Taxonomy

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This article is about taxonomy in the field of biology.

Taxonomy is the science of describing, naming, and classifying living and extinct organisms. The term is also used in a wider sense, to refer to the classification of things or the principles underlying the classification of things. In this sense, almost anything – animate objects, inanimate objects, places, qnd events – may be classified according to some taxonomic scheme. The term taxonomy is derived from the Greek taxis ("arrangement"; from the verb tassein, to classify") and nomos ("law" or "science", such as used in "economy."

An important science, taxonomy is basic to all biological disciplines, since each require the correct names and descriptions of the organisms being studied. However, taxonomy is also dependent on other disciplines, such as genetics, physiology, ecology, and anatomy, since they provide information needed by taxonomists for their work.

Naming, describing and classsifying living organisms is also a natural activity of humans, since it is essential to our daily activities. Even the Bible references the naming of living things as one of the first activities of humankind. Without such knowledge, it would be difficult to communicate, let alone indicate to others what plant is poisonous, what plant is edible, and so forth. Some further feel that beyond naming and describing, the human mind naturally organizes its knowledge of the world into systems.

Taxonomy is a dynamic science, which has gone through many trends. Since the publication of Darwin's The Origin of Species, taxonomy has been closely tied to the mechanism of descent, rather than simply delineation of species boundaries, and the extent to which subjective findings are presented as fact is of some concern.

Scope of taxonomic studies

For a long time, the term taxonomy was unambiguous, but over time the word was applied in a wider sense, to the classificaiton of things, or tghe principles underling the classifcation. Ammost anything, animate objects, iniamate objects, places, qnd events, may be classified according to some taxonomic scheme. For example, stellar and galactic classification in astronomy.

Original meaning, however, refers to:

including the principles, rules and procedures used in classification.

. Systematics Agenda 2000: Charting the Biosphere (SA2000), a global initiative to discover, describe and classify the world's species, and produced from the input of 27 standing committees and over 300 scientists, defines taxonomy as "the science of discovering, describing, and classifying species or groups of species." SA2000 was luanched by the American Society of Plant Taxonomists, the Society of Systematic Biologists, and the Willi Hennig Society, in cooperation wiht the Association of Systematic Collections.

United Kingdom Parlimanet, defines as :

original meaning actual definition biological classification systematics

sometimes used interchangeable with sstematics or systematic biology. Over time,

Another source of confusion is the relationship to systematics. The words "taxonomy" and "systematics" have a similar history and similar meanings: over time these have been used as synonyms, as overlapping or as completely complementary. Systematics (as a science) deals with the relationships between taxa, especially at the higher levels, these days often based to a great extent on DNA from mitochondria and chloroplasts. The latter, sometimes known as molecular systematics, is doing well, likely at the expense of taxonomy (Wheeler, 2004). Systematics or systematic biology: scientific disciipline, to discover, describe, name, and classify living things and investigate the evolutionary relationship between them.

systematics: the study of the kinds and diversity of organisms and any and all relationships among them. includes not only the traditional activities of taxonomy, but also the investigation of such things as evolution, natural variation, speciation, etc. howeve, much disagreemetn on the technical differences between taxonomy and systematics and they are often used interchangeably.

SA2000: systematics: the science dedicated to the discovery, organization, and interpretation of biological diversity, includes taxonomy and phylogenetic analysis.

subdisciplines wihtin taxonomy alpha taxonomy: describing new species and defining boundaries between species species descriptions. preparation of keys, specimen identification; cataloguing beta taxonomy: arrangement into a natural system of classification; classification; identification of natural groups; phylogenetic reconstruciton

gamma taxoonmy: analysis of evolutionary trends

precise and universal system of rules by all botanists and zoologiests International Code of Zoological Nomenclature (ICZN) International Code of Botanical Nomenclature (ICBN)

taxon: a tasonomic group of any rank, e.g. family, gens, species, subspecies, etc.

any named or namable enty (subspecies, species, genus, family, etc.

Scientific or biological classification

Scientific classification or biological classification is how biologists group and categorize extinct and living species of organisms. Modern classification has its roots in the system of Carolus Linnaeus, who grouped species according to shared physical characteristics. These groupings have been revised since Linnaeus to improve consistency with the Darwinian principle of common descent. Molecular systematics, which uses genomic DNA analysis, has driven many recent revisions and is likely to continue to do so. Scientific classification belongs to the science of taxonomy or biological systematics.

