taxonomy

—taxonomic /tak'seuh nom"ik/, taxonomical, adj. —taxonomically, adv. —taxonomist, taxonomer, n.

/tak son"euh mee/, n.

1. the science or technique of classification.

2. Biol. the science dealing with the description, identification, naming, and classification of organisms.

[1805-15; F taxonomie. See TAXO-, -NOMY]

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In biology, the classification of organisms into a hierarchy of groupings, from the general to the particular, that reflect evolutionary and usually morphological relationships: kingdom, phylum, class, order, family, genus, species.

The black-capped chickadee, for example, is an animal (kingdom Animalia) with a dorsal nerve cord (phylum Chordata) and feathers (class Aves: birds) that perches (order Passeriformes: perching birds) and is small with a short bill (family Paridae), a song that sounds like "chik-a-dee" (genus Parus), and a black-capped head (species atricapillus). 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.

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▪ biology

Introduction

      in a broad sense, the science of classification, but more strictly the classification of living and extinct organisms—i.e., biological classification. The term is derived from the Greek taxis (“arrangement”) and nomos (“law”). Taxonomy is, therefore, the methodology and principles of systematic botany and zoology and sets up arrangements of the kinds of plants and animals in hierarchies of superior and subordinate groups.

      Popularly, classifications of living organisms arise according to need and are often superficial. Anglo-Saxon terms such as worm and fish have been used to refer, respectively, to any creeping thing—snake, earthworm, intestinal parasite, or dragon—and to any swimming or aquatic thing. Although the term fish is common to the names shellfish, crayfish, and starfish, there are more anatomical differences between a shellfish and a starfish than there are between a bony fish and a man. Vernacular names vary widely. The American robin (Turdus migratorius), for example, is not the English robin (Erithacus rubecula), and the mountain ash (Sorbus) has only a superficial resemblance to a true ash.

      Biologists, however, have attempted to view all living organisms with equal thoroughness and thus have devised a formal classification. A formal classification provides the basis for a relatively uniform and internationally understood nomenclature, thereby simplifying cross-referencing and retrieval of information.

      The usage of the terms taxonomy and systematics with regard to biological classification varies greatly. American evolutionist Ernst Mayr (Mayr, Ernst) has stated that “taxonomy is the theory and practice of classifying organisms” and “systematics is the science of the diversity of organisms”; the latter in such a sense, therefore, has considerable interrelations with evolution, ecology, genetics, behaviour, and comparative physiology that taxonomy need not have.

Historical background

      People who live close to nature usually have an excellent working knowledge of the elements of the local fauna and flora important to them and also often recognize many of the larger groups of living things (e.g., fishes, birds, and mammals). Their knowledge, however, is according to need, and such people generalize only rarely.

From the Greeks to the Renaissance

      The first great generalizer in classification was Aristotle, who virtually invented the science of logic, of which for 2,000 years classification was a part. Greeks had constant contact with the sea and marine life, and Aristotle seems to have studied it intensively during his stay on the island of Lesbos. In his writings, he described a large number of natural groups, and, although he ranked them from simple to complex, his order was not an evolutionary one. He was far ahead of his time, however, in separating invertebrate animals into different groups and was aware that whales, dolphins, and porpoises had mammalian characters and were not fish. Lacking the microscope, he could not, of course, deal with the minute forms of life.

      The Aristotelian method dominated classification until the 19th century. His scheme was, in effect, that the classification of a living thing by its nature—i.e., what it really is, as against superficial resemblances—requires the examination of many specimens, the discarding of variable characters (since they must be accidental, not essential), and the establishment of constant characters. These can then be used to develop a definition that states the essence of the living thing—what makes it what it is and thus cannot be altered; the essence is, of course, immutable. The model for this procedure is to be seen in mathematics, especially geometry, which fascinated the Greeks. Mathematics seemed to them the type and exemplar of perfect knowledge, since its deductions from axioms were certain and its definitions perfect, irrespective of whether a perfect geometrical figure could ever be drawn. But the Aristotelian procedure applied to living things is not by deduction from stated and known axioms; rather, it is by induction from observed examples and thus does not lead to the immutable essence but to a lexical definition. Although it provided for centuries a procedure for attempting to define living things by careful analysis, it neglected the variation of living things. It is of interest that the few people who understood Charles Darwin's Origin of Species in the mid-19th century were empiricists who did not believe in an essence of each form.

      Aristotle and his pupil in botany, Theophrastus, had no notable successors for 1,400 years. In about the 12th century AD, botanical works necessary to medicine began to contain accurate illustrations of plants, and a few began to arrange similar plants together. Encyclopaedists also began to bring together classical wisdom and some contemporary observations. The first flowering of the Renaissance in biology produced, in 1543, Andreas Vesalius' treatise on human anatomy and, in 1545, the first university botanic garden, founded in Padua, Italy. After this time, work in botany and zoology flourished. John Ray (Ray, John) summarized in the late 17th century the available systematic knowledge, with useful classifications. He distinguished the monocotyledonous plants from the dicotyledonous (dicotyledon) ones in 1703, recognized the true affinities of the whales, and gave a workable definition of the species concept, which had already become the basic unit of biological classification. He tempered the Aristotelian logic of classification with empirical observation.

The Linnaean system

      Carolus Linnaeus (Linnaeus, Carolus), who is usually regarded as the founder of modern taxonomy and whose books are considered the beginning of modern botanical and zoological nomenclature, drew up rules for assigning names to plants and animals and was the first to use binomial nomenclature consistently (1758). Although he introduced the standard hierarchy of class, order, genus, and species, his main success in his own day was providing workable keys, making it possible to identify plants and animals from his books. For plants he made use of the hitherto neglected smaller parts of the flower.

      Linnaeus attempted a natural classification but did not get far. His concept of a natural classification was Aristotelian; i.e., it was based on Aristotle's idea of the essential features of living things and on his logic. He was less accurate than Aristotle in his classification of animals, breaking them up into mammals, birds, reptiles, fishes, insects, and worms. The first four, as he defined them, are obvious groups and generally recognized; the last two incorporate about seven of Aristotle's groups.

