Biology:Nomenclature codes

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Short description: Rulebooks of taxonomic nomenclature, in biology

Nomenclature codes or codes of nomenclature are the various rulebooks that govern the naming of living organisms. Standardizing the scientific names of biological organisms allows researchers to discuss findings (including the discovery of new species).

As the study of biology became increasingly specialized, specific codes were adopted for different types of organism.

To an end-user who only deals with names of species, with some awareness that species are assignable to genera, families, and other taxa of higher ranks, it may not be noticeable that there is more than one code, but beyond this basic level these are rather different in the way they work.

Binomial Nomenclature

In taxonomy, binomial nomenclature ("two-term naming system"), also called binary nomenclature, is a formal system of naming species of living things by giving each a name composed of two parts, both of which use Latin grammatical forms, although they can be based on words from other languages. Such a name is called a binomial name (which may be shortened to just "binomial"), a binomen, binominal name, or a scientific name; more informally it is also historically called a Latin name. In the ICZN, the system is also called binominal nomenclature,[1] "binomi'N'al" with an "N" before the "al", which is not a typographic error, meaning "two-name naming system".[2]

The first part of the name – the generic name – identifies the genus to which the species belongs, whereas the second part – the specific name or specific epithet – distinguishes the species within the genus. For example, modern humans belong to the genus Homo and within this genus to the species Homo sapiens. Tyrannosaurus rex is likely the most widely known binomial.[3]

The formal introduction of this system of naming species is credited to Carl Linnaeus, effectively beginning with his work Species Plantarum in 1753.[4] But as early as 1622, Gaspard Bauhin introduced in his book Pinax theatri botanici (English, Illustrated exposition of plants) containing many names of genera that were later adopted by Linnaeus.[5] The introduction of two-part names (binominal nomenclature) for species by Linnaeus was a welcome simplification because as our knowledge of biodiversity expanded, so did the length of the names, many of which had become unwieldy.[6]

Codification of Scientific Names

With all naturalists worldwide adopting binominal nomenclature, there arose several schools of thought about the details. It became ever more apparent that a detailed body of rules was necessary to govern scientific names. From the mid-19th century onwards, there were several initiatives to arrive at worldwide-accepted sets of rules. Presently nomenclature codes govern the naming of:

Differences between codes

Starting point

The starting point, that is the time from which these codes are in effect (usually retroactively), varies from group to group, and sometimes from rank to rank.[7] In botany and mycology, the starting point is often 1 May 1753 (Linnaeus, Species plantarum). In zoology, it is 1 January 1758 (Linnaeus, Systema Naturae, 10th Edition). On the other hand, bacteriology started anew, making a clean sweep in 1980 (Skerman et al., "Approved Lists of Bacterial Names"), although maintaining the original authors and dates of publication.[8]

Exceptions in botany:[9][10][11]

  • Spermatophyta and Pteridophyta, suprageneric names: 4 August 1789 (Jussieu, Genera plantarum);
  • Musci (except Sphagnaceae): 1 January 1801 (Hedwig, Species muscorum);
  • Sphagnaceae and Hepaticae (including Anthocerotae), suprageneric names: 4 August 1789 (Jussieu, Genera plantarum);
  • (Fungi:) Microsporidia are governed by the ICZN (treated as animals), and see below for fossil fungi;[12]
  • (Algae:)
    • Nostocaceae homocysteae: 1 January 1892 (Gomont, "Monographie des Oscillariées");
    • Nostocaceae heterocysteae: 1 January 1886 (Bornet & Flahault, "Révision des Nostocacées hétérocystées");
    • Desmidiaceae: 1 January 1848 (Ralfs, British Desmidieae);
    • Oedogoniaceae: 1 January 1900 (Hirn, "Monographie und Iconographie der Oedogoniaceen");
  • Fossil plants, algae (diatoms excepted) and fungi: 31 December 1820 (Sternberg, Flora der Vorwelt).

Exceptions in zoology:[13]

  • Spiders: 1757 (Clerck, Aranei Svecici).