Taxonomies are frequently hierarchical in structure.

Mathematically, a hierarchical taxonomy is a tree structure of classifications for a given set of objects. At the top of this structure is a single classification, the root node, that applies to all objects. Nodes below this root are more specific classifications that apply to subsets of the total set of classified objects. So for instance in common schemes of scientific classification of organisms, the root is the Organism (as this applies to all living things, it is implied rather than stated explicitly). Below this are the Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species, with various other ranks sometimes inserted.

Most authorities recognize five kingdoms: monerans (prokaryotes), protists, fungi (see fungus), plants, and animals. Carolus Linnaeus established the scheme of using Latin generic and specific names in the mid-18th century; his work was extensively revised by later biologists.

Domains are a relatively new grouping. The three-domain system was first invented in 1990, but not generally accepted until later. Now, the majority of biologists accept the domain system, but a large minority use the five-kingdom method. One main characteristic of the three-domain method is the separation of Archaea and Bacteria, previously grouped into the single kingdom Bacteria (sometimes Monera). A small minority of scientists add Archaea as a sixth kingdom but do not accept the domain method.

Examples

The usual classifications of five species follow: the fruit fly so familiar in genetics laboratories (Drosophila melanogaster), humans (Homo sapiens), the peas used by Gregor Mendel in his discovery of genetics (Pisum sativum), the fly agaric mushroom Amanita muscaria, and the bacterium Escherichia coli. The eight major ranks are given in bold; a selection of minor ranks are given as well.

Rank	Fruit fly	Human	Pea	Fly Agaric	E. coli
Domain	Eukarya	Eukarya	Eukarya	Eukarya	Bacteria
Kingdom	Animalia	Animalia	Plantae	Fungi	Monera
Phylum or Division	Arthropoda	Chordata	Magnoliophyta	Basidiomycota	Eubacteria
Subphylum or subdivision	Hexapoda	Vertebrata	Magnoliophytina	Hymenomycotina
Class	Insecta	Mammalia	Magnoliopsida	Homobasidiomycetae	Proteobacteria
Subclass	Pterygota	Placentalia	Magnoliidae	Hymenomycetes
Order	Diptera	Primates	Fabales	Agaricales	Enterobacteriales
Suborder	Brachycera	Haplorrhini	Fabineae	Agaricineae
Family	Drosophilidae	Hominidae	Fabaceae	Amanitaceae	Enterobacteriaceae
Subfamily	Drosophilinae	Homininae	Faboideae	Amanitoideae
Genus	Drosophila	Homo	Pisum	Amanita	Escherichia
Species	D. melanogaster	H. sapiens	P. sativum	A. muscaria	E. coli

Notes:

• Botanists and mycologists use systematic naming conventions for higher taxa, using the Latin stem of the type genus for that taxon, plus a standard ending (See below for a list of standard endings). For example, the rose family Rosaceae is named after the stem "Ros-" of the type genus Rosa plus the standard ending "-aceae" for a family.
• Zoologists use similar conventions for higher taxa, but only up to the rank of superfamily.
• Higher taxa and especially intermediate taxa are prone to revision as new information about relationships is discovered. For example, the traditional classification of primates (class Mammalia — subclass Theria — infraclass Eutheria — order Primates) is challenged by new classifications such as McKenna and Bell (class Mammalia — subclass Theriformes — infraclass Holotheria — order Primates). See mammal classification for a discussion. These differences arise because there are only a small number of ranks available and a large number of branching points in the fossil record.
• Within species further units may be recognised. Animals may be classified into subspecies (for example, Homo sapiens sapiens, modern humans). Plants may be classified into subspecies (for example, Pisum sativum subsp. sativum, the garden pea) or varieties (for example, Pisum sativum var. macrocarpon, snow pea), with cultivated plants getting a cultivar name (for example, Pisum sativum var. macrocarpon 'Snowbird'). Bacteria may be classified by strains (for example Escherichia coli O157:H7, a strain that can cause food poisoning).

Group suffixes

Taxa above the genus level are often given names derived from the Latin (or Latinized) stem of the type genus, plus a standard suffix. The suffixes used to form these names depend on the kingdom, and sometimes the phylum and class, as set out in the table below.