      The standard Aristotelian definition of a form was by genus and differentia. The genus defined the general kind of thing being described; the differentia gave its special character. A genus, for example, might be “Bird” and the species “Feeding in water,” or the genus might be “Animal” and the species “Bird.” The two together made up the definition, which could be used as a name. Unfortunately, when many species of a genus became known, the differentia became longer and longer. In some of his books Linnaeus printed in the margin a catch name, the name of the genus and one word from the differentia or from some former name; in this way he created the binomial, or binary, nomenclature. Thus, modern man is Homo sapiens, Neanderthal man Homo neanderthalensis, the gorilla Gorilla gorilla, and so on.

Classification since Linnaeus

      Classification since Linnaeus has incorporated newly discovered information and more closely approaches a natural system. When the life history of barnacles was discovered, for example, they could no longer be associated with mollusks because it became clear that they were arthropods (jointed-legged animals such as crabs and insects). Jean-Baptiste Lamarck (Lamarck, Jean-Baptiste), an excellent taxonomist despite his misconceptions about evolution, first separated spiders and crustaceans from insects as separate classes; he also introduced the distinction, no longer accepted by all workers as wholly valid, between vertebrates—i.e., those with backbones, such as fishes, amphibians, reptiles, birds, and mammals—and invertebrates, which have no backbones. The invertebrates, defined by a feature they lack rather than by those they have, constitute in fact about 90 percent of the diversity of all animals. The mixed group “Infusoria,” which included all the microscopic forms that would appear when hay was let stand in water, was broken up into empirically recognized groups by the French biologist Felix Dujardin. The German biologist Ernst Haeckel (Haeckel, Ernst) proposed the term Protista in 1866 to include chiefly the unicellular plants and animals because he realized that, at the one-celled level, there could no longer be a clear distinction between plants and animals.

      The process of clarifying relationships continues—only in 1898 were agents of disease discovered (viruses (virus)) that would pass through the finest filters, and it was not until 1935 that the first completely purified virus was obtained. Primitive spore-bearing land plants (Psilophyta) from the Cambrian Period, which dates from 570,000,000 years ago, were discovered in Canada in 1859. The German botanist Wilhelm Hofmeister (Hofmeister, Wilhelm) in 1851 gave the first good account of the alterations of generations (alternation of generations) in various nonflowering (cryptogamous) plants, on which many major divisions of higher plants are based. The phylum Pogonophora (beardworms (beardworm)) was recognized only in the 20th century.

      The immediate impact of Darwinian (Darwin, Charles) evolution on classification was negligible for many groups of organisms, and unfortunate for others. As taxonomists began to accept evolution, they recognized that what had been described as natural affinity—i.e., the more or less close similarity of forms with many of the same characters—could be explained as relationship by evolutionary descent. In groups with little or no fossil record, a change in interpretation rather than alteration of classifications was the result. Unfortunately, some authorities, believing that they could derive the group from some evolutionary principle, would proceed to reclassify it. The classification of earthworms and their allies (Oligochaeta), for example, which had been studied by using the most complex organism easily obtainable and by then arranging progressively simple forms below it, was changed after the theory of evolution appeared. The most simple oligochaete, the tiny freshwater worm Aeolosoma, was considered to be most primitive, and classifiers arranged progressively complex forms above it. Later, when it was realized that Aeolosoma might well have been secondarily simplified (i.e., evolved from a more complex form), the tendency was to start in the middle of the series, and work in both directions. Biassed names for the major subgroups (Archioligochaeta, Neoligochaeta) were widely accepted, when in fact there was no evidence for the actual course of evolution of this and other animal groups. Groups with good fossil records suffered less from this type of reclassification because good fossil material allowed the placing of forms according to natural affinities; knowledge of the strata in which they were found allowed the formulation of a phylogenetic tree (i.e., one based on evolutionary relationships), or dendrite (also called a dendrogram), irrespective of theory.

      The long-term impact of Darwinian evolution has been different and very important. It indicates that the basic arrangement of living things, if enough information were available, would be a phylogenetic tree rather than a set of discrete classes. Many groups are so poorly known, however, that the arrangement of organisms into a dendrite is impossible. Extensive and detailed fossil sequences—the laying out of actual specimens—must be broken up arbitrarily. Many groups, especially at the species level, show great geographical variation, so that a simple definition of species is impossible. Difficulties of classification at the species level are considerable. Many plants show reticulate (chain) evolution, in which species form, then subsequently hybridize, resulting in the formation of new species. And because many plants and animals have abandoned sexual reproduction, the usual criteria for the species—interbreeding within a pool of individuals—cannot be applied. Nothing about the viruses, moreover, seems to correspond to the species of higher organisms.

The objectives of biological classification

      A classification or arrangement of any sort cannot be handled without reference to the purpose or purposes for which it is being made. An arrangement based on everything known about a particular class of objects is likely to be the most useful for many particular purposes. One in which objects are grouped according to easily observed and described characteristics allows easy identification of the objects. If the purpose of a classification is to provide information unknown to or not remembered by the user but relating to something the name of which is known, an alphabetical arrangement may be best. Specialists may want a classification relating only to one aspect of a subject. A chemist analyzing the essential oils of plants, for instance, is interested only in the oil content of plants and probably requires such information in far greater detail than would anyone else.

      Classification is used in biology for two totally different purposes, often in combination, namely, identifying and making natural groups. The specimen or a group of similar specimens must be compared with descriptions of what is already known. This type of classification, called a key, provides as briefly and as reliably as possible the most obvious characteristics useful in identification. Very often they are set out as a dichotomous key with opposing pairs of characters. The butterflies of a region, for example, might first be separated into those with a lot of white on the wings and those with very little; then each group could be subdivided on the basis of other characters. One disadvantage of such classifications, which are useful for well-known groups, is that a mistake may produce a ridiculous answer, since the groups under each division need have nothing in common but the chosen character (e.g., white on the butterfly wings). In addition, if the group being keyed is large or given to great variation, the key may be extremely complex and may rely on characters difficult to evaluate. Moreover, if the form in question is a new one or one that is not in the key (being, perhaps, unrecorded from the region to which the key applies), it may be identified incorrectly. Many unrelated butterflies have a lot of white on the wings—a few swallowtails, the well-known cabbage whites, some of the South American dismorphiines, and a few satyrids. Should identification of an undescribed form of fritillary butterfly containing much white on the wings be desired, the use of a key could result in an incorrect identification of the butterfly. In order to avoid such mistakes, it is necessary to consider many characters of the organism: not merely one aspect of the wings but their anatomy and the features of the various stages in the life cycle.

