TAXONOMY

CONCEPT

Taxonomy is the area of the biological sciences devoted to the identification, naming, and classification of living things according to apparent common characteristics. It is far from a simple subject, particularly owing to many disputes over the rules for classifying plants and animals. In terms of real-life application, taxonomy, on the one hand, is related to the entire world of life on Earth, but on the other hand, it might seem an ivory-tower discipline that it has nothing to do with the lives of ordinary people. Nonetheless, to understand the very science of life, which is biology, it is essential to understand taxonomy. Each discipline has its own form of taxonomy: people cannot really grasp politics, for instance, without knowing such basics of political classification as the difference between a dictatorship and a democracy or a representative government and one with an absolute ruler. In the biological sciences, before one can begin to appreciate the many varieties of organisms on Earth, it is essential to comprehend the fundamental ideas about how those organisms are related—or, in areas of dispute, may be related—to one another.

HOW IT WORKS

Taxonomy in Context

The term taxonomy is actually just one of several related words describing various aspects of classification in the biological sciences. In keeping with the spirit of order and intellectual tidiness that governs all efforts to classify, let us start with the most general concept, which happens to be classification itself. Classification is a very broad term, with applications far beyond the biological sciences, that simply refers to the act of systematically arranging ideas or objects into categories according to specific criteria.

While its meaning is narrower than that of classification, even taxonomy still has broader applications than the way in which it is used in the biological sciences. In a general sense, taxonomy refers to the study of classification or to methods of classification—for example, "political taxonomy," as we used it in the introduction to this essay. Literary critics sometimes refer to a writer's taxonomy of characters. Within the biological sciences, however, the term designates specifically a subdiscipline involving the process and study of the identification, naming, and classification of organisms according to apparent common characteristics.

PHYLOGENY AND NOMENCLATURE.

Two other terms that one is likely to run across in the study of taxonomy are phylogeny and nomenclature. Phylogeny is the evolutionary history of organisms, particularly as that history refers to the relationships between life-forms and the broad lines of descent that unite them. Taxonomy is less fundamental a concept than phylogeny. Whereas taxonomy is a human effort to give order to all the data, phylogeny is the true evolutionary relationship between living organisms. Some scientists call phylogeny the tree of life, meaning that it represents the underlying hierarchical structure by which life-forms evolved and are related to one another.

The word naming was used earlier in the definition of taxonomy because it is a familiar, easily understandable word. However, a more accurate term, and one that helps illuminate the distinction between taxonomy and systematics, is nomenclature. The latter can be defined as the act or process of naming as a well as a system of names, particularly one used in a specific science or discipline.

Homologous and Analogous Features

Before going on to discuss methods of classification, it is important to note just which characteristics of an organism's morphological aspect (i.e., structure or form) are important to scientists working in the field of taxonomy. In theorizing relationships between species, taxonomists are not interested in what are known as analogous features, those characteristics that are superficially similar but not as a result of any common evolutionary origin. Rather, they are interested in homologous features, or features that have a common evolutionary origin, even though they may differ in terms of morphological form.

One example of a shared evolutionary characteristic, discussed briefly in the essay Evolution, is the pentadactyl limb, a five-digit appendage common to mammals and found, in modified form, among birds. This is a homologous feature, indicating a common ancestor that likewise had limbs with five digits at the end. By contrast, there is no indication of a close evolutionary relationship in the fact that birds, butterflies, and bats all have wings that are similar in shape. Rather, the laws of physics require that a wing be of a certain shape in order to hold an object aloft, which is why the contour of an airplane wing, when viewed from the side, is remarkably like that of a bird's wing where it joins the animal's body.

Cladistics and Numerical Taxonomy

Cladistics is a system of taxonomy that distinguishes taxonomic groups or entities on the basis of shared derived characteristics, hypothesizing evolutionary relationships to arrange them in a tree like, branching hierarchy. The expression derived characteristics in this definition means that the characteristics that unite two types of organism are not necessarily present in a shared evolutionary ancestor. Rather, they have developed over the course of evolutionary history since the time of that shared ancestor.

In explaining cladistics to the ordinary human being, the vast majority of science writers seem to be at a loss as to how to make the topic comprehensible. Thus, such terms as derived characteristics and its opposite, primitive characteristics, usually are left undefined. A welcome exception is Paul Willis, who, in an on-line article for the Australian Broadcasting Corporation (see Where to Learn More) gave a wonderful illustration that was an attempt to analyze the relationships between a mouse, a lizard, and a fish.

