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.
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.
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:
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:
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. 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.
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.
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 19th 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.
… 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.
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. Thus, Ernst Mayr 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.
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. By extension, macrotaxonomy is the study of groups at higher taxonomic ranks, from subgenus and above only, than species.
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.
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.
Organisms were first classified by Aristotle (Greece, 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: plants and animals. 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. 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.
Taxonomy in the Middle Ages was largely based on the Aristotelian system, 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, again deriving ultimately from Aristotle. Aristotelian system did not classify plants or fungi, due to the lack of microscope at the time, as his ideas were based on arranging the complete world in a single continuum, as per the scala naturae (the Natural Ladder). This, as well, was taken into consideration in the Great chain of being. 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.
During the Renaissance, the Age of Reason, and the Enlightenment, categorizing organisms became more prevalent, and taxonomic works became ambitious enough to replace the ancient texts. 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". His magnum opus De Plantis came out in 1583, and described more than 1500 plant species. Two large plant families that he first recognized are still in use today: the Asteraceae and Brassicaceae. Then in the 17th century John Ray (England, 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 (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.
The Swedish botanist Carl Linnaeus (1707–1778) ushered in a new era of taxonomy. With his major works Systema Naturae 1st Edition in 1735, Species Plantarum 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. Thus the Linnaean system was born, and is still used in essentially the same way today as it was in the 18th century. Currently, 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). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean.
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. 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. 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.
With Darwin's theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle of common descent. 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. Using the then newly discovered fossils of Archaeopteryx and Hesperornis, Thomas Henry Huxley pronounced that they had evolved from dinosaurs, a group formally named by Richard Owen in 1842. The resulting description, that of dinosaurs "giving rise to" or being "the ancestors of" birds, is the essential hallmark of evolutionary taxonomic thinking. As more and more fossil groups were found and recognized in the late 19th and early 20th centuries, palaeontologists worked to understand the history of animals through the ages by linking together known groups. With the modern evolutionary synthesis of the early 1940s, an essentially modern understanding of 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 method has emerged since the 1960s. In 1958, Julian Huxley 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, ignoring ranks. 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, 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.
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. First proposed in 1977, Carl Woese's three-domain system was 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), with the Eukaryota for all organisms whose cells contain a nucleus. A small number of scientists include a sixth kingdom, Archaea, 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 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. 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.
|Woese et al.
|2 kingdoms||3 kingdoms||2 empires||4 kingdoms||5 kingdoms||3 domains||2 empires, 6 kingdoms||2 empires, 7 kingdoms|
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, which covers eukaryotes only with an emphasis on protists, and Ruggiero et al., 2015, covering both eukaryotes and prokaryotes to the rank of Order, although both exclude fossil representatives.
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. 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.
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.[Note 1]
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, 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:
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.
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 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., for Linnaeus, is commonly used. In botany, there is, in fact, 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.
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 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. 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.
Modern taxonomy uses database 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, which attempts to list every documented species. 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.
'The All-Species Living Tree' Project is a collaboration between various academic groups/institutes, such as ARB, SILVA rRNA database project, and LPSN, with the aim of assembling a database of 16S rRNA sequences of all validly published species of Bacteria and Archaea. At one stage, 23S sequences were also collected, but this has since stopped.Currently there are over 10,950 species in the aligned dataset and several more are being added either as new species are discovered or species that are not represented in the database are sequenced. Initially the latter group consisted of 7% of species.Body plan
A body plan, Bauplan (German plural Baupläne), or ground plan is a set of morphological features common to many members of a phylum of animals. The vertebrate body plan is one of many: invertebrates consist of many phyla.
This term, usually applied to animals, envisages a "blueprint" encompassing aspects such as symmetry, segmentation and limb disposition. Evolutionary developmental biology seeks to explain the origins of diverse body plans.
Body plans have historically been considered to have evolved in a flash in the Cambrian explosion, but a more nuanced understanding of animal evolution suggests gradual development of body plans throughout the early Palaeozoic.Catalogue of Life
The Catalogue of Life is an online database that provides the world’s most comprehensive and authoritative index of known species of animals, plants, fungi and micro-organisms. It was created in 2001 as a partnership between the global Species 2000 and the American Integrated Taxonomic Information System. The Catalogue interface is available in twelve languages and is used by research scientists, citizen scientists, educators, and policy makers. The Catalogue is also used by the Biodiversity Heritage Library, the Barcode of Life Data System, Encyclopedia of Life, and the Global Biodiversity Information Facility. The Catalogue currently compiles data from 168 peer-reviewed taxonomic databases, that are maintained by specialist institutions around the world. As of 2018, the Catalogue lists 1,744,204 of the world's 2.2m extant species known to taxonomists on the planet at present time.Circumscription (taxonomy)
In biological taxonomy, circumscription is the definition of a taxon, that is, a group of organisms.
