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).[1] 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.[2]

In bacteriology, a type species is assigned for each genus.[3]

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.

Whooper Swan - geograph.org.uk - 1370869
Cygnus cygnus, the whooper swan, is the type species of the genus Cygnus.

Use in zoology

A type species is both a concept and a practical system that is used in the classification and nomenclature (naming) of animals. The "type species" represents the reference species and thus "definition" for a particular genus name. Whenever a taxon containing multiple species must be divided into more than one genus, the type species automatically assigns the name of the original taxon to one of the resulting new taxa, the one that includes the type species.

The term "type species" is regulated in zoological nomenclature by article 42.3 of the International Code of Zoological Nomenclature, which defines a type species as the name-bearing type of the name of a genus or subgenus (a "genus-group name"). In the Glossary, type species is defined as

The nominal species that is the name-bearing type of a nominal genus or subgenus.[4]

The type species permanently attaches a formal name (the generic name) to a genus by providing just one species within that genus to which the genus name is permanently linked (i.e. the genus must include that species if it is to bear the name). The species name in turn is fixed, in theory, to a type specimen.

For example, the type species for the land snail genus Monacha is Helix cartusiana, the name under which the species was first described, known as Monacha cartusiana when placed in the genus Monacha. That genus is currently placed within the family Hygromiidae. The type genus for that family is the genus Hygromia.

The concept of the type species in zoology was introduced by Pierre André Latreille.[5]

Citing

The International Code of Zoological Nomenclature states that the original name (binomen) of the type species should always be cited. It gives an example in Article 67.1. Astacus marinus Fabricius, 1775 was later designated as the type species of the genus Homarus, thus giving it the name Homarus marinus (Fabricius, 1775). However, the type species of Homarus should always be cited using its original name, i.e. Astacus marinus Fabricius, 1775.[1]

Although the International Code of Nomenclature for algae, fungi, and plants does not contain the same explicit statement, examples make it clear that the original name is used, so that the "type species" of a genus name need not have a name within that genus. Thus in Article 10, Ex. 3, the type of the genus name Elodes is quoted as the type of the species name Hypericum aegypticum, not as the type of the species name Elodes aegyptica.[2] (Elodes is not now considered distinct from Hypericum.)

See also

References

  1. ^ a b "International Code of Zoological Nomenclature, Fourth Edition, adopted by the International Union of Biological Sciences". International Commission on Zoological Nomenclature. 1999. Article 67.1
  2. ^ a b International Code of Nomenclature for algae, fungi, and plants (ICN) articles 7 through 10 (Melbourne Code, 2012)
  3. ^ "Chapter 3: Rules of Nomenclature with Recommendations; Section 4. Nomenclatural Types and Their Designation", International Code of Nomenclature of Bacteria: Bacteriological Code, 1990 Revision
  4. ^ ICZN Code Glossary
  5. ^ Claude Dupuis (1974). "Pierre André Latreille (1762–1833): the foremost entomologist of his time" (PDF). Annual Review of Entomology. 19: 1–14. doi:10.1146/annurev.en.19.010174.000245.
Acacia

Acacia, commonly known as the wattles or acacias, is a large genus of shrubs and trees in the subfamily Mimosoideae of the pea family Fabaceae. Initially it comprised a group of plant species native to Africa and Australia, with the first species A. nilotica described by Linnaeus. Controversy erupted in the early 2000s when it became evident that the genus as it stood was not monophyletic, and that several divergent lineages needed to be placed in separate genera. It turned out that one lineage comprising over 900 species mainly native to Australia was not closely related to the mainly African lineage that contained A. nilotica—the first and type species. This meant that the Australian lineage (by far the most prolific in number of species) would need to be renamed. Botanist Les Pedley named this group Racosperma, which was inconsistently adopted. Australian botanists proposed that this would be more disruptive than setting a different type species (A. penninervis) and allowing this large number of species to remain Acacia, resulting in the two African lineages being renamed Vachellia and Senegalia, and the two New World lineages renamed Acaciella and Mariosousa. This was officially adopted, but many botanists from Africa and elsewhere disagreed that this was necessary.

A number of species have been introduced to various parts of the world, and two million hectares of commercial plantations have been established. The heterogeneous group varies considerably in habit, from mat-like subshrubs to canopy trees in forest.