      Unfortunately, little is known about many of the vast variety of living things. In poorly known groups—and most living things are poorly known—the first objective is identification. There are, for example, about 250,000 species of beetles; many are known only from a single specimen of the adult. In such groups the tendency is to produce classifications which, though purporting to be natural ones, are actually dichotomous keys. Although most common earthworms have on each body segment four pairs of special bristles (chaetae) that are used in locomotion, some species have many chaetae arranged in a complete ring around the body on each segment (perichaetine condition). Because the chaetae are an easily observed character, the latter species were once placed together as a natural group, the family Perichaetidae; knowledge of other aspects of earthworm anatomy, however, made it obvious that several different groups had independently evolved the perichaetine condition. Many current so-called natural groups, especially those at the lower levels of classification, are probably not natural at all but are based on some easily observed characters.

      A natural classification is advantageous in that it groups together forms that seem fundamentally to be related. Information utilized in the definition of a group thus need not be repeated for each constituent. This provides concision and efficient information storage. A certain amount of prediction is also possible—a new form with a few ascertained characters similar to those of a natural group probably has other similar characters. As long as no difficult intermediary forms are found, all of the different types can be classified into definite discrete categories. Biological classification has progressed from artificial or key classifications to a natural classification; it has also been realized that division into sharply separated groups often is not possible. Formal classification thus sometimes obscures actual relationships.

The taxonomic process

      Basically, no special theory lies behind modern taxonomic methods. In effect, taxonomic methods depend on: (1) obtaining a suitable specimen (collecting, preserving and, when necessary, making special preparations); (2) comparing the specimen with the known range of variation of living things; (3) correctly identifying the specimen if it has been described, or preparing a description showing similarities to and differences from known forms, or, if the specimen is new, naming it according to internationally recognized codes of nomenclature; (4) determining the best position for the specimen in existing classifications and determining what revision the classification may require as a consequence of the new discovery; and (5) using available evidence to suggest the course of the specimen's evolution. Prerequisite to these activities is a recognized system of ranks in classifying; recognized rules for nomenclature; and a procedure for verification, irrespective of the group being examined. A group of related organisms to which a taxonomic name is given is called a taxon (plural taxa).

Ranks

      The goal of classifying is to place an organism into an already existing group or to create a new group for it, based on its resemblances to and differences from known forms. To this end, a hierarchy of categories is recognized; for example, an ordinary flowering plant, on the basis of gross structure, is clearly one of the higher green plants, not a fungus, bacterium, or animal, it can easily be placed in the Kingdom Plantae (or Metaphyta). If the body of the plant has distinct leaves, roots, a stem, and flowers, it is placed with the other true flowering plants in the division Magnoliophyta (or Angiospermae), one subcategory of the Plantae. If it is a lily, with sword-like leaves, with the parts of the flowers in multiples of three, and with one cotyledon (the incipient leaf) in the embryo, it belongs with other lilies, tulips, palms, orchids, grasses, and sedges in a subgroup of the Magnoliophyta, which is called the class Liliatae (or Monocotyledones).

       Obligatory Hierarchy of Ranks, TableIn this class, it is placed, rather than with orchids or grasses, in a subgroup of the Liliatae, the order Liliales; this procedure is continued to the species level. Should the plant be different from any lily yet known, a new species is named, as well as higher taxa, if necessary. If the plant is a new species within a well-known genus, a new species name is simply added to the appropriate genus. If the plant is very different from any known monocot it might require, even if only a single new species, the naming of a new genus, family, order, or higher taxon; there is no restriction on the number of forms in any particular group. The number of ranks that is recognized in a hierarchy is a matter of widely varying opinion. Shown in Table 1 (Obligatory Hierarchy of Ranks, Table) are seven ranks that are accepted as obligatory by zoologists and botanists. In botany, the term division is often used as an equivalent to the term phylum of zoology. The number of ranks is expanded as necessaryby using the prefixes sub-, super-, and infra- (e.g., subclass, superorder) and by adding other intermediate ranks, such as brigade, cohort, section, or tribe. Given in full, the zoological hierarchy for the timber wolf of the Canadian subarctic would be as follows:

      Kingdom Animalia

      Subkingdom Metazoa

      Phylum Chordata

      Subphylum Vertebrata

      Superclass Tetrapoda

      Class Mammalia

      Subclass Theria

      Infraclass Eutheria

      Cohort Ferungulata

      Superorder Ferae

      Order Carnivora

      Suborder Fissipeda

      Superfamily Canoidea

      Family Canidae

      Subfamily Caninae

      Tribe (none described for this group)

      Genus Canis

      Subgenus (none described for this group)

      Species Canis lupus (wolf)

      Subspecies Canis lupus occidentalis (northern timber wolf)

      Although the name of the species is binomial (e.g., Canis lupus) and that of the subspecies trinomial (C. lupus occidentalis for the northern timber wolf; C. lupus lupus for the northern European wolf), all other names are single words. In zoology, convention dictates that the names of superfamilies end in -oidea, and the code dictates that the names of families end in -idae, those of subfamilies in -inae, and those of tribes in -ini. Unfortunately, there are no widely accepted rules for other major divisions of living things because each major group of animals and plants has its own taxonomic history, and old names tend to be preserved. Apart from a few accepted endings, the names of groups of high rank are not standardized and must be memorized.