One goal of biological taxonomy is to achieve a stable circumscription for every taxon. Achieving stability is not yet a certainty in most taxa, and many that had been regarded as stable for decades are in upheaval in the light of rapid developments in molecular phylogenetics. In essence, new discoveries may invalidate the application of irrelevant attributes used in established or obsolete circumscriptions, or present new attributes useful in cladistic taxonomy.
An example of a taxonomic group with unstable circumscription is Anacardiaceae, a family of flowering plants. Some experts favor a circumscription in which this family includes the Blepharocaryaceae, Julianaceae, and Podoaceae, which are sometimes considered to be separate families.EPPO Code
An EPPO code, formerly known as a Bayer code, is an encoded identifier that is used by the European and Mediterranean Plant Protection Organization (EPPO), in a system designed to uniquely identify organisms – namely plants, pests and pathogens – that are important to agriculture and crop protection. EPPO codes are a core component of a database of names, both scientific and vernacular. Although originally started by the Bayer Corporation, the official list of codes is now maintained by EPPO.Encyclopedia of Life
The Encyclopedia of Life (EOL) is a free, online collaborative encyclopedia intended to document all of the 1.9 million living species known to science. It is compiled from existing databases and from contributions by experts and non-experts throughout the world. It aims to build one "infinitely expandable" page for each species, including video, sound, images, graphics, as well as text. In addition, the Encyclopedia incorporates content from the Biodiversity Heritage Library, which digitizes millions of pages of printed literature from the world's major natural history libraries. The project was initially backed by a US$50 million funding commitment, led by the MacArthur Foundation and the Sloan Foundation, who provided US$20 million and US$5 million, respectively. The additional US$25 million came from five cornerstone institutions—the Field Museum, Harvard University, the Marine Biological Laboratory, the Missouri Botanical Garden, and the Smithsonian Institution. The project was initially led by Jim Edwards and the development team by David Patterson. Today, participating institutions and individual donors continue to support EOL through financial contributions.Form classification
Form classification is the classification of organisms based on their morphology, which does not necessarily reflect their biological relationships. Form classification, generally restricted to palaeontology, reflects uncertainty; the goal of science is to move "form taxa" to biological taxa whose affinity is known.Form taxonomy is restricted to fossils that preserve too few characters for a conclusive taxonomic definition or assessment of their biological affinity, but whose study is made easier if a binomial name is available by which to identify them. The term "form classification" is preferred to "form taxonomy"; taxonomy suggests that the classification implies a biological affinity, whereas form classification is about giving a name to a group of morphologically-similar organisms that may not be related.A "parataxon" (not to be confused with parataxonomy), or "sciotaxon" (Gr. "shadow taxon"), is a classification based on incomplete data: for instance, the larval stage of an organism that cannot be matched up with an adult. It reflects a paucity of data that makes biological classification impossible. A sciotaxon is defined as a taxon thought to be equivalent to a true taxon (orthotaxon), but whose identity cannot be established because the two candidate taxa are preserved in different ways and thus cannot be compared directly.Homonym (biology)
In biology, a homonym is a name for a taxon that is identical in spelling to another such name, that belongs to a different taxon.
The rule in the International Code of Zoological Nomenclature is that the first such name to be published is the senior homonym and is to be used (it is "valid"); any others are junior homonyms and must be replaced with new names. It is, however, possible that if a senior homonym is archaic, and not in "prevailing usage," it may be declared a nomen oblitum and rendered unavailable, while the junior homonym is preserved as a nomen protectum.
Cuvier proposed the genus Echidna in 1797 for the spiny anteater.
However, Forster had already published the name Echidna in 1777 for a genus of moray eels.
Forster's use thus has priority, with Cuvier's being a junior homonym.
Illiger published the replacement name Tachyglossus in 1811.Similarly, the International Code of Nomenclature for algae, fungi, and plants (ICN) specifies that the first published of two or more homonyms is to be used: a later homonym is "illegitimate" and is not to be used unless conserved (or sanctioned, in the case of fungi).