Alvernaviridae

Alvernaviridae is a family of viruses. Dinoflagellates serve as natural hosts. There is currently only one species in this family: the type species Heterocapsa circularisquama RNA virus 01. Diseases associated with this family include: control of the host population possibly through lysis of the host cell.

Bunyavirales

Bunyavirales is an order of negative-sense single-stranded RNA viruses. It is the only order in the class Ellioviricetes. It was formerly known as Bunyaviridae family of viruses. The name Bunyavirales derives from Bunyamwera, where the original type species Bunyamwera orthobunyavirus was first discovered. Ellioviricetes is named in honor of late virologist Richard M. Elliott for his early work on bunyaviruses.In 2017, the ICTV reclassified the family Bunyaviridae as Bunyavirales, a taxonomic shift from a family of viruses to an order of viruses. The body made these decisions in a 2016 convening in Budapest. Primary reasons for this alteration revolve around these observations: approximately half of viruses in the former Bunyaviridae were at the time unassigned to a genus; novel viruses discovered that were characteristic of and clustered around Bunyaviridae based on phylogenetic analyses had bi-segmented genomes (as opposed to Bunyaviridae's tri-segmentation); and plant viruses also lacking tri-segmentation were previously known to be "bunya-like" yet were not properly assigned to the family Bunyaviridae based upon the past taxonomic classifications. All five genera formerly in the family Bunyaviridae (Hantavirus, Nairovirus, Orthobunyavirus, Phlebovirus, Tospovirus) are now novel viral families, some of which have been combined. These new families include: Hantaviridae, Feraviridae, Fimoviridae, Jonviridae, Nairoviridae, Peribunyaviridae, Phasmaviridae, Phenuiviridae, and Tospoviridae.

This order of viruses belong to the fifth group of the Baltimore classification, the so-called negative-sense single stranded ribonucleic acid (−)ssRNA. They are enveloped RNA viruses. Though generally found in arthropods or rodents, certain viruses in this order occasionally infect humans. Some of them also infect plants.A majority of bunyaviruses are vector-borne. With the exception of Hantaviruses, all viruses in the Bunyavirales order are transmitted by arthropods (mosquitos, tick, or sandfly). Hantaviruses are transmitted through contact with deer mice feces. Incidence of infection is closely linked to vector activity, for example, mosquito-borne viruses are more common in the summer.Human infections with certain members of Bunyavirales, such as Crimean-Congo hemorrhagic fever orthonairovirus, are associated with high levels of morbidity and mortality, consequently handling of these viruses must occur with a Biosafety level 4 laboratory. They are also the cause of severe fever with thrombocytopenia syndrome.Hanta virus or Hantavirus Hemorrhagic fever, common in Korea, Scandinavia, Russia, and western North America, is associated with high fever, lung edema and pulmonary failure. Mortality is around 55%. The antibody reaction plays an important role in decreasing levels of viremia.

Carmotetraviridae

Carmotetraviridae is a family of viruses; there is currently only one genus in this family, Alphacarmotetravirus, and one species in this genus, the type species Providence virus. Lepidopteran insects serve as natural hosts.

Emaravirus

Emaravirus is a genus of plant viruses. The genus has nine species. The type species European mountain ash ringspot-associated emaravirus is associated with a leaf mottling and ringspot disease of European mountain ash Sorbus aucuparia. It can be transmitted by grafting and possibly mites.

Haloarchaea

Haloarchaea (halophilic archaea, halophilic archaebacteria, halobacteria) are a class of the Euryarchaeota, found in water saturated or nearly saturated with salt. Halobacteria are now recognized as archaea, rather than bacteria and are one of the largest groups. The name 'halobacteria' was assigned to this group of organisms before the existence of the domain Archaea was realized, and remains valid according to taxonomic rules. In a non-taxonomic context, halophilic archaea are referred to as haloarchaea to distinguish them from halophilic bacteria.

These microorganisms are members of the halophile community, in that they require high salt concentrations to grow, with most species requiring more than 2.0M NaCl for growth and survival. They are a distinct evolutionary branch of the Archaea distinguished by possession of ether-linked lipids and the absence of murein in their cell walls.

