Genetypes

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Genetypes is a taxonomic concept proposed in 2010 to describe any genetic sequences from type specimens. [1] [2] This nomenclature integrates molecular systematics and terms used in biological taxonomy. This nomenclature is designed to label, or flag, genetic sequences that were sampled from type specimens. The nomenclature of genetypes proposes that genetic sequences from a holotype should be referred to as a “hologenetype” (from “holotype” and “genetype”), sequences from a topotype should be a “topogenetype”, and so forth. In addition, the genetic marker(s) used should be incorporated into the nomenclature (e.g. paragenetype ND2).

The genetypes nomenclatural system could be used to flag “gold standard” sequences that due to their direct link to type specimens will be more credible than standard sequences whose species identification may be problematic. Misidentifications plague many sequences on GenBank [ citation needed ] and having some sequences that are linked to type specimens will help locate and manage misidentifications and to create positively identified "gold standard" sequences available for comparison. It is suggested that this nomenclature be used in publications and databases that display or discuss sequences from type specimens. [3] [2]

Examples of genetypes include:

The genetypes concept was superseded by the GenSeq concept, proposed in 2013 due to some confusion among researchers that genetypes were equivalent to name-bearing types. [6] [ clarification needed ]

See also

Related Research Articles

<span class="mw-page-title-main">Holotype</span> Example of an organism used to describe its species

A holotype is a single physical example of an organism, known to have been used when the species was formally described. It is either the single such physical example or one of several examples, but explicitly designated as the holotype. Under the International Code of Zoological Nomenclature (ICZN), a holotype is one of several kinds of name-bearing types. In the International Code of Nomenclature for algae, fungi, and plants (ICN) and ICZN, the definitions of types are similar in intent but not identical in terminology or underlying concept.

<span class="mw-page-title-main">Type species</span> Term used in biological nomenclature

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<span class="mw-page-title-main">Type (biology)</span> Specimen(s) to which a scientific name is formally attached

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<i>Nemadactylus macropterus</i> Species of fish

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The Singapore whiskered bat is or was a possible species of vesper bat endemic to Singapore. No specimens have been found since its original scientific description in 1840 by Dutch zoologist Coenraad Temminck. Modern analysis of the type specimen found it to have skull fragments from another species and the skin to be in too poor a condition to confirm as distinct species.

<span class="mw-page-title-main">Oblong turtle</span> Species of turtle

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<span class="mw-page-title-main">Gobiiformes</span> Order of fishes

The Gobiiformes are an order of fish that includes the gobies and their relatives. The order, which was previously considered a suborder of Perciformes, is made up of about 2,211 species that are divided between seven families. Phylogenetic relationships of the Gobiiformes have been elucidated using molecular data. Gobiiforms are primarily small species that live in marine water, but roughly 10% of these species inhabit fresh water. This order is composed chiefly of benthic or burrowing species; like many other benthic fishes, most gobiiforms do not have a gas bladder or any other means of controlling their buoyancy in water, so they must spend most of their time on or near the bottom. Gobiiformes means "Goby-like".

<span class="mw-page-title-main">Cavefish</span>

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<span class="mw-page-title-main">Prosanta Chakrabarty</span>

Prosanta Chakrabarty is an American ichthyologist and professor of ichthyology, evolution and systematics at Louisiana State University. He studied at McGill University where he received a bachelor of science in Applied Zoology and at the University of Michigan where he obtained his PhD in Ecology and Evolution. Among other professional positions he was a Program Director for the National Science Foundation and is currently the President-Elect of the American Society of Ichthyologist and Herpetologist. He was named a TED Fellow in 2016, and a TED Senior Fellow in 2018. He was named an Elected Fellow of the AAAS for "distinguished contributions to evolutionary biology, focusing on the bioluminescent systems and historical biogeography of freshwater fishes, and for effectively communicating science to the public."

Carole C. Baldwin is a research zoologist, curator of fishes, and the vertebrate zoology department chair at the National Museum of Natural History. She researches the diversity and evolution of coral reef and deep sea fishes through integrative taxonomy. She is on the board of directors of the National Aquarium in Washington, D.C. She is a senior author on the educational seafood cookbook One Fish, Two Fish, Crawfish, Bluefish - The Smithsonian Sustainable Seafood Cookbook, and the principal investigator on the Deep Reef Observation Project (DROP) which researches reefs to 300 meter depths. She was inducted into the Women Divers Hall of Fame in 2003.

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Symmetrolestes is an extinct genus of small spalacotheriid mammal from the Early Cretaceous period of Japan. The genus contains one species known as S. parvus, the type fossil is from fluvial deposits located in the Dinosaur Quarry in the Kitadani Formation, near the city of Katsuyama which lies alongside valley of the Sugiyamagawa River. It was described by Tsubamoto and Rougier in 2004 keeping the Holotype at the National Science Museum, Tokyo, Japan.

The Wells and Wellington affair was a dispute about the publication of three papers in the Australian Journal of Herpetology in 1983 and 1985. The periodical was established in 1981 as a peer-reviewed scientific journal focusing on the study of amphibians and reptiles (herpetology). Its first two issues were published under the editorship of Richard W. Wells, a first-year biology student at Australia's University of New England. Wells then ceased communicating with the journal's editorial board for two years before suddenly publishing three papers without peer review in the journal in 1983 and 1985. Coauthored by himself and high school teacher Cliff Ross Wellington, the papers reorganized the taxonomy of all of Australia's and New Zealand's amphibians and reptiles and proposed over 700 changes to the binomial nomenclature of the region's herpetofauna.

References

  1. Chakrabarty, Prosanta (2010). "Genetypes: a concept to help integrate molecular systematics and traditional taxonomy" (PDF). Zootaxa. 2632: 67–68. doi: 10.11646/zootaxa.2632.1.4 .
  2. 1 2 Harrison, I. J.; Chakrabarty, P.; Freyhof, J.; Craig, J. F. (May 2011). "Correct nomenclature and recommendations for preserving and cataloguing voucher material and genetic sequences". Journal of Fish Biology. 78 (5): 1283–1290. doi: 10.1111/j.1095-8649.2011.02979.x . PMID   21539541.
  3. "JFB Instruction to Authors". Journal of Fish Biology.[ permanent dead link ]
  4. Byrkjedal, Ingvar; Jan Yde Poulsen; John Galbraith (2011). "Leptoderma macrophthalmum n.sp., a new species of smooth-head (Otocephala: Alepocephalidae) from the Mid Atlantic Ridge" (PDF). Zootaxa. 2876: 49–56. doi:10.11646/zootaxa.2876.1.5.
  5. 1 2 Chakrabarty, Prosanta (2010). "Status and phylogeny of Milyeringidae (Teleostei: Gobiiformes), with the description of a new blind cave-fish from Australia, Milyeringa brooksi, n. sp" (PDF). Zootaxa. 2557: 19–28. doi:10.11646/zootaxa.2557.1.2.
  6. Chakrabarty, Prosanta; Warren, Melanie; Page, Lawrence; Baldwin, Carole (2013). "GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources". ZooKeys (346): 29–41. doi:10.3897/zookeys.346.5753. PMC   3821064 . PMID   24223486.