      The discovery of the only living coelacanth fish of the genus Latimeria, in 1938, caused virtually no disturbance of the accepted classification, since the suborder Coelacanthi was already well known from fossils. When certain unusual worms were discovered in the depths of the oceans about ten years later, however, it was necessary to create a new phylum, Pogonophora (beardworm), for them since they showed no close affinities to any other known animals. The phylum Pogonophora, as usually classified, has one class—the animals in the phylum are relatively similar—but there are two orders, several families and genera, and more than 100 species. Both of these examples have been widely accepted by authorities in their respective areas of taxonomy and may be considered stable taxa.

      It cannot be too strongly emphasized that there are no explicit taxonomic characters that define a phylum, class, order, or other rank. A feature characteristic of one phylum may vary in another phylum among closely related members of a class, order, or some lower group. The complex carbohydrate cellulose is characteristic of two kingdoms of plants; among animals, however, cellulose occurs only in one subphylum of one phylum. It would simplify the work of the taxonomist if characters diagnostic of phylum rank in animals were always taken from one feature, the skeleton, for example; those of class rank, from the respiratory organs; and so on down the taxonomic hierarchy. Such a system, however, would produce an unnatural classification.

      The taxonomist must first recognize natural groups and then decide on the rank that should be assigned them. Are seasquirts, for instance, so clearly linked by the structure of the extraordinary immature form (larva) to the phylum Chordata, which includes all the vertebrates, that they should be called a subphylum; or should their extremely modified adult organization be deemed more important, with the result that seasquirts might be recognized as a separate phylum, albeit clearly related to the Chordata? At present, this sort of question has no precise answer.

      Some biologists believe that “numerical taxonomy,” a system of quantifying characteristics of taxa and subjecting the results to multivariate analysis, may eventually produce quantitative measures of overall differences among groups, and that agreement can be achieved so as to establish the maximal difference allowed each taxonomic level. Although such agreement may be possible, many difficulties exist. An order in one authority's classification may be a superorder or class in another. Most of the established classifications of the better known groups result from a general consensus among practicing taxonomists. It follows that no complete definition of a group can be made until the group itself has been recognized, after which its common (or most usual) characters can be formally stated. As further information is obtained about the group, it is subject to taxonomic revision.

Nomenclature

      Communication among biologists requires a recognized nomenclature, especially for the units in most common use. The internationally accepted taxonomic nomenclature is the Linnaean system, which, although founded on Linnaeus' rules and procedures, has been greatly modified through the years. There are separate international codes of nomenclature in botany (first published in 1901), in zoology (1906), and in microbiology (bacteria and viruses, 1948). The Linnaean binomial system is not employed for viruses. There is also a code, which was established in 1953, for the nomenclature of cultivated plants, many of which are artificially produced and are unknown in the wild.

      The codes, the authority for each of which stems from a corresponding international congress, differ in various details, but all include the following elements: the naming of species by two words treated as Latin; a law of priority that the first validly published and validly binomial name for a given taxon is the correct one and that any others must become synonyms; recognition that a valid binomen can apply to only one taxon, so that a name may be used both in botany and in zoology but for only one plant taxon and one animal taxon; that if taxonomic opinion about the status of a taxon is changed, the valid name can change also; and, lastly, that the exact sense in which a name is used be determined by reference to a type. Rules are also given for the obligate categories of the hierarchy and for what constitutes valid publication of a name. Finally, recommendations are given on the process of deriving names.

      Linnaeus believed that there were not more than a few thousand genera of living things, each with some clearly marked character, and that the good taxonomist could memorize them all, especially if their names were well chosen. Thus, although the naming of the species might often involve much research, the genus at least could be easily found.

      At the present time, in many taxa, the species has a definite biological meaning—it is defined as a group of individuals that can breed among themselves but do not normally breed with other forms. Among microorganisms and other groups in which sexual reproduction need not occur, this criterion fails.

      In botanical practice, matters more usually resemble the Linnean situation. Many sorts of chromosomal variants (individuals with different arrangements of chromosomes, or hereditary material, which prevent interbreeding) and marked ecotypes (individuals whose external form is affected by the conditions of soil, moisture, and other environmental factors), as well as other forms, that would clearly be classified as separate species by the zoologist may be lumped together unrecognized or considered subspecies by the botanist. Botanists commonly use the terms variety and form to designate genetically controlled variants within plant populations below the subspecies level.

      The use of a strictly biological species definition would enormously increase rather than reduce the number of names in use in botany. A recognized species of flowering plant may consist of several “chromosomal races”—i.e., identical in external appearance but genetically incompatible and, thus, effectively separate species. Such various forms are often identifiable only by cytological examination, which requires fresh material and extensive laboratory work. Many botanists have said that there has been so little stability in the accepted nomenclature that further upheavals would be intolerable and render identification impossible for many applied botanists who may not require such refinements. To postpone recognition of such forms, however, will probably cause upheaval in the future.

      Some species of birds are widespread over the archipelagos of the Southwest Pacific, where nearly every island may have a form sufficiently distinct to be given some kind of taxonomic recognition. For example, 73 races are currently recognized for the )golden whistler (Pachycephala pectoralis (golden whistler)). Before the realization that species could vary geographically, each island form was named as a separate species (as many of the races of P. pectoralis actually were). It is often believed—and often it is only belief rather than fact—however, that all of these now genetically isolated populations arose as local differentiations of a single stock; thus, they are now usually classed in zoological usage as subspecies of one polytypic species. The term polytypic indicates that a separate description (and type specimen) is needed for each of the distinct populations, instead of one for the entire species. The use of a trinomial designation for each subspecies (e.g., Pachycephala pectoralis bougainvillei) indicates that it is regarded as simply a local representative (in this case, on Bougainville Island in the Solomons) of a more widely distributed species. The decision on whether to consider such island forms as representatives of one species depends partly on whether, in the judgment of the taxonomist, populations from adjacent islands are sufficiently similar to allow free interbreeding.

Verification and validation by type specimens

      The determination of the exact organism designated by a particular name usually requires more than the mere reading of the description or the definition of the taxon to which the name applies. New forms, which may have become known since the description was written, may differ in characteristics not originally considered; or later workers may discover, by inspection of the original material, that the original author inadvertently confused two or more forms. No description can be guaranteed to be exhaustive for all time. Validation of the use of a name requires examination of the original specimen. It must, therefore, be unambiguously designated.