Example: the later homonym Myroxylon L.f. (1782), in the family Leguminosae, is conserved against the earlier homonym Myroxylon J.R.Forst. & G.Forst. (1775) (now called Xylosma, in the family Salicaceae).Incertae sedis
Incertae sedis (Latin for "of uncertain placement") or problematica are terms 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 at specific taxonomic levels is indicated by incertae familiae (of uncertain family), incerti subordinis (of uncertain suborder), incerti ordinis (of uncertain order) and similar terms.Interim Register of Marine and Nonmarine Genera
The Interim Register of Marine and Nonmarine Genera (IRMNG) is a taxonomic database containing the scientific names of the genus, species, and higher ranks of many plants, animals and other kingdoms, both living and extinct, within a standardized taxonomic hierarchy, with associated machine-readable information on habitat (e.g. marine/nonmarine) and extant/fossil status for the majority of entries. The database aspires to provide complete coverage of both accepted and unaccepted genus names across all kingdoms, with a subset only of species names included as a lower priority. In its March 2019 release, IRMNG contained 490,095 genus names, of which 236,514 were listed as "accepted", 120,194 "unaccepted", 7,391 of "other" status i.e. interim unpublished, nomen dubium, nomen nudum, taxon inquirendum or temporary name, and 125,996 as "uncertain" (unassessed for taxonomic status at this time). The data originate from a range of (frequently domain-specific) print, online and database sources, and are reorganised into a common data structure to support a variety of online queries, generation of individual taxon pages, and bulk data supply to other biodiversity informatics projects. IRMNG content can be queried and displayed freely via the web, and download files of the data down to the taxonomic rank of genus as at specific dates are available in the Darwin Core Archive (DwC-A) format.
The data include homonyms (with their authorities), including both available (validly published) and selected unavailable names.IRMNG was initiated in 2006 by the Ocean Biogeographic Information System (OBIS) Australia at CSIRO Marine and Atmospheric Research, and since has been hosted by the Flanders Marine Institute (VLIZ) since 2016. VLIZ also hosts the World Register of Marine Species (WoRMS), using a common infrastructure.Content from IRMNG is used by several global Biodiversity Informatics projects including Open Tree of Life, the Global Biodiversity Information Facility (GBIF), and the Encyclopedia of Life (EOL), in addition to others including the Atlas of Living Australia and the Global Names Architecture (GNA)'s Global Names Resolver. From 2018 onwards, IRMNG data are also being used to populate the taxonomic hierarchy and provide generic names for a range of taxa in the areas of protists (kingdoms Protozoa and Chromista) and plant algae (Charophyta, Chlorophyta, Glaucophyta and Rhodophyta) in the Catalogue of Life. IRMNG identifiers have also been associated with numerous Wikipedia taxon pages, based on content harvested from IRMNG and stored in Wikidata.IRMNG was initiated and designed by Tony Rees. For his work on this and other projects, GBIF awarded him the 2014 Ebbe Nielsen Prize. The citation said, in part:
IRMNG in particular has been a tool of enormous importance to GBIF and others in supplying much of the detail for a global taxonomic classification of all life and as high-value taxon trait data in a form which can readily be reused in data validation and to enhance species pages.
IRMNG is now managed and curated by Rees, with assistance from the VLIZ team.Plazi
Plazi is a Swiss-based international non-profit association supporting and promoting the development of persistent and openly accessible digital bio-taxonomic literature. Plazi is maintaining a digital taxonomic literature repository to enable archiving of taxonomic treatments, enhances submitted taxonomic treatments by creating version in the XML formats TaxonX
and Taxpub, and educates about the importance of maintaining open access to scientific discourse and data. It is a contributor to the evolving e-taxonomy in the field of Biodiversity Informatics.The approach was originally developed in a binational National Science Foundation (NSF) and
German Research Foundation (DFG) digital library program to the American Museum of Natural History and the University of Karlsruhe, respectively, to create an XML schema modeling the content of bio-systematic literature. The TaxonX schema is applied to legacy publications using GoldenGATE, a semiautomatic editor. In its current state GoldenGATE is a complex mark up tool allowing community involvement in the process of rendering documents into semantically enhanced documents.
Plazi developed ways to make distribution records in published taxonomic literature accessible through a TAPIR service that is harvested by the Global Biodiversity Information Facility (GBIF). Similarly, the Species Page Model (SPM) transfer schema has been implemented to allow harvesting of treatments (the scientific descriptions of species and higher taxa) by third parties such as the Encyclopedia of Life (EOL). If available, the treatments are enhanced with links to external databases such as GenBank, The Hymenoptera Name Server for scientific names or ZooBank, the registry of zoological names.
Plazi claims it adheres to copyright law and argues that taxonomic treatments do not qualify as literary and artistic work. Plazi claims that such works are therefore in the public domain and can be freely used and disseminated (with scientific practice requiring appropriate citation).Royal Entomological Society Handbooks
Handbooks for the Identification of British Insects is a series of books produced by the Royal Entomological Society (RES). The aim of the Handbooks is to provide illustrated identification keys to the insects of Britain, together with concise morphological, biological and distributional information. The series also includes several Check Lists of British Insects. All books contain line drawings, with the most recent volumes including colour photographs. In recent years, new volumes in the series have been published by Field Studies Council, and benefit from association with the AIDGAP identification guides and Synopses of the British Fauna.Segregate (taxonomy)
In taxonomy, a segregate, or a segregate taxon is created when a taxon is split off from another taxon. This other taxon will be better known, usually bigger, and will continue to exist, even after the segregate taxon has been split off. A segregate will be either new or ephemeral: there is a tendency for taxonomists to disagree on segregates, and later workers often reunite a segregate with the 'mother' taxon.