Haloarchaea can grow aerobically or anaerobically. Parts of the membranes of haloarchaea are purplish in color, and large blooms of haloarchaea appear reddish, from the pigment bacteriorhodopsin, related to the retinal pigment rhodopsin, which it uses to transform light energy into chemical energy by a process unrelated to chlorophyll-based photosynthesis.

Haloarchaea have a potential to solubilize phosphorus. Phosphorus-solubilizing halophilic archaea may well play a role in P (phosphorus) nutrition to vegetation growing in hypersaline soils. Haloarchaea may also have application as inoculants for crops growing in hypersaline regions.

Iflaviridae

Iflaviridae is a family of positive sense RNA viruses insect-infecting viruses. Some of the insects commonly infected by iflaviruses include aphids, leafhoppers, flies, bees, ants, silkworms and wasps. The name "Ifla" is derived from the name "Infectious flacherie virus", for the type species. There is only one genus (Iflavirus) and 14 species in this family, including the type species Infectious flacherie virus.

International Code of Zoological Nomenclature

The International Code of Zoological Nomenclature (ICZN) is a widely accepted convention in zoology that rules the formal scientific naming of organisms treated as animals. It is also informally known as the ICZN Code, for its publisher, the International Commission on Zoological Nomenclature (which shares the acronym "ICZN"). The rules principally regulate:

How names are correctly established in the frame of binominal nomenclature

Which name must be used in case of name conflicts

How scientific literature must cite namesZoological nomenclature is independent of other systems of nomenclature, for example botanical nomenclature. This implies that animals can have the same generic names as plants.

The rules and recommendations have one fundamental aim: to provide the maximum universality and continuity in the naming of all animals, except where taxonomic judgment dictates otherwise. The code is meant to guide only the nomenclature of animals, while leaving zoologists freedom in classifying new taxa.

In other words, whether a species itself is or is not a recognized entity is a subjective decision, but what name should be applied to it is not. The code applies only to the latter. A new animal name published without adherence to the code may be deemed simply "unavailable" if it fails to meet certain criteria, or fall entirely out of the province of science (e.g., the "scientific name" for the Loch Ness Monster).

The rules in the code determine what names are valid for any taxon in the family group, genus group, and species group. It has additional (but more limited) provisions on names in higher ranks. The code recognizes no case law. Any dispute is decided first by applying the code directly, and not by reference to precedent.

The code is also retroactive or retrospective, which means that previous editions of the code, or previous other rules and conventions have no force any more today, and the nomenclatural acts published 'back in the old times' must be evaluated only under the present edition of the code. In cases of disputes concerning the interpretation, the usual procedure is to consult the French Code, lastly a case can be brought to the commission who has the right to publish a final decision.

Marnaviridae

Marnaviridae is a family of positive-stranded RNA viruses in the order Picornavirales. The first marnavirus that was isolated, and which is the type species for the family, infects a Microphyte: the toxic bloom-forming Raphidophyte, Heterosigma akashiwo. Algae therefore seem to serve as natural hosts. There is only one genus (Marnavirus) and one species in this family, the type species Heterosigma akashiwo RNA virus (HaRNAV).HaRNAV was isolated from water collected in the Strait of Georgia in British Columbia, Canada, from a concentrated virus assemblage using the host Heterosigma akashiwo (NEPCC 522).Although the International Committee on the Taxonomy of Viruses currently only recognizes one member of the family, environmental sequencing of the RNA-dependent RNA polymerase has shown that there are many related viruses in the sea that show a high degree of temporal and spatial diversity.

Megabirnaviridae

Megabirnaviridae is a family of viruses with one genus Megabirnavirus. Fungi serve as natural hosts. There is only one species in this family: the type species Rosellinia necatrix megabirnavirus 1. Diseases associated with this family include: reduced host virulence.

Pacullidae

Pacullidae is a family of araneomorph spiders. It was merged into Tetrablemmidae by Brignoli in 1973 and by Lehtinen in 1981. In 2016, a large phylogenetic study proposed reviving the family. As of May 2018, the family is accepted by the World Spider Catalog.

Podoviridae

Podoviridae is a family of viruses in the order Caudovirales. Bacteria serve as natural hosts. There are currently 50 species in this family, divided among 20 genera. This family is characterized by having very short, noncontractile tails.