      At one time an author might have taken his description from a series of specimens, or partly (or even wholly) from other authors' descriptions or figures, as Linnaeus often did. Much of the controversy over the validity of certain names in current use, especially those dating from the late 18th century, stems from the difficulty in determining the identity of the material used by the original authors. In modern practice, a single type specimen must be designated for a new species or subspecies name. The type should always be placed in a reliable public institution, where it can be properly cared for and made available to taxonomists. For many microorganisms, type cultures are maintained in qualified institutions. Because of the short generation time of microorganisms, however, they may actually evolve during storage.

      A complex nomenclature is applied to the different sorts of type specimens. The holotype is a single specimen designated by the original describer of the form (a species or subspecies only) and available to those who want to verify the status of other specimens. When no holotype exists, as is frequently the case, a neotype is selected and so designated by someone who subsequently revises the taxon; the neotype occupies a position equivalent to that of the holotype. The first type validly designated has priority over all other type specimens. Paratypes are specimens used, along with the holotype, in the original designation of a new form; they must be part of the same series (i.e., collected at the same immediate locality and at the same time) as the holotype. For a taxon above the species level, the type is a taxon of the next lower rank (for a genus, for instance, it is a species); from the level of the genus to that of the superfamily there are rules regarding the formation of a group name from the name of the type group. The genus Homo (man) is the type genus of the family Hominidae, for example, and the code forbids its removal from the family Hominidae as long as the Hominidae is treated as a valid family and the name Homo is taxonomically valid. Whatever the remainder of its contents, the family that contains the genus Homo must be the Hominidae.

      Indiscriminate collecting is of little use today, but huge areas of the Earth still are poorly known biologically, at least as far as many groups are concerned, and there remain many groups for which the small number of properly collected and prepared specimens precludes any thorough taxonomic analysis. Even in well-studied groups, such as the higher vertebrates, new methods of analyzing material often necessitate special collecting. The determination of variation within species or populations may necessitate the study of more specimens than are available, even when (as is usual) the specialist can utilize material from many institutions. Usually, collecting is done to fill gaps (in geographical range, geological formations, or taxonomic categories) already brought to light by specialists reviewing the available material. The well-informed collector of living things knows where to go, what to look for, and how to spot anything especially valuable or extraordinary.

      The actual techniques of collecting and preserving vary greatly from one group of organisms to another—soil protozoa, fungi, or pines are neither collected nor preserved in the same manner as birds. Some animals can be preserved only in weak alcohol; others macerate (decompose) in it. Certain earthworms “preserved” in weak alcohol simply flow out of their own skins when lifted out. Special methods are used after long experience to preserve characters of special value in taxonomy. Some methods make specimens difficult to observe; this is especially true of material that has to be sectioned or otherwise made into preparations suitable for microscopic observation.

      After taxonomic material has been collected and preserved, its value can be lost unless it is accurately and completely labelled. Only rarely is unlabelled or insufficiently labelled material of any use. The taxonomist normally must know the locality of collection of each specimen (or lot of specimens), often the habitat (e.g., type of forest, marsh, type of seawater), the date, the name of the collector, and the original field number given to the specimen or lot. To this information is added the catalog number of the collection and the sex (if not already determined in the field and if relevant). The scientific identity of the specimen, as determined by an acknowledged specialist, is usually added to the label at the museum. Also included is the name of the specialist who identified the specimen. Later revisions of the classification and additional knowledge of the organism may result in later alterations of the scientific name, but the original labels must still be kept unaltered.

      Other information may also be required; for example, the males and females of some insect groups are extremely different in appearance, and males and females of the same species may have to be identified. The capture of a pair in the wild actually in copulation gives a strong (but, surprisingly, not absolute) indication that the male and female belong to the same species; the labels of each specimen (if they are separated) indicate the specimen with which it was mating.

Evaluating taxonomic characters

      Comparison of material depends to some extent on the purposes of the comparison. For mere identification, a suitable key, with attention given only to the characters in it, may be enough in well-known groups. If the form is likely to be a new one, its general position is determined by observing as many characters as possible and by comparing them with the definitions and descriptions in a natural classification. The new specimen is compared with its nearest known relatives, usually with reference to type material. Any character may be of taxonomic use. In general, taxonomists tend to work from preserved material, so that their findings can be checked. For extinct forms, of course, only preserved material (fossils) is available.

      Many biochemical, physiological, or behavioral characters may be at least as good as anatomical characters for discriminating between closely related species or for suggesting relationships. There has been a tendency in recent years rather to discount anatomical characters, but when they are obtainable in quantity (as for most plants and animals), they probably represent as large a sample of the effects of the organism's heredity as can be got, short of complete genetic analysis. Enthusiasts in genetics often stress that the only real basis for classification is the actual genotype of each organism—i.e., the hereditary information by which the organism is formed. It is impossible to obtain such information for extinct forms, and the time required to obtain it for most existing ones would be enormous, even if the techniques were available. An important development, however, has been the hybridization technique employing deoxyribonucleic acid ( DNA), the substance by which hereditary information is coded. With this technique, it has been possible to determine similarities in parts of DNA molecules from different organisms but not the nature of their differences.

      In making comparisons, resemblances resulting from convergence must be considered. Whales and bony fishes, for example, have similar body shapes for the same function—progression through water; their internal features, however, are widely different. In this case, the convergence is evident because of the large number of characters that link whales to other mammals and not to the fishes and because the fossil record for the vertebrates provides a fair indication of the actual evolutionary sequence from primitive fishes through primitive amphibians to primitive reptiles, mammal-like reptiles, and mammals. In the absence of a good fossil record it may be difficult or impossible to identify positively a case of convergence; yet it has been asserted that the occurrence of convergence must not be stated unless it has been “proved.” To obey this assertion would be to make the method of analysis dictate in part the results achieved.