"They've all got backbones," Willis wrote," so the feature 'backbone' is useless [as an indication of evolutionary branching]; it's a 'primitive' character that tells you nothing. But the [derived] feature 'four legs' is useful because it's an evolutionary novelty shared only between the lizard and the mouse. This implies that the lizard and mouse are more closely related to each other than either is to the fish. Put another way, the lizard and the mouse share a common ancestor that had four legs." Willis went on to note that "the more evolutionary novelties we can find that support a particular relationship, the greater our confidence that the relationship is correct. 'Air breathing,' 'neck' and 'amniotic egg' are another three evolutionary novelties that tie the lizard and the mouse together and leave the fish as a more distant relative."

NUMERICAL TAXONOMY.

Cladistics, the most widely applied approach to taxonomy, has undergone considerable change since it was introduced by the German zoologist Willi Hennig (1913-1976) in the 1950s. Particularly important has been the marriage of cladistics with another taxonomic idea born in the mid-twentieth century, phenetics, or numerical taxonomy. Introduced by the Austrian biologist Robert Reuven Sokal (1926-) and the English microbiologist Peter Henry Andrews Sneath (1923-), numerical taxonomy is an approach in which specific morphological characteristics of an organism are measured and assigned numerical value, so that similarities between taxa (taxonomic groups or entities) can be compared mathematically. These mathematical comparisons are performed through the use of algorithms, or specific step-by-step mathematical procedures for computing the answer to a particular problem. The aim of numerical taxonomy is to remove all subjectivity (such as the taxonomist's "intuition") from the process of classification. Initially, many traditional taxonomists rejected numerical taxonomy, because its results sometimes contradicted their own decades-long studies of comparative morphological features. Nearly all modern taxonomists apply numerical methods in taxonomy, although there is often heated debate as to which particular algorithms should be used.

Identification, Classification, and Nomenclature

Earlier, taxonomy was defined in terms of its relationship to the identification, classification, and nomenclature of taxa. Let us now briefly consider each in turn, with the understanding that they are exceedingly complex, technical subjects that can be treated here in the most cursory fashion. The process of identification is a particularly complex one. When an apparently new taxon is discovered, a taxonomist prepares an organized written description of the characteristics of similar species, which are referred to as a taxonomic key. Instead of using pictures, which often poorly convey the natural variations in morphological features, taxonomists prefer to use a taxonomic key in written form, which provides much more detail and exactitude.

To put it in colloquial terms, by referring to a taxonomic key, a taxonomist may determine that if an organism "looks like a duck and quacks like a duck, it must be a duck"—only, in this instance, the taxa being compared are much more specific than the common term duck and the characteristics much more precisely described. (For one thing, there are several dozen species in the genus Anas, which includes all "proper" ducks, and many more species in the family Anatidae, or waterfowl, that are commonly called by "duck names"—including such amusingly named species as the ruddy duck, lack duck, freckled duck, and comb duck.) If there is no already established "duck" that the species in question resembles, the taxonomist may have discovered an entirely new genus, family, order, class, or even phylum.

A taxonomist may use what is called a dichotomous key, which presents series of alternatives much like a flow chart. For example, if the flowers of a sample in question are white and the stem is woody, then (depending on additional alternatives) it could be either species A or species B. If the flowers are not white and the stem is herbaceous (non-woody), then, presented with another set of additional alternatives, it is possible that the plant is either species C or species D.

CLASSIFICATION.

In discussing cladistics and phenetics, we touched briefly on the process of classification. Suffice it to say that this process is far more complex and technically elaborate than these few paragraphs can begin to suggest. We return later to specifics of classification as they relate to systems and innovations introduced by the Greek philosopher Aristotle (384-322 b.c.), the Swedish botanist Carolus Linnaeus (1707-1778), and the English naturalist Charles Darwin (1809-1882), the three most important men in the history of taxonomy before the twentieth century. For the present, our focus is on the overall ranking system.

There are many possible ranks of classification but only seven that are part of what is known as the obligatory taxonomy, or obligatory hierarchy. These ranks are kingdom, phylum, class, order, family, genus, and species. Listed here are all possible ranks, with obligatory ranks in italics.

