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 employed in a wider sense, to refer to the classification of things, including inanimate objects, places and events, or to the principles underlying the classification of things.) 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 the information provided by other disciplines, such as genetics, physiology, ecology, and anatomy.

Naming, describing and classifying living organisms is a natural and integral activity of humans. 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. Even the Bible references the naming of living things as one of the first activities of humanity. Some further feel that, beyond naming and describing, the human mind naturally organizes its knowledge of the world into systems.

Taxonomy, systematics, and alpha taxonomy: Defining terms

For a long time, the term taxonomy was unambiguous and used for the classification of living and once-living organisms, and the principles, rules and procedures employed in such classification. This use of the term is sometimes referred to as "biological classification" or "scientific classification." Beyond classification, the discipline or science of taxonomy historically included the discovering, naming, and describing of organisms.

Over time, however, the word taxonomy came to take on a broader meaning, referring to the classification of things, or the principles underlying the classification. Almost anything may be classified according to some taxonomic scheme, such as stellar and galactic classifications, or classifications of events and places.

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

The Select Committee on Science and Technology of the United Kingdom Parliament also offers an official definition for taxonomy: "We use taxonomy to refer to the activities of naming and classifying organisms, as well as producing publications detailing all known members of a particular gropup of living things."

The term "systematics" (and "systematic biology") is sometimes used interchangeably with the term taxonomy. The words have a similar history and similar meanings: over time these have been used as synonyms, as overlapping, or as completely complementary.

In general, however, the term systematics (as a science) includes an aspect of phylogenetic analysis (the study of evolutionary relatedness among various groups of organisms). That is, it deals not only discovering, describing, naming, and classifying living things, but also an investigation of the evolutionary relationship between taxa (a taxonomic group of any rank, such as sub-species, species, family, genus, etc.), especially at the higher levels. Thus, according to this perspective, systematics not only includes the traditional activities of taxonomy, but also the investigation of evolutionary relationships, variation, speciation, and so forth. However, there remains disagreements on the technical differences between the two terms, taxonomy and systematics, and they are often used interchangeably.

These days, systematics is 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).

"Alpha taxonomy" is the sub-discipline of taxonomy, and is concerned with describing new species, and defining boundaries between species. It includes finding new species, preparing species descriptions, developing keys for identification, and cataloging the species. "Beta taxonomy" is another sub-discipline, and deals with the arrangement of species into a natural system of classification.

Universal codes

Codes have been created to provide a universal and precise system of rules for the taxonomic classification of plants, animals, and bacteria. The International Code of Zoological Nomenclature (ICZN) is a set of rules in zoology to provide the maximum universality and continuity in classifying animals according to taxonomic judgment. The International Code of Botanical Nomenclature (ICBN) is the set of rules and recommendations dealing with the formal botanical names that are given to plants. Its intent is that each taxonomic group ("taxon", plural "taxa") of plants has only one correct name, accepted worldwide. The International Code of Nomenclature of Bacteria (ICNB) governs the scientific names for bacteria.

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. Groupings have been revised since Linnaeus to reflect 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 classifications (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
• Species.

Various other ranks are sometimes inserted, such as sub-Class and superfamily.

Carolus Linnaeus established the scheme of using Latin generic and specific names in the mid-18th century (see species; his work was extensively revised by later biologists.

Domain and Kingdom systems

At the top of the taxonomic classification of organisms, one can find either Domain or Kingdom.

For two centuries, from the mid-18th century until the mid-20th century, organisms were generally considered to belong to one of two kingdoms, Plantae (plants, including bacteria) or Animalia (animals, including protozoa). This system was proposed by Carolus Linnaeus in the mid-18th century. However, this classification had obvious difficulties, including the difficulty of placing fungi, protists, and prokaryotes. There are single-celled organisms that fall between the two categories, such as Euglena that can photosynthesize food from sunlight and yet feed by consuming organic matter.

In 1969, American ecologist Robert H. Whittaked proposed a system with five kingdoms: Monera (prokaryotes — bacteria and blue-green algae), Protista (unicellular, multicellular, and colonial protists), Fungi, Plantae, and Animalia. This system was widely used for three decades, and remains popular today.

More recently, a classification level higher than a kingdom has been devised, called a "Domain." Also called a "Superregnum" or "Superkingdom," a Domain is the top-level grouping of organisms in scientific classification. One of the reasons such a classification has been developed is because research has revealed the unique nature of anaerobic bacteria (called Archaeobacteria, or simply Archaea). These "living fossils" are genetically and metabolically very different from oxygen-breathing organisms. Various numbers of Kingdoms are recognized under the Domain category.

In the three-domain system, which was introduced by Carl Woese in 1990, the three groupings are:

Archaea; Bacteria; and Eukaryota. This scheme emphasizes the separation of prokaryotes into two groups, the Bacteria (originally labelled Eubacteria) and the Archaea (originally labelled Archaebacteria).

In some classifications, authorities keep the Kingdom system as the higher level classification, but recognize a sixth Kingdom, the Archaebacteria. In the Domain system, various numbers of Kingdoms are recognized under the Domain category, such as five or six or more.

Coexisting with these schemes is one dividing living organisms into the two main divisions of prokaryote (cells that lack a nucleous: bacteria, etc.) and eukaryote (cells that have a nucleus and membrane-bound organelles: animals, plants, fungi, and protists).

In summary, today there are several competing top classifications of life:

• The three-domain system of Carl Woese, with top-level groupings of Archaea, Eubacteria, and Eukaryota domains;
• The two-empire system, with top-level groupings of Prokaryota (or Monera) and Eukaryota empires.
• The five-kingdom system with top-level groupings of Protista, Monera, Fungi, Plantae, and Animalia.
• The six-kingdom system with top-level groupings of Archaebacteria, Protista, Monera, Fungi, Plantae, and Animalia.

Overall, the majority of biologists accept the domain system, but a large minority use the five-kingdom method. A small minority of scientists add Archaea or Archaebacteria 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). These differences arise because there are only a small number of ranks available and a large number of proposed 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.

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.

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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