      In some forms, especially internal parasites (parasitism), great modification has occurred in adapting to a parasitic way of life. The “root system” of the “tumour” (in reality a parasite) found under the abdomen (“tail”) of some crabs, for example, penetrates through the crab's body; the parasite is unrecognizable as a close relative of the barnacles (crustaceans not far removed from the crabs themselves) without the free-swimming larval stage, which shows its affinities. Transient or inconspicuous characters may be of great importance in indicating affinities; the complete life cycle of a specimen may have to be observed before its affinities can be determined. Although such characters may be useless for identification and for definition of a natural group if only a few forms in a group show them, they may be of the utmost importance in understanding relationships. Characters are therefore weighted to some extent by the taxonomist according to their utility for different purposes. Any characters intrinsic to the organism can be used in classification. Extrinsic characters, including the position of fossils in a geological sequence and geographical distribution of fossil and recent forms, may force the taxonomist to look more closely at the intrinsic characters.

      Weighting or nonweighting (i.e., by the degree of importance) of characters has been a subject of great dispute. On the one hand it has been pointed out that weighting is often demonstrably arbitrary and always imprecise. On the other, it has been said that if characters were actually examined without weighting, some obvious cases of extreme convergence would have to be classed with each other instead of in their proper place. A classification based on unweighted characters is called a phenetic one (based on appearances) as opposed to a phyletic one, in which characters are weighted by their presumed importance in indicating lines of descent. The quarrel results in part from a misunderstanding of aims.

      At present, the classification of living things is a rough, non-quantitative sketch of their diversity. A properly surveyed map of this diversity would advance classification enormously. If, on such a map, the diving petrels (Pelecanoides) of the Southern Hemisphere and the little auk (Plautus) of the Northern Hemisphere were closer to each other than to their own phylogenetic (phylogeny) relatives (the other petrels, fulmars, and albatrosses; and the guillemots, terns, gulls, and shorebirds, respectively), this would show the extent of their convergence, which is certainly great, but it would not be a reason for combining them in a separate group. In recent years numerical techniques have been developed for estimating overall resemblance or phenetic distance. For these methods, it is necessary to use large numbers of characters taken from each form and, as far as possible, at random; this involves enormous labour. The mathematical techniques are not as yet wholly satisfactory, some having been borrowed from statistical analysis and applied to taxonomic problems without any consideration of whether they were designed to answer the questions asked by the taxonomist.

      It is worth noting that if there were a complete fossil record for any group, then simply placing any form nearest to those most like it (which must be its immediate ancestors or descendants) would produce an arrangement in which all cases of parallelism and convergence would be revealed. Since evolution occurs by descent with modification, this arrangement would presumably reflect the greatest use of the information available about the group and thus would also be the most useful general arrangement. For such groups, the phenetic arrangement is the phyletic one also.

Making a classification

      When some idea has been obtained of the constituent forms in a group and of the similarity and dissimilarity that they bear to each other, it is necessary to fit a hierarchical system to them. As already indicated, for groups with good fossil records, a dendritic, or branching, arrangement is desired, and classification must be partly arbitrary because of lack of knowledge. If the taxonomist has two compact groups of species, those within each group agreeing closely with each other in many characters and differing sharply from members of the other group in others, there is no difficulty in classification except in ranking. If each group contains a scattering of forms, any one close to another but the most divergent members in each group less like each other than they are like certain of the other group, breaking up the groups into definite classes becomes arbitrary.

      A particularly difficult case arises when these forms also occur in time series: the present-day dogs, cats, hyenas, and other carnivores differ greatly from each other, but at one time their ancestors were much alike; presumably, therefore, they came from one ancestral stock. Paleontologists trace back each taxonomic line and are inclined to carry their separations of taxonomic groups as far backward in time as possible, until the earliest members of related groups are far more like each other than each is to the rest of the later members of the group to which it is assigned. This separation of groups is extreme phyletic splitting, but cutting off a large basal group containing all the primitive members may require arbitrary breaks in the many lines of descent and will obscure the evolutionary relationships. There is no answer to this dilemma except to avoid extremes.

      A similar difficulty arises when the same character complex has arisen independently in related lines. The American paleontologist George Gaylord Simpson (Simpson, George Gaylord), for example, has pointed out that mammalian characters such as the single jawbone (dentary) have arisen several times in groups of the extinct mammal-like reptiles. To use Sir Julian Huxley's useful terminology, the definition of the Mammalia expresses a grade of organization (the attainment of a particular level of advancement), not a clade (a single phyletic group or line). Some taxonomists insist that in an evolutionary classification every group must be truly monophyletic—that is, spring from a single ancestral stock. Usually, this cannot be ascertained; the fossil material is insufficient or, as with many soft-bodied forms, nonexistent. Definite convergence must not be overlooked if it can be detected.

      How far groups should be split to show phyletic lines and what rank should be given each group and subgroup thus are matters for reasonable compromise. The resulting classification, if fossils are unknown, may be frankly “natural” or phenetic, as is often explicitly the case with the flowering plants and is actually the case with many animal groups. If sufficient fossils are available, the resulting classification may be consonant with what is known about the evolution of the group or with what is merely conjectured. In reality, many classifications are conjectural or tendentious, and simpler and more natural ones might be closer to the available facts.

      Even when only mere fragments are dealt with, a classification of some sort may still be necessary. Large numbers of leaves, some stems, trunks or roots, many seeds, and few flowers are known as fossils and may be of interest to the evolutionist. It may be many decades before a particular sort of fossilized leaf can be associated with a particular sort of branch, let alone trunk, flower, or seed. It is customary to construct form groups (i.e., a genus or species name is assigned to the fossilized material based on its structure) in order to classify fossilized remains and to give them valid binomial names. When (if ever) two or more bits of fossil material are identified as belonging to one organism, one name only is retained. This procedure is best known for plants, but one phylum of animals (the Conodonta) is made up of enigmatic structures that are obviously some part of something animal.

A.J. Cain

Current systems of classification

Division of organisms into kingdoms

      As long as the only known plants were those that grew fixed in one place and all known animals moved about and took in food, the greater groups of organisms were obvious. Even in the time of Linnaeus, however, many biologists wondered about such animal groups as corals and sponges, which were fixed in position and in some ways even flowerlike. Were they zoophytes—animal-plants—intermediate between the two kingdoms?