• Kingdom
• Subkingdom
• Phylum
• Subphylum
• Superclass
• Class
• Subclass
• Infraclass
• Cohort
• Superorder
• Order
• Suborder
• Superfamily
• Family
• Subfamily
• Tribe
• Genus
• Subgenus
• Species
• Subspecies

The reader occasionally may come across nonobligatory ranks, most notably subphylum, but for the most part the only ranks referred to in this book are the obligatory ones.

NOMENCLATURE.

In accordance with a tradition established by Linnaeus, all group names are in Latin, thus facilitating ease of communication. There are some rules concerning names of groups: for instance, those of families use the suffix-idae. In the world of taxonomy, however, few rules are accepted universally. Even as basic a term as phylum is not universal, since botanists prefer the word division.

The proper name of any ranking more general than species is capitalized (e.g., phylum Chordata), with species and subspecies names in lowercase. Genus, species, and subspecies names are rendered in italics (e.g., Homo sapiens, or "man the wise"), while proper names of the more general groupings are presented in ordinary type (e.g., class Mammalia). If the same name appears a second time in the same article, the genus name usually is abbreviated: thus, H. sapiens.

Just as most people (with such rare exceptions as Cher and Madonna) are identified by two names, a personal and a family name, taxonomy makes use of a system called binomial nomenclature, in which each type of plant or animal is given a two-word name, with the first name identifying the genus and the second the species. In binomial nomenclature, the genus name is analogous to the family name, inasmuch as there are many species within a genus, and the species name is like a personal name. The difference is that whereas there may be thousands of boys and men named John Smith, there is only one species called Homo sapiens. Beyond the species name, there may be subspecies names: humans are subspecies sapiens, so our full species name with subspecies is Homo sapiens sapiens. Additional rules govern the inclusion of a name or an abbreviation, at the end of the species or subspecies name, to recognize the individual who first identified it.

REAL-LIFE APPLICATIONS

The Urge to Classify

One might ask what all the fuss is about. Why is classification so important? We attempt to answer that question from a few angles, including a brief look at the lengthy historical quest to develop a workable taxonomic system. But what was the original impulse that motivated that quest? One clue can be found in the Greek roots of the word taxonomy: taxis, or "arrangement," and nomos, or "law." The search for a taxonomic system represents humankind's desire to make order out of the complexities with which nature presents us. When it comes to the organization of ideas (including ideas about the varieties of life-forms), this desire for order is more than a mere preference. It is a necessity.

THE ANALOGY TO A LIBRARY.

Imagine a library without any organizational system, with books simply crammed willy-nilly on the shelves. Such a place would be totally chaotic, and if one happened to find a book one was looking for, it would be a case of pure luck. The odds would be weighted heavily against such luck, especially in a university library or a large municipal or regional one. Just as a good-size university library has upward of a million volumes, and many large university libraries have several million, so there are at least a couple of million identified species, and the total may be much larger. Some entomologists (scientists who study insects) speculate that there may be ten million species of insect alone.

THE LURE OF A NEW SPECIES.

When a zoologist or botanist discovers what he or she believes to be a new species, the taxonomic system provides a standard against which to check it—rather as you would do if you thought you had discovered a book that was not in the library. If the "new" species matches an established one, that may be the end of the story—unless the scientist has discovered a new aspect of the species or a new subspecies. And if there is no match in the taxonomic "library," the scientist has discovered an entirely new life-form, with all the grand and terrifying ramifications that may ensue.

The new species might be an herb from which a cure can be synthesized for a devastating disease, or it could be a parasite that carries a new and previously unknown malady. Whatever it is, it is better to know about it than not to know, and though the vast majority of "new" species are not nearly as exciting as the preceding paragraph would imply, each has its part to play in the overall balance of life. Discovery of new species is particularly important when those species are endangered or might be in the process of disappearing even as they are identified.

Nonscientific Taxonomy

Without knowing anything about scientific taxonomy, almost anyone can begin to classify animals and perhaps plants. If we limit the discussion purely to animals, there are many basic parameters according to which we could classify them, just off the tops of our heads, as it were. For example, there are aquatic and terrestrial animals, and these general groupings can be broken down further according to biome or habitat (see Biomes). There are animals that walk, fly, swim, slither, or move by some other means. Animals can be divided according to their forms of reproduction, whether asexual or sexual, oviparous or viviparous (expelling or retaining a fertilized egg, respectively), and so on. As discussed in Food Webs, animals may be classified as herbivores, carnivores, omnivores, or detritivores or as primary, secondary, or tertiary consumers. They may be endothermic or ectothermic (warm-blooded or cold-blooded), and they may be covered with scales, feathers, fur, or skin. (In the last case, that skin may be protected by either mucus or hair.)

