Phylogeny and Systematics
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The criteria by which we group organisms is one thing; the manner in which we give them names, what those names mean and how we define them, is another. The approach to naming groups (nomenclature) most familiar to all of us was invented by Karl von Linne, a.k.a. Carolus Linnaeus. He invented binomial nomenclature by snipping the then-often-used <genus> + <lots of attributes of a species> down to <genus> + <some distinctive attribute of a species>. He also rationalized nomenclature, using the same name for both sexes and for adults and juveniles of a species. Like many of his contemporaries, he used Latin, which has the nice feature of being nationalistically neutral.
His hierarchy of taxa (singular: taxon) was kingdom, class, order, genus, and species, but later taxonomists added phylum, division, family, and various sub- and supertaxa, and even such taxa as domain, cohort, tribe, and section.
Taxonomic names and parts of names come from a variety of sources, though they must all be Latinized. Aside from personal and place names, taxonomic name parts are almost always words drawn from Latin and Classical Greek, with other languages occasionally represented. They are often common names (Homo, Canis, Bos, Equus, Columba, Salmo, Apis, Lilium, Rosa, Quercus, Pinus, etc.), and also words for various features and descriptions of them. Compound words are very common, though this sometimes leads to jawbreakers like Strongylocentrotus purpuratus (the purple sea urchin, found off the North American coast of the Pacific, often used as a model system). Higher-level taxa are often named after genera that they contain.
Several taxonomic ranks have standardized suffixes. Animal families end in -idae, plant families in -aceae, bird orders in -iformes, plant orders in -ales, etc. However, genera and lower-ranking taxa do not; genus names are singular nouns, while species names are either singular nouns, adjectives, or genitives (Latin's of-case). Also, taxon names above the genus are all plurals or collectives, whether or not they have some standardized suffix. Such conventions allow comparison of the ranks of different taxa at a glance.
Many organisms have received different names from different taxonomists; such conflicts are resolved by using the first-bestowed name. Thus, Apatosaurus pushed out Brontosaurus and Hyracotherium pushed out Eohippus. Although the international codes of nomenclature have no rules against it, this rule of priority has meant that some inappropriate names -- names that don't accurately reflect the content or characters of taxa -- have survived. The chimpanzee, Pan troglodytes, got its species name because Linnaeus believed that it lives in caves; it actually lives in forests. Also, Basilosaurus ("king lizard") turned out to be an early cetacean rather than a marine reptile upon closer examination.
Questions of which name is appropriate for any given taxon can become complicated if multiple options exist. For this reason, the various Codes of Nomenclature have developed to guide decisions on name usage. The two most significant codes are the International Code of Zoological Nomenclature (ICZN) for animals and the International Code of Botanical Nomenclature (ICBN) for plants (zoology and botany had become separate disciplines by the time the codes were developed, hence the separate codes). Other organisms -- fungi and protists -- are governed by one or the other code based on whether they were traditionally regarded as plants or animals, so fungi and algae fall under the Botanical Code, while most protozoa fall under the Zoological Code. Bacteria were originally governed by the Botanical Code, but conflicts between the provisions of the Botanical Code and the requirements of bacterial taxonomy led to the establishment of the International Code of Nomenclature of Bacteria (ICNB). Additional separate codes exist for viruses and cultivated plants (horticulturally-developed varieties and hybrids). Different codes may have different opinions on what constitutes a validly-publiched name, but all codes agree that the oldest name for a taxon is generally valid, and require the identification of some kind of type. Traditionally, names described under different codes do not count as homonyms, so Prunella is both a genus of birds and a member of the mint family, while Bacillus is both a bacterium and a stick insect (the Bacteriological Code does forbid the use of names that have previously been used in the other codes, but identical names may exist if the bacterial genus was named first).
A small number of taxa (photosynthetic flagellates and their close relatives, and slime moulds) have been included with both plants and animals at various times in the past, so have been regarded by different authors as falling under both the Zoological and Botanical Codes. This can cause confusion, as the correct name for a taxon may differ between the codes -- a name may be validly published under one code but not under the other, or be a homonym under one code but not the other. Cavalier-Smith (1998) divided eukaryotes into five kingdoms -- the paraphyletic kingdom Protozoa and the monophyletic kingdoms Animalia, Fungi, Chromista and Plantae -- and suggested that Animalia and Protozoa should fall under the Zoological Code, while Plantae, Fungi and Chromista would fall under the Botanical Code. However, Microsporidia in Fungi and various non-photosynthetic taxa in Chromista have been generally treated in the past under the Zoological Code, while dinoflagellates (Protozoa) have probably been more often treated under the Botanical Code than the Zoological Code.
It should be stressed that all codes of nomenclature make a distinction between nomenclaturally valid (or available) names and biologically valid names. The former qualification deals with whether a name is validly published or not, while the latter deals with whether or not it is distinct from other taxa. For instance, the name Homo neanderthalensis for Neanderthal Man was published by King in 1864, but authors differ as to whether Neanderthal Man (or Woman) represents a separate species from modern humans (Homo sapiens Linnaeus 1758). Therefore, Homo neanderthalensis is undoubtably a nomenclaturally valid name, but may not be a biologically valid name.
Occasionally, situations may arise where the correct name for a taxon is uncertain under the Codes, or where strict applications of the Code's regulations would cause confusion for researchers (see entries for nomen conservandum and nomen oblitum). All Codes have an administrative board that adjudicates such cases -- these are the International Commission on Zoological Nomenclature, the International Association for Plant Taxonomy and the International Committee on Systematics of Prokaryotes for the Zoological, Botanical and Bacteriological Codes, respectively. - EvoWiki
International Commission on Zoological Nomenclature
International Association for Plant Taxonomy
International Committe on Systematics of Prokaryotes
This page incorporates material from EvoWiki and so is licensed under the Attribution-NonCommercial-ShareAlike Creative Commons License). EvoWiki url: http://wiki.cotch.net/index.php/Taxonomy_and_Phylogeny Codes of nomenclature CKT070322; page MAK120229