      A more serious problem of classification arose with the invention of the microscope and the discovery of microscopic forms of life. It became apparent that many of these microorganisms held both animal and plant characteristics and could not simply be classified in either kingdom. For example, Euglena is a unicellular organism with chlorophyll characteristic of a plant, yet with such animal features as an eyespot and locomotion by means of a flagellum.

      Some microorganisms are parasitic inside animals and ingest complicated materials as food, while related microorganisms obtain their nutrients through photosynthesis. It has been proposed that the unicellular forms of microorganisms be placed in a separate kingdom, the Protista. Some biologists do not find this to be a happy solution, however, as some of the “unicellular” plants occur in “colonies” of various numbers of cells and may even have specialized reproductive cells.

      In the mid-20th century, biologists recognized two vastly different cell types, procaryote (prokaryote) and eucaryote (eukaryote), and based a division of the living and extinct world on these two broad categorizations. The divisions were based primarily on the absence or presence, respectively, of a membrane-bound nucleus containing the genetic material of the cell, as well as on other organizational and structural features. Many classifications of living organisms adopted such a division and further created two superkingdoms, Prokaryota and Eukaryota. Within the Prokaryota was placed the kingdom Monera (the bacteria, blue-green algae, and a recently described bacterial group called the Archaebacteria [also called Archaeobacteria]). The Eukaryota comprised all other living organisms.

      Viruses (virus) are far more difficult to classify. They are known only as parasites; no free-living forms have been found. They have a far simpler structure than bacteria and reproduce by injecting their hereditary material, which is either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) but not both (as in all other living things), into cells of other organisms. In effect, viruses utilize the host's protein-synthesizing mechanism to reproduce. The individual virus particle (virion), therefore, does not grow and divide by fission as do bacteria. Some biologists have speculated that viruses are genes that have gotten out of control and become parasitic; others have denied that viruses can be considered living at all. Many are highly important disease producers in plants, animals, and bacteria.

      The principal characteristic shared by bacteria and viruses is that the hereditary material is not contained within a special nuclear membrane. Such a procaryotic (prokaryote) condition might be postulated by evolutionists as primitive when compared with forms with a complex nucleus, as in eucaryotic organisms (eukaryote). Viruses, as they now exist, may be the simplest of living things, but it is not known how much they are modified from ancestral forms that are assumed not to have been parasitic and that were evidently on the main line of evolution; nor is their relation to bacteria known.

      Another procaryotic group, the blue-green algae, is traditionally placed with the other algae (e.g., seaweeds) and studied more by botanists than by microbiologists. Blue-green algae may be either unicellular or filamentous, and they behave like true plants, photosynthesizing in a way that resembles green plants rather than bacteria. Many move by gliding, as do some bacteria and some true unicellular algae. They are often extremely abundant around hot springs or at the edges of muddy ponds, and, though they are resistant to harsh environments, blue-green algae are killed by many drugs (e.g., antibiotics) used against bacteria. Perhaps they are best regarded as representing a group close to the main evolutionary line that gave rise to the eucaryotic plants.

      Another problem relates to the position of the fungi (fungus), a large group including such familiar forms as mushrooms, toadstools, molds, and yeasts. (Although some authorities place the true slime molds [Myxomycetes] with the fungi, others point to the many characteristics they share with the protists.) The fungi are eucaryotic, lack chlorophyll (and therefore cannot photosynthesize as do green plants), and have rigid walls to the “cells,” or filaments (hyphae) that sometimes contain cellulose, as do green plants. Some fungi walls or filaments are made of chitin, the major constituent of the external skeleton of insects and other arthropods, or even of other structural compounds. A fungal “cell” usually contains many nuclei. Asexual and sexual spores are usually produced; some produce motile spores with flagella, like the spores of some algae. The sexual cycle is often very complex. Because fungi in general grow and produce “fruit” like ordinary plants, they have traditionally been included with them; but the differences between the fungi and the plants seem considerable.

      The preceding considerations exemplify the difficulties inherent in producing a generally accepted classification, even at the highest levels. Since the earliest attempts at classifying the living world into two kingdoms, Plantae and Animalia, biologists have debated the relationships among all organisms. Most biologists, however, accept the fundamental differences in cell structure that separates the superkingdoms Eukaryota and Prokaryota.

       four-kingdom scheme of classificationThe two-kingdom classification of organisms has not been a suitable alternative since the discovery of a microscopic group of organisms. One four-kingdom classification (Table (four-kingdom scheme of classification)) recognizes the kingdoms Virus, Monera, Plantae, and Animalia within the superkingdoms Prokaryota and Eukaryota. Separate kingdoms are not recognized for the microorganisms (Protista) or for the fungi, which are placed in the plant kingdom. Another classification recognizes Protista (including the fungi and protozoans) rather than viruses.

A classification of living organisms

      Recent advances in biochemical and electron microscopic techniques, as well as in testing that investigates the genetic relatedness among species, have redefined previously established taxonomic relationships and have fortified support for a five-kingdom classification of living organisms. This alternative scheme is presented below and is used in the major biological articles. In it, the procaryotic Monera continue to comprise the bacteria, although techniques in genetic homology have defined a new group of bacteria, the Archaebacteria, that some biologists believe may be as different from bacteria as bacteria are from other eucaryotic organisms. The eucaryotic kingdoms now include the Plantae, Animalia, Protista, and Fungi, or Mycota.