On and on go the categories, and if one is inclined toward a classifying mind, this kind of mental exercise can be fun. Certainly, little children enjoy it, and many educational programs and games call on the child to group animals thus. Although these kinds of groupings, and the efforts to place animals into one group or another, constitute a form of classification, there is a great difference between this and scientific taxonomy.

SCIENCE VERSUS "COMMON SENSE."

Taxonomy is tied closely to evolutionary study, and Darwin's theory of evolution was a turning point in the history of scientific classification. Thus, taxonomists are concerned more with the evolutionary patterns that link organisms than they are with what may be only superficial similarities. Habitat, for instance, is significant in studying biomes, but it seldom plays a role in taxonomy. Nor is the ability to fly, as we have noted, necessarily an indicator of taxonomic similarities.

A striking example of the difference between scientific taxonomy and "common sense" classification is the fact that whales and dolphins are grouped along with other mammals (class Mammalia) rather than with fish and other creatures that most readily come to mind when thinking of aquatic organisms. In fact, whales and dolphins share not only a wide array of primitive characteristics with mammals (for example, the pentadactyl limb described earlier) but also the derived characteristic that defines mammal : the secreting of milk from mammary glands, by which a mother feeds her young. Not only is it impossible to get milk from a fish (even family Chanidae, known by the common name "milkfish"), but fish lack even that primitive characteristic, the pentadactyl limb, that links mammals, at least distantly, with nonmammalian creatures, such as birds (class Aves).

COMMON TERMS AND FOLK TAXONOMY.

For the sake of convenience, in many places throughout this book, common terms such as bird, horse, fish, and so forth are used. But common terms are far from adequate in a scientific context, because such terminology can be deceptive, as exemplified by the nonduck "ducks" mentioned earlier. Likewise, shellfish and starfish are not "fish" as that term is usually understood. But while common terminology can be misleading, sometimes correlations with scientific taxonomy can be found in what is known as folk taxonomy. The latter is a term for the taxonomic systems applied in relatively isolated non-Western societies. For example, the folk taxonomy of native peoples in New Guinea identified 136 bird species in the mountains of that island, a figure that came amazingly close to the 137 species identified by the German-born American evolutionary biologist Ernst Mayr (1904-) when he studied New Guinea's birds using scientific methods.

Aristotle, Linnaeus, Darwin, and Beyond

Among his many other accomplishments as a thinker, Aristotle is regarded as the father of the biological sciences and of taxonomy. Among the dominant ideas in his work as a philosopher are the concepts of hierarchy and classification, and thus he took readily to the idea of classifying things. At his school in Athens, he put his students to work on all sorts of taxonomic pursuits, from listing the champions at the Pythian Games (a festival like the Olympics) to classifying the constitutions of various Greek city-states to analyzing the body parts of animals. Aristotle himself dissected hundreds of animals to understand what made them tick, and he proved to be some 2,000 years ahead of his time in recognizing that the dolphin is a mammal and not a fish. His system of classification, however, was a far cry from the ideas that developed in nineteenth-century taxonomy; rather than searching for evolutionary lines of descent, he ranked animals in order of their physical complexity.

In most aspects of his other work, Aristotle established sharp distinctions between his own ideas and those of his teacher, Plato (427?-347 b.c.). For example, Aristotle rejected Plato's position that every idea we can conceive is but a dim reflection of an essential concept—for example, that our idea of "red" is only a shadowy copy of the perfect notion of "redness." Yet in his taxonomy, Aristotle seemed to hark back to his days as Plato's star pupil. The Aristotelian principles of classification were governed by the idea that there are constant, unchanging "essences" that unite classes of organisms. This idea of essences is completely at odds with the empirical (experience-based) mentality that governs taxonomy today. Nonetheless, for two millennia, Aristotelian ideas represented the cutting edge in taxonomy and much else.

THE MIDDLE AGES AND RENAISSANCE.