Workings

There are also differences in the way codes work. For example, the ICN (the code for algae, fungi and plants) forbids tautonyms, while the ICZN, (the animal code) allows them.

Terminology

These codes differ in terminology, and there is a long-term project to "harmonize" this. For instance, the ICN uses "valid" in "valid publication of a name" (=the act of publishing a formal name), with "establishing a name" as the ICZN equivalent. The ICZN uses "valid" in "valid name" (="correct name"), with "correct name" as the ICN equivalent. Harmonization is making very limited progress.

Types

There are differences in respect of what kinds of types are used. The bacteriological code prefers living type cultures, but allows other kinds. There has been ongoing debate regarding which kind of type is more useful in a case like cyanobacteria.[14]

Other codes

BioCode

A more radical approach was made in 1997 when the IUBS/IUMS International Committee on Bionomenclature (ICB) presented the long debated Draft BioCode, proposed to replace all existing Codes with an harmonization of them.[15][16] The originally planned implementation date for the BioCode draft was January 1, 2000, but agreement to replace the existing Codes was not reached.

In 2011, a revised BioCode was proposed that, instead of replacing the existing Codes, would provide a unified context for them, referring to them when necessary.[17][18][19] Changes in the existing codes are slowly being made in the proposed directions.[20][21] However, participants of the last serious discussion of the draft Biocode concluded that it would probably not be implemented in their lifetimes.[22]

PhyloCode

Main page: Biology:PhyloCode

Many authors encountered problems in using the Linnean system in phylogenetic classification.[23] In fact, early proponents of rank-based nomenclature, such as Alphonse de Candolle and the authors of the 1886 version of the American Ornithologists' Union code of nomenclature already envisioned that in the future, rank-based nomenclature would have to be abandoned.[24][6] Another Code that was developed since 1998 is the PhyloCode, which now regulates names defined under phylogenetic nomenclature instead of the traditional Linnaean nomenclature. This new approach requires using phylogenetic definitions that refer to "specifiers", analogous to "type" under rank-based nomenclature. Such definitions delimit taxa under a given phylogeny, and this kind of nomenclature does not require use of absolute ranks. The Code took effect in 2020, with the publication of Phylonyms, a monograph that includes a list of the first names established under that code.

Ambiregnal protists

Some protists, sometimes called ambiregnal protists, have been considered to be both protozoa and algae, or protozoa and fungi, and names for these have been published under either or both of the ICZN and the ICN.[25][26] The resulting double language throughout protist classification schemes resulted in confusion.[27][28][29]

Groups claimed by both protozoologists and phycologists include euglenids, dinoflagellates, cryptomonads, haptophytes, glaucophytes, many heterokonts (e.g., chrysophytes, raphidophytes, silicoflagellates, some xanthophytes, proteromonads), some monadoid green algae (volvocaleans and prasinophytes), choanoflagellates, bicosoecids, ebriids and chlorarachniophytes.

Slime molds, plasmodial forms and other "fungus-like" organisms claimed by both protozoologists and mycologists include mycetozoans, plasmodiophorids, acrasids, and labyrinthulomycetess. Fungi claimed by both protozoologists and mycologists include chytrids, blastoclads, and the gut fungi.

Other problematic groups are the Cyanobacteria (ICNP/ICN) and Microsporidia (ICZN/ICN).

Unregulated taxa

The zoological code does not regulate names of taxa lower than subspecies or higher than superfamily. There are many attempts to introduce some order on the nomenclature of these taxa,[30][31] including the PhyloCode, the Duplostensional Nomenclatural System,[32][33] and circumscriptional nomenclature.[34][35]

The botanical code is applied primarily to the ranks of superfamily and below. There are some rules for names above the rank of superfamily, but the principle of priority does not apply to them, and the principle of typification is optional. These names may be either automatically typified names or be descriptive names.[36][37] In some circumstances, a taxon has two possible names (e.g., Chrysophyceae Pascher, 1914, nom. descrip.; Hibberd, 1976, nom. typificatum). Descriptive names are problematic, once that, if a taxon is split, it is not obvious which new group takes the existing name. Meanwhile, with typified names, the existing name is taken by the new group that still bears the type of this name. However, typified names present special problems for microorganisms.[29]