      The protists are predominantly unicellular, microscopic, nonvascular organisms that do not generally form tissues. Exhibiting all modes of nutrition, protists are frequently motile organisms, primarily using flagella, cilia, or pseudopodia. The fungi, also nonvascular organisms, exhibit an osmotrophic type of heterotrophic nutrition. Although the mycelium may be complex, they also exhibit only simple tissue differentiation, if any at all. Their cell walls usually contain chitin, and they commonly release spores during reproduction. The plants are multicellular, multitissued, autotrophic organisms with cellulose-containing cell walls. The vascular plants possess roots, stems, leaves, and complex reproductive organs. Their life cycle shows an alternation of haploid (gametophyte) and diploid (sporophyte) generations. The animals are multicellular, multitissued, heterotrophic organisms whose cells are not surrounded by cell walls. Animals generally are independently motile, which has led to the development of organ and tissue systems. The monerans, the only procaryotic kingdom in this classification scheme, is principally made up of the bacteria. They are generally free-living, unicellular organisms that reproduce by fission. Their genetic material is concentrated in a non-membrane-bound nuclear area. Motility in bacteria is by a flagellar structure that is different from the eucaryotic flagellum. Most bacteria have an envelope that contains a unique cell wall, peptidoglycan, the chemical nature of which imparts a special staining property that is taxonomically significant (i.e., gram-positive, gram-negative, acid-fast).

      The use of “division” by botanists and “phylum” by zoologists for equivalent categories leads to a rather awkward situation in the Protista, a group of interest to both botanists and zoologists. As used below, the terms follow prevailing usage: phylum for the primarily animal-like protozoa and division for other protistan groups that are more plantlike and of interest primarily to botanists.

      The discussion above shows the difficulty involved in classification; for example, one traditional classification of the Aschelminthes, presented below and in the article aschelminth, divides the phylum Aschelminthes into five classes: Rotifera, Gastrotricha, Kinorhyncha, Nematoda, and Nematomorpha. An alternative classification elevates these classes to phyla, and still another classification establishes different relationships between the groups: phylum Gastrotricha, phylum Rotifera, phylum Nematoda (containing classes Adenophorea, Secernentea, and Nematomorpha), and phylum Introverta (containing classes Kinorhyncha, Loricifera, Priapulida, and Acanthocephala). The true relationships between these pseudocoelomates remain to be established.

Kingdom Monera (moneran) ( bacteria, archaebacteria, and blue-green algae)

 Kingdom Protista (protist) (protists)

 Algae other than the blue-green algae, protozoa, and slime molds.Kingdom Fungi (fungi)

 Kingdom Plantae (Metaphyta or Embryophyta; nonvascular and vascular plants)

 Includes mosses, liverworts, hornworts, whisk ferns, club mosses, horsetails, ferns, cycads, conifers, gnetophytes, ginkgophytes, and flowering plants.

      Division Bryophyta (mosses, liverworts, and hornworts)

 

      Division Psilotophyta (whisk ferns or psilopsids)

 

      Division Lycophyta (club mosses and quillworts)

 

      Division Sphenophyta (horsetails)

 

      Division Polypodiophyta (ferns)

 

      Division Coniferophyta

 Includes pines, yews, spruces, firs, junipers, redwoods, and others.

      Division Ginkgophyta (ginkgoes)

 

      Division Cycadophyta (cycads)

 

      Division Gnetophyta (gnetophytes)

 

      Division Magnoliophyta (flowering plants)

 Includes monocots (grasses, rushes, sedges, cattails and pondweeds, palms, pineapple and other bromeliads, lilies, bananas, ginger, orchids, and others) and dicots or broad-leaved plants (most trees, buttercups, poppies, roses, violets, cacti, mints, squashes, sunflowers, and many others).

Kingdom Animalia (or Metazoa)

 

      Subkingdom Parazoa (sponges)

 

      Phylum Porifera (sponges)

 

      Subkingdom Eumetazoa

 

      Phylum Mesozoa (mesozoans)

 

      Phylum Cnidaria (or Coelenterata; cnidarians)

 

      Phylum Ctenophora (ctenophores)

 

      Phylum Platyhelminthes (flatworms)

 

      Phylum Nemertea (or Rhynchocoela; ribbonworms)

 

      Phylum (or class) Acanthocephala (spiny-headed worms)

 

      Phylum Aschelminthes

 

      Phylum Priapulida (priapulids)

 

      Phylum Annelida (annelid worms)

 

      Phylum Tardigrada

 

      Phylum Onychophora

 

      Phylum Arthropoda (arthropods)

 

      Phylum Mollusca (mollusks)

 

      Phylum Bryozoa (or Ectoprocta; bryozoans)

 

      Phylum Phoronida (phoronid worms)

 

      Phylum Brachiopoda (brachiopods)

 

      Phylum Sipuncula (sipunculid worms)

 

      Phylum Chaetognatha (arrowworms)

 

      Phylum Echiurida (spoonworms)

 

      Phylum Echinodermata (echinoderms)

 

      Phylum Hemichordata (hemichordates)

 

      Phylum Pogonophora (beardworms)

 

      Phylum Chordata (chordates)

 

Ed.

Additional Reading

Willi Hennig, Phylogenetic Systematics (1966, reissued 1979), is a statement of phylogenetic principles. Mark Ridley, Evolution and Classification: The Reformation of Cladism (1986), offers a very clear and readable account of the different philosophical approaches used in taxonomy and systematics. General texts include George Gaylord Simpson, Principles of Animal Taxonomy (1961, reissued 1990); Lynn Margulis and Karlene V. Schwartz, Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth, 2nd ed. (1988), a survey of the lives and relationships of many groups of organisms; Godfrey M. Hewitt, Andrew W.B. Johnston, and J. Peter W. Young (eds.), Molecular Techniques in Taxonomy (1991), covering various topics and methods in molecular systematics; V.V. Sivarajan, Introduction to the Principles of Plant Taxonomy, ed. by N.K.P. Robson, 2nd ed. (1991), an overview of the established concepts of plant systematics for beginning students; Peter L. Forey et al., Cladistics: A Practical Course in Systematics (1992), an introduction to the theory and practice of cladistics; and Ernst Mayr and Peter D. Ashlock, Principles of Systematic Zoology, 2nd ed. (1991). Also of interest are S.P. Lapage et al. (eds.), International Code of Nomenclature of Bacteria, 1990 revision (1992); W. Greuter et al. (eds.), International Code of Botanical Nomenclature (Tokyo Code) (1994); and W.D.L. Ride et al. (eds.), International Code of Zoological Nomenclature, 3rd ed. (1985).A.J. Cain Ed.

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