. J. Godfray & S. Knapp. 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.
  10. ↑ Singh, Gurcharan (2004). Plant systematics: an integrated approach. Science Publishers. ISBN 1578083516. p. 20.
  11. 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.
  12. ↑ 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.
  13. ↑ Ernst Mayr (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
  14. ↑ Mayr, E. (1982). "Chapter 6:Microtaxonomy, the science of species". The Growth of Biological Thought: Diversity, Evolution, and Inheritance. Belknap Press of Harvard University Press. ISBN 9780674364462.
  15. ↑ Datta 1988.
  16. ↑ Stace 1989.
  17. ↑ Stuessy 2009.
  18. 1 2 Knapp, S. (2010). "What's in a name? A history of taxonomy".
  19. 1 2 3 Manktelow, M. (2010) History of Taxonomy. Lecture from Dept. of Systematic Biology, Uppsala University.
  20. ↑ Mayr, E. (1982) The Growth of Biological Thought. Belknap P. of Harvard U.P, Cambridge (Mass.).
  21. ↑ Linnaeus, C. (1735) Systema naturae, sive regna tria naturae systematice proposita per classes, ordines, genera, & species. Haak, Leiden
  22. ↑ Linnaeus, C. (1753) Species Plantarum. Stockholm, Sweden.
  23. ↑ Linnaeus, C. (1758) Systema naturae, sive regna tria naturae systematice proposita per classes, ordines, genera, & species, 10th Edition. Haak, Leiden
  24. ↑ Donk, M.A. (1957). "Typification and later starting-points" (PDF). Taxon 6: 245–256. doi:10.2307/1217493. JSTOR 1217493.
  25. ↑ Secord, James A. (2000). "Victorian Sensation: The Extraordinary Publication, Reception, and Secret Authorship of Vestiges of the Natural History of Creation". Chicago: University of Chicago Press. ISBN 978-0-226-74410-0. Archived from the original on May 16, 2008.
  26. ↑ Huxley, T. H. (1876): Lectures on Evolution. New York Tribune. Extra. no 36. In Collected Essays IV: pp 46–138 original text w/ figures
  27. ↑ Rudwick, M. J. S. (1985). The Meaning of Fossils: Episodes in the History of Palaeontology. University of Chicago Press. p. 24. ISBN 0-226-73103-0.
  28. ↑ Cracraft, Joel and Donaghue, Michael J. (eds.) (2004). Assembling the Tree of Life. Oxford, England: Oxford University Press. ISBN 0195172345. pp. 45, 78 and 555
  29. 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.
  30. ↑ Luketa S. (2012). "New views on the megaclassification of life" (PDF). Protistology 7 (4): 218–237.
  31. ↑ Linnaeus, C. (1735). Systemae Naturae, sive regna tria naturae, systematics proposita per classes, ordines, genera & species.
  32. ↑ Haeckel, E. (1866). Generelle Morphologie der Organismen. Reimer, Berlin.
  33. ↑ 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.
  34. ↑ Copeland, H. (1938). "The kingdoms of organisms". Quarterly Review of Biology 13: 383–420. doi:10.1086/394568.
  35. ↑ 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.
  36. ↑ 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.
  37. ↑ "What is taxonomy?". Natural History Museum London.
  38. ↑ "How can I describe new species?". International Commission on Zoological Nomenclature.
  39. ↑ "About the Catalogue of Life: 2012 Annual Checklist". Catalogue of Life. Integrated Taxonomic Information System (ITIS). Retrieved 22 May 2012.

Bibliography

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