See also

References

  1. ↑ International Commission on Zoological Nomenclature 1999, Chapter 2, Article 5. Principle of Binominal Nomenclature ("Article 5. Principle of Binominal Nomenclature | International Code of Zoological Nomenclature". https://code.iczn.org/chapter-2-the-number-of-words-in-the-scientific-names-of-animals/article-5-principle-of-binominal-nomenclature/. )
  2. ↑ International Commission on Zoological Nomenclature 1999, Glossary – "binomen", "nomenclature, binominal" ("Glossary | International Code of Zoological Nomenclature". https://code.iczn.org/glossary/. )
  3. ↑ Busby, Arthur III (1997). A Guide to Rocks and Fossils. p. 103. 
  4. ↑ Knapp, Sandra. "What's in a name? A history of taxonomy: Linnaeus and the birth of modern taxonomy". NHM.ac.uk. Natural History Museum, London. http://www.nhm.ac.uk/nature-online/science-of-natural-history/taxonomy-systematics/history-taxonomy/session1/index.html. 
  5. ↑ Bauhin, Gaspard. "Pinax theatri botanici". Kyoto University Library. http://edb.kulib.kyoto-u.ac.jp/exhibit-e/b07/b07cont.html. 
  6. ↑ 6.0 6.1 Laurin, Michel (3 August 2023). The Advent of PhyloCode: The Continuing Evolution of Biological Nomenclature. CRC Press. doi:10.1201/9781003092827. ISBN 978-1-003-09282-7. https://www.taylorfrancis.com/books/mono/10.1201/9781003092827/advent-phylocode-michel-laurin. 
  7. ↑ Nicolson, Dan (1991). "A history of botanical nomenclature". Annals of the Missouri Botanical Garden 78 (1): 33–56. doi:10.2307/2399589. https://archive.org/details/cbarchive_53278_ahistoryofbotanicalnomenclatur1991. 
  8. ↑ Skerman, V. B. D.; McGowan, V.; Sneath, P. H. A. (1980). "Approved lists of bacterial names". Int. J. Syst. Bacteriol. 30: 225–420. doi:10.1099/00207713-30-1-225. 
  9. ↑ Chitwood, B. G. (1958). "The designation of official names for higher taxa of invertebrates". Bull. Zool. Nomencl. 15: 860–895. doi:10.5962/bhl.part.19410. https://www.biodiversitylibrary.org/page/12219511#page/292/mode/1up. 
  10. ↑ Silva, P. C. (1958). "Later starting points in algae". Taxon 7 (7): 181–184. doi:10.2307/1216399. http://www.iapt-taxon.org/historic/Congress/IBC_1959/Prop058.pdf. 
  11. ↑ (Turland et al. 2018 {{{2}}})
  12. ↑ (Turland at al. 2018 {{{2}}})
  13. ↑ ICZN - International Commission on Zoological Nomenclature (1999). International Code of Zoological Nomenclature. Fourth Edition. The International Trust for Zoological Nomenclature, London, UK. 306 pp., [1].
  14. ↑ Oren, Aharon (2004). "A proposal for further integration of the cyanobacteria under the Bacteriological Code". International Journal of Systematic and Evolutionary Microbiology 54 (Pt. 5): 1895–1902. doi:10.1099/ijs.0.03008-0. PMID 15388760. 
  15. ↑ "Draft BioCode". 1997. http://www.bgbm.org/IAPT/biocode/default.htm. 
  16. ↑ McNeill, John (4 November 1996). "Chapter 2. The BioCode: Integrated biological Nomenclature for the 21st Century?". http://www.plantsystematics.org/reveal/pbio/nomcl/mcne.html. 
  17. ↑ "The Draft BioCode (2011)". International Committee on Bionomenclature (ICB). http://www.bgbm.org/biodivinf/docs/biocode2011/biocode2.html. 