Pseudoviridae

The Pseudoviridae are a family of viruses, including the following genera:

Genus Pseudovirus; type species: Saccharomyces cerevisiae Ty1 virus

Genus Hemivirus; type species: Drosophila melanogaster copia virus

Genus Sirevirus; type species: Glycine max SIRE1 virusA further Pseudoviridae species without classified genus is Phaseolus vulgaris Tpv2-6 virus.

Quadriviridae

Quadriviridae is a family of viruses with a single genus Quadrivirus. Fungi serve as natural hosts. There is currently only one species in this family: the type species Rosellinia necatrix quadrivirus 1.

Retrovirus

A retrovirus is a type of RNA virus that inserts a copy of its genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Such viruses are either single stranded RNA (e.g. HIV) or double stranded DNA (e.g. Hepatitis B virus) viruses.

Once inside the host cell's cytoplasm, the virus uses its own reverse transcriptase enzyme to produce DNA from its RNA genome, the reverse of the usual pattern, thus retro (backwards). The new DNA is then incorporated into the host cell genome by an integrase enzyme, at which point the retroviral DNA is referred to as a provirus. The host cell then treats the viral DNA as part of its own genome, transcribing and translating the viral genes along with the cell's own genes, producing the proteins required to assemble new copies of the virus. It is difficult to detect the virus until it has infected the host. At that point, the infection will persist indefinitely.

In most viruses, DNA is transcribed into RNA, and then RNA is translated into protein. However, retroviruses function differently, as their RNA is reverse-transcribed into DNA, which is integrated into the host cell's genome (when it becomes a provirus), and then undergoes the usual transcription and translational processes to express the genes carried by the virus. The information contained in a retroviral gene is thus used to generate the corresponding protein via the sequence: RNA → DNA → RNA → polypeptide. This extends the fundamental process identified by Francis Crick (one gene-one peptide) in which the sequence is DNA → RNA → peptide (proteins are made of one or more polypeptide chains; for example, haemoglobin is a four-chain peptide).

Retroviruses are valuable research tools in molecular biology, and they have been used successfully in gene delivery systems.

Rhizidiovirus

Rhizidiovirus is a genus of viruses. Stramenopiles (fungi and hyphochytridiomycota) serve as natural hosts. There is only one species in this genus: the type species Rhizidiomyces virus.

Tetraviridae

The Tetraviridae were a family of viruses so named because they have a T=4 symmetry (T is the triangulation number), are extremely host specific, and infect moths and butterflies of the following genera:

Genus Betatetravirus; type species: Nudaurelia capensis β virus (see Nudaurelia cytherea capensis)

Genus Omegatetravirus; type species: Nudaurelia capensis ω virusThis family was divided into three families by the ICTV in 2011: Alphatetraviridae, Carmotetraviridae and Permutotetraviridae.

Type (biology)

In biology, a type is a particular specimen (or in some cases a group of specimens) of an organism to which the scientific name of that organism is formally attached. In other words, a type is an example that serves to anchor or centralize the defining features of that particular taxon. In older usage (pre-1900 in botany), a type was a taxon rather than a specimen.A taxon is a scientifically named grouping of organisms with other like organisms, a set that includes some organisms and excludes others, based on a detailed published description (for example a species description) and on the provision of type material, which is usually available to scientists for examination in a major museum research collection, or similar institution.

Virus classification

Virus classification is the process of naming viruses and placing them into a taxonomic system. Similar to the classification systems used for cellular organisms, virus classification is the subject of ongoing debate and proposals. This is mainly due to the pseudo-living nature of viruses, which is to say they are non-living particles with some chemical characteristics similar to those of life, or non-cellular life. As such, they do not fit neatly into the established biological classification system in place for cellular organisms.

Viruses are mainly classified by phenotypic characteristics, such as morphology, nucleic acid type, mode of replication, host organisms, and the type of disease they cause. The formal taxonomic classification of viruses is the responsibility of the International Committee on Taxonomy of Viruses (ICTV) system, although the Baltimore classification system can be used to place viruses into one of seven groups based on their manner of mRNA synthesis. Specific naming conventions and further classification guidelines are set out by the ICTV.

A catalogue of all the world's known viruses has been proposed; some related preliminary efforts have been accomplished.

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