Taxonomy and naming

Common and scientific namesedit

The commonly used names for kinds of organisms are often ambiguous: "cat" could mean the domestic cat, Felis catus, or the cat family, Felidae. Another problem with common names is that they often vary from place to place, so that puma, cougar, catamount, panther, painter and mountain lion all mean Puma concolor in various parts of America, while "panther" may also mean the jaguar (Panthera onca) of Latin America or the leopard (Panthera pardus) of Africa and Asia. In contrast, the scientific names of species are chosen to be unique and universal; they are in two parts used together: the genus as in Puma, and the specific epithet as in concolor.

Species descriptionedit

A species is given a taxonomic name when a type specimen is described formally, in a publication that assigns it a unique scientific name. The description typically provides means for identifying the new species, differentiating it from other previously described and related or confusable species and provides a validly published name (in botany) or an available name (in zoology) when the paper is accepted for publication. The type material is usually held in a permanent repository, often the research collection of a major museum or university, that allows independent verification and the means to compare specimens. Describers of new species are asked to choose names that, in the words of the International Code of Zoological Nomenclature, are "appropriate, compact, euphonious, memorable, and do not cause offence".

Abbreviationsedit

Books and articles sometimes intentionally do not identify species fully and use the abbreviation "sp." in the singular or "spp." (standing for species pluralis, the Latin for multiple species) in the plural in place of the specific name or epithet (e.g. Canis sp.). This commonly occurs when authors are confident that some individuals belong to a particular genus but are not sure to which exact species they belong, as is common in paleontology.

Authors may also use "spp." as a short way of saying that something applies to many species within a genus, but not to all. If scientists mean that something applies to all species within a genus, they use the genus name without the specific name or epithet. The names of genera and species are usually printed in italics. However, abbreviations such as "sp." should not be italicised.

When a species' identity is not clear, a specialist may use "cf." before the epithet to indicate that confirmation is required. The abbreviations "nr." (near) or "aff." (affine) may be used when the identity is unclear but when the species appears to be similar to the species mentioned after.

Identification codesedit

With the rise of online databases, codes have been devised to provide identifiers for species that are already defined, including:

• National Center for Biotechnology Information (NCBI) employs a numeric 'taxid' or Taxonomy identifier, a "stable unique identifier", e.g., the taxid of Homo sapiens is 9606.
• Kyoto Encyclopedia of Genes and Genomes (KEGG) employs a three- or four-letter code for a limited number of organisms; in this code, for example, H. sapiens is simply hsa.
• UniProt employs an "organism mnemonic" of not more than five alphanumeric characters, e.g., HUMAN for H. sapiens.
• Integrated Taxonomic Information System (ITIS) provides a unique number for each species. The LSID for Homo sapiens is urn:lsid:catalogueoflife.org:taxon:4da6736d-d35f-11e6-9d3f-bc764e092680:col20170225.

Lumping and splittingedit

The naming of a particular species, including which genus (and higher taxa) it is placed in, is a hypothesis about the evolutionary relationships and distinguishability of that group of organisms. As further information comes to hand, the hypothesis may be corroborated or refuted. Sometimes, especially in the past when communication was more difficult, taxonomists working in isolation have given two distinct names to individual organisms later identified as the same species. When two species names are discovered to apply to the same species, the older species name is given priority and usually retained, and the newer name considered as a junior synonym, a process called synonymy. Dividing a taxon into multiple, often new, taxa is called splitting. Taxonomists are often referred to as "lumpers" or "splitters" by their colleagues, depending on their personal approach to recognising differences or commonalities between organisms. The circumscription of taxa, considered a taxonomic decision at the discretion of cognizant specialists, is not governed by the Codes of Zoological or Botanical Nomenclature.

Broad and narrow sensesedit

The nomenclatural codes that guide the naming of species, including the ICZN for animals and the ICN for plants, do not make rules for defining the boundaries of the species. Research can change the boundaries, also known as circumscription, based on new evidence. Species may then need to be distinguished by the boundary definitions used, and in such cases the names may be qualified with sensu stricto ("in the narrow sense") to denote usage in the exact meaning given by an author such as the person who named the species, while the antonym sensu lato ("in the broad sense") denotes a wider usage, for instance including other subspecies. Other abbreviations such as "auct." ("author"), and qualifiers such as "non" ("not") may be used to further clarify the sense in which the specified authors delineated or described the species.