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Genetypes

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Genetypes

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 will be a “topogenetype,” and so forth. In addition, the genetic marker(s) used should also 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 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:

  • Leptoderma macrophthalmum hologenetype mitogenome - AP011500 [4]
  • Milyeringa brooksi paragenetype COI - HM590595[5]
  • Milyeringa brooksi paragenetype NDI - HM590607[5]


The genetypes concept was superseded by the GenSeq concept, proposed in 2013 due to some confusion among researchers that genetypes were equivalent to name-bearing types.[6]

See also

References

  1. ^ Chakrabarty, Prosanta (2010). "Genetypes: a concept to help integrate molecular systematics and traditional taxonomy". Zootaxa 2632: 67–68. 
  2. ^ a b 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.  
  3. ^ "JFB Instruction to Authors". Journal of Fish Biology. 
  4. ^ Byrkjedal, Ingvar; Jan Yde Poulsen & John Galbraith (2011). n.sp., a new species of smooth-head (Otocephala: Alepocephalidae) from the Mid Atlantic Ridge"Leptoderma macrophthalmum". Zootaxa 2876: 49–56. 
  5. ^ a b Chakrabarty, Prosanta (2010). , n. sp."Milyeringa brooksi"Status and phylogeny of Milyeringidae (Teleostei: Gobiiformes), with the description of a new blind cave-fish from Australia, . Zootaxa 2557: 19–28. 
  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.  
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