Rank	Plants	Algae	Fungi	Animals
Division/Phylum	-phyta		-mycota
Subdivision/Subphylum	-phytina		-mycotina
Class	-opsida	-phyceae	-mycetes
Subclass	-idae	-phycidae	-mycetidae
Superorder	-anae
Order	-ales
Suborder	-ineae
Infraorder	-aria
Superfamily	-acea			-oidea
Family	-aceae			-idae
Subfamily	-oideae			-inae
Tribe	-eae			-ini
Subtribe	-inae			-ina

Notes

• The stem of a word may not be straightforward to deduce from the nominative form as it appears in the name of the genus. For example, Latin "homo" (human) has stem "homin-", thus Hominidae, not "Homidae".
• For animals, there are standard suffixes for taxa only up to the rank of superfamily (ICZN article 27.2).

Historical developments

"classification is a natural occupation of humans and one of the most necessary of pastitimes. It is essential to our daily lives and is started almost as soon as we're born. We need to classify and name things so we know that we're talking about the same thing." "Taxonomy is probably the oldest science — plants classified as poisonous vs. edible."

The earliest known system of classifying forms of life comes from the Greek philosopher Aristotle, who classified animals based on their means of transportation (air, land, or water).

In 1172 Ibn Rushd (Averroes), who was a judge (Qadi) in Seville, translated and abridged Aristotle's book de Anima (On the Soul) into Arabic. His original commentary is now lost, but its translation into Latin by Michael Scot survives.

An important advance was made by the Swiss professor, Conrad von Gesner (1516–1565). Gesner's work was a critical compilation of life known at the time.

The exploration of parts of the New World next brought to hand descriptions and specimens of many novel forms of animal life. In the latter part of the 16th century and the beginning of the 17th, careful study of animals commenced, which, directed first to familiar kinds, was gradually extended until it formed a sufficient body of knowledge to serve as an anatomical basis for classification. Advances in using this knowledge to classify living beings bear a debt to the research of medical anatomists, such as Fabricius (1537–1619), Petrus Severinus (1580–1656), William Harvey (1578–1657), and Edward Tyson (1649–1708). Advances in classification due to the work of entomologists and the first microscopists is due to the research of people like Marcello Malpighi (1628–1694), Jan Swammerdam (1637–1680), and Robert Hooke (1635–1702).Successive developments in the history of insect classification may be followed on the website [1]by clicking on succeeding works in chronological order.

John Ray (1627–1705) was an English naturalist who published important works on plants, animals, and natural theology. The approach he took to the classification of plants in his Historia Plantarum was an important step towards modern taxonomy. Ray rejected the system of dichotomous division by which species were classified according to a pre-conceived, either/or type system, and instead classified plants according to similarities and differences that emerged from observation.

Linnaeus

Two years after John Ray's death, Carolus Linnaeus (1707–1778) was born. His great work, the Systema Naturae, ran through twelve editions during his lifetime (1st ed. 1735). In this work nature was divided into three realms: mineral, vegetable and animal. Linnaeus used four ranks: class, order, genus, and species.

Linnaeus is best known for his introduction of the method still used to formulate the scientific name of every species. Before Linnaeus, long many-worded names had been used, but as these names gave a description of the species, they were not fixed. By consistently using a two-word Latin name — the genus name followed by the specific epithet — Linnaeus separated nomenclature from taxonomy. This convention for naming species is referred to as binomial nomenclature.

Today, nomenclature is regulated by Nomenclature Codes, which allows names divided into ranks: see rank (botany) and rank (zoology).

Whereas Linnaeus classified for ease of identification, it is now generally accepted that classification should reflect the Darwinian principle of common descent.

Since the 1960s a trend called cladistic taxonomy or cladism has emerged, arranging taxa in an evolutionary tree. If a taxon includes all the descendants of some ancestral form, it is called monophyletic, as opposed to paraphyletic. Other groups are called polyphyletic.

A new formal code of nomenclature, the PhyloCode, is currently under development, intended to deal with clades rather than taxa. It is unclear, should this be implemented, how the different codes will coexist.

The term taxonomy is derived from the Greek taxis (“arrangement”; from the verb tassein, to classify") and nomos (“law”, science, cf "economy").

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