If a segregate is generally accepted as a 'good' taxon it ceases to be a segregate. Thus, this is a way of indicating change in the taxonomic status. It should not be confused with, for example, the subdivision of a genus into subgenera.
For example, the genus Alsobia is a segregate from the genus Episcia; The genera Filipendula and Aruncus are segregates from the genus Spiraea.Synonym (taxonomy)
In scientific nomenclature, a synonym is a scientific name that applies to a taxon that (now) goes by a different scientific name, although the term is used somewhat differently in the zoological code of nomenclature. For example, Linnaeus was the first to give a scientific name (under the currently used system of scientific nomenclature) to the Norway spruce, which he called Pinus abies. This name is no longer in use: it is now a synonym of the current scientific name, Picea abies.
Unlike synonyms in other contexts, in taxonomy a synonym is not interchangeable with the name of which it is a synonym. In taxonomy, synonyms are not equals, but have a different status. For any taxon with a particular circumscription, position, and rank, only one scientific name is considered to be the correct one at any given time (this correct name is to be determined by applying the relevant code of nomenclature). A synonym cannot exist in isolation: it is always an alternative to a different scientific name. Given that the correct name of a taxon depends on the taxonomic viewpoint used (resulting in a particular circumscription, position and rank) a name that is one taxonomist's synonym may be another taxonomist's correct name (and vice versa).
Synonyms may arise whenever the same taxon is described and named more than once, independently. They may also arise when existing taxa are changed, as when two taxa are joined to become one, a species is moved to a different genus, a variety is moved to a different species, etc. Synonyms also come about when the codes of nomenclature change, so that older names are no longer acceptable; for example, Erica herbacea L. has been rejected in favour of Erica carnea L. and is thus its synonym.Taxonomic sequence
Taxonomic sequence (also known as systematic, phyletic or taxonomic order) is a sequence followed in listing of taxa which aids ease of use and roughly reflects the evolutionary relationships among the taxa. Taxonomic sequences can exist for taxa within any rank, that is, a list of families, genera, species can each have a sequence.
Early biologists used the concept of "age" or "primitiveness" of the groups in question to derive an order of arrangement, with "older" or more "primitive" groups being listed first and more recent or "advanced" ones last. A modern understanding of evolutionary biology has brought about a more robust framework for the taxonomic ordering of lists. A list may be seen as a rough one-dimensional representation of a phylogenetic tree. Taxonomic sequences are essentially heuristic devices that help in arrangements of linear systems such as books and information retrieval systems. Since phylogenetic relationships are complex and non-linear, there is no unique way to define the sequence, although they generally have the more basal listed first with species that cluster in a tight group included next to each other.The organization of field guides and taxonomic monographs may either follow or prescribe the taxonomic sequence; changes in these sequences are often introduced by new publications.Type genus
In biological classification, especially zoology, the type genus is the genus which defines a biological family and the root of the family name.Type species
In zoological nomenclature, a type species (species typica) is the species name with which the name of a genus or subgenus is considered to be permanently taxonomically associated, i.e., the species that contains the biological type specimen(s). A similar concept is used for suprageneric groups called a type genus.
In botanical nomenclature, these terms have no formal standing under the code of nomenclature, but are sometimes borrowed from zoological nomenclature. In botany, the type of a genus name is a specimen (or, rarely, an illustration) which is also the type of a species name. The species name that has that type can also be referred to as the type of the genus name. Names of genus and family ranks, the various subdivisions of those ranks, and some higher-rank names based on genus names, have such types.In bacteriology, a type species is assigned for each genus.Every named genus or subgenus in zoology, whether or not currently recognized as valid, is theoretically associated with a type species. In practice, however, there is a backlog of untypified names defined in older publications when it was not required to specify a type.Wikispecies
Wikispecies is a wiki-based online project supported by the Wikimedia Foundation. Its aim is to create a comprehensive free content catalogue of all species; the project is directed at scientists, rather than at the general public. Jimmy Wales stated that editors are not required to fax in their degrees, but that submissions will have to pass muster with a technical audience. Wikispecies is available under the GNU Free Documentation License and CC BY-SA 3.0.
Started in September 2004, with biologists across the world invited to contribute, the project had grown a framework encompassing the Linnaean taxonomy with links to Wikipedia articles on individual species by April 2005.Zootaxa
Zootaxa is a peer-reviewed scientific mega journal for animal taxonomists. It is published by Magnolia Press (Auckland, New Zealand). The journal was established by Zhi-Qiang Zhang in 2001 and new issues are published multiple times a week. As of December 2012 more than 26,300 new taxa have been described in the journal. Print and online versions are available.
|Apostles of Linnaeus|