  18. ↑ Greuter, W.; Garrity, G.; Hawksworth, D. L.; Jahn, R.; Kirk, P. M.; Knapp, S.; McNeill, J.; Michel, E. et al. (2011). "Draft BioCode (2011): Principles and rules regulating the naming of organisms". Taxon 60: 201–212. doi:10.1002/tax.601019. 
  19. ↑ Hawksworth, D. L. (2011). "Introducing the Draft BioCode (2011)". Taxon 60 (1): 199–200. doi:10.1002/tax.601018. http://iczn.org/content/introducing-draft-biocode-2011. 
  20. ↑ DL Hawksworth (2011) BioCode 2011. Introduction. http://www.bionomenclature.net/biocode2011.html
  21. ↑ Werner Greuter (2011) BioCode 2011. Explanatory prologue. http://www.bionomenclature.net/biocode2011.html
  22. ↑ Oren, Aharon (2019). in Bergey's Manual of Systematics of Archaea and Bacteria (1 ed.). Wiley. p. 1-12. doi:10.1002/9781118960608.bm00004.pub2. ISBN 978-1-118-96060-8. https://doi.org/10.1002/9781118960608.bm00004.pub2. 
  23. ↑ de Queiroz, K.; Gauthier, J. (December 1990). "Phylogeny as a Central Principle in Taxonomy: Phylogenetic Definitions of Taxon Names". Systematic Zoology 39 (4): 307–322. doi:10.2307/2992353. http://vertebrates.si.edu/herps/herps_pdfs/deQueiroz_pdfs/1990deQ_GauSZ.pdf. 
  24. ↑ Laurin, Michel (23 July 2023). "The PhyloCode : The logical outcome of millennia of evolution of biological nomenclature?". Zoologica Scripta 52 (6): 543–555. doi:10.1111/zsc.12625. ISSN 0300-3256. https://doi.org/10.1111/zsc.12625. 
  25. ↑ Corliss, J. O. (1995). "The ambiregnal protists and the codes of nomenclature: A brief review of the problem and of proposed solutions". Bulletin of Zoological Nomenclature 52: 11–17. doi:10.5962/bhl.part.6717. http://biostor.org/reference/2636. 
  26. ↑ (McNeill et al. 2012 {{{2}}})
  27. ↑ Adl, S. M. et al. Diversity, Nomenclature, and Taxonomy of Protists. Systematic Biology, p. 684-689, 2007, [2].
  28. ↑ Elbrächter, M. et al. Establishing an Agenda for Calcareous Dinoflagellates Research (Thoracosphaeraceae, Dinophyceae) including a nomenclatural synopsis of generic names. Taxon 57, p. 1289–1303, 2008, [3]
  29. ↑ 29.0 29.1 (Lahr et al. 2012 {{{2}}})
  30. ↑ Dubois, A. (2006). Proposed Rules for the incorporation of nomina of higher-ranked zoological taxa in the International Code of Zoological Nomenclature. 2. The proposed Rules and their rationale. Zoosystema, 28 (1): 165‒258, [4].
  31. ↑ Frost, D. R. et al. (2006). The Amphibian Tree of Life. Bulletin of the American Museum of Natural History 297: 1–291, [5],
  32. ↑ Dubois, Alain (2015). "The Duplostensional Nomenclatural System for higher zoological nomenclature". Dumerilia 5: 1–108. 
  33. ↑ Dubois, Alain; Ohler, Annemarie; Pyron, R. Alexander (26 February 2021). "New concepts and methods for phylogenetic taxonomy and nomenclature in zoology, exemplified by a new ranked cladonomy of recent amphibians (Lissamphibia)". Megataxa 5 (1). doi:10.11646/megataxa.5.1.1. ISSN 2703-3090. 
  34. ↑ Klüge, N. J. (2010). Circumscriptional names of higher taxa in Hexapoda. Bionomina, 1, 15-55, [6].
  35. ↑ Kluge, N. J. (1999). "A system of alternative nomenclatures of supra-species taxa. Linnaean and post-Linnaean principles of systematics". Entomological Review 79 (2): 133–147. 
  36. ↑ (McNeill et al. 2012 {{{2}}})
  37. ↑ (Turland et al. 2018 {{{2}}})

Bibliography

External links



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