After Aristotle and his brilliant student Theophrastus (371?-287? b.c.), the father of botany, there would be no Western biological theorists of remotely comparable stature until the time of the Renaissance. In the meantime, taxonomy, as with so many other areas of learning in Europe, declined badly. During the Middle Ages, what passed for taxonomic writings consisted primarily of bestiaries, books full of fanciful and imaginary creatures, such as the unicorn. The first signs of scientific reawakening in the biological sciences in general, and taxonomy in particular, came with plant and animal catalogues by such great medieval scholars as Peter Abelard (1079-1142) and Albertus Magnus (ca. 1200-1280). Even so, their work consisted primarily of summations of existing Aristotelian knowledge rather than new contributions.

In the sixteenth century, the Swiss scientist Konrad von Gessner (1516-1565) wrote Historia animalium (1551-1558), a groundbreaking work that included descriptions of many animals never before seen by most Europeans. Gesner also denounced the practice of including fictitious animals in bestiaries. Around the same time, the discoveries of new plant and animal species in the New World began to point up the need for a taxonomy that went beyond Aristotle's. The first scholar of the modern era to attack this problem was the Italian botanist Andrea Cesalpino (1519-1603), but nearly two centuries would pass before the development of a workable classification system.

LINNAEUS AND OTHERS.

The man who revolutionized taxonomy was born Carl von Linné but adopted the Latinized name Carolus Linnaeus. Even that late in scientific history, scholars still wrote chiefly in Latin, not because they were trying to adhere to tradition but because it remained a common language between educated people of different countries. Thus, Linnaeus's great work, which he first published in 1737 but revised numerous times, was named Systema naturae, or "The Natural System." Thanks to Linnaeus, Latin became enshrined permanently as the language of taxonomy the world over, but this was far from his only accomplishment.

It was Linnaeus who introduced binomial nomenclature, in a 1758 revision of his Systema, and also Linnaeus who established several of the obligatory rankings. Moreover, he instituted the first taxonomic keys, and his system, first applied in botany, became accepted in the zoological community as well. Others, including Baron Georges Cuvier (1769-1832), Michel Adanson (1727-1806), and Comte Georges Buffon (1707-1788), refined Linnaeus's system, but he stands as a towering figure in the discipline.

Later, the French natural philosopher Jean Baptiste de Lamarck (1744-1829) proposed a distinction between vertebrates, or animals with spinal columns, and invertebrates. Today this distinction is not considered as useful as it once was, since it is lopsided—that is, there are nine times as many invertebrates as vertebrates in the animal kingdom—but at the time, it represented an advancement. Less questionable were the distinctions introduced in 1866 by the German biologist Ernst Haeckel (1834-1919) between plants, animals, and single-cell organisms. As Haeckel reasoned, at the level of unicellular organisms, distinctions between plant and animal really make no sense.

DARWIN AND THE TWENTIETH CENTURY.

By far the most influential figure in taxonomy during the nineteenth century was the man also recognized as the most influential figure in all of biology during that era: Darwin. Whereas Linnaeus had retained the Aristotelian focus on the "essence" of the animal's features, Darwin swept away such notions and, in his Origin of Species (1859), proposed that the "community of descent" is "the one known cause of close similarity in organic beings" and therefore the only reasonable basis for taxonomic classification systems. As result of Darwin's work, taxonomists became much more oriented toward the representation of phylogeny in their classification systems. Therefore, instead of simply naming and cataloguing species, modern taxonomists also try to construct evolutionary trees showing the relationships between different species.

Since Darwin's time, taxonomy has seen numerous innovations, including the introduction of cladistics by Hennig and of numerical taxonomy by Sokal and Sneath. Taxonomists today make use of something unknown at the time of Darwin: DNA (deoxyribonucleic acid, a molecule that contains genetic codes for inheritance), which provides a wealth of evidence showing relationships between creatures. For example, a comparison of human and chimpanzee DNA reveals that we share more than 98% of the same genetic material, indicating that the two lines of descent are related more closely than either is to apes.

The Five Kingdoms

There are several taxonomic systems, distinguished in part by the number of different kingdoms that each system recognizes. The system used in this book is that of five kingdoms, listed here, which is the result of modifications by the American biologists Lynn Margulis (1938-) and Karlene V. Schwartz (1936-) to the work of earlier taxonomists. (It should be noted that biologists are increasingly using a system of six kingdoms under three domains: eubacteria, arachaea, and eukaryotes. For the sake of simplicity, however, the five-kingdom system is used here.) These five kingdoms are as follows:

Monera : bacteria, blue-green algae, and spirochetes (spiral-shaped, undulating bacteria). Members of this kingdom, consisting of some 10,000 or more known species, are single-cell prokaryotes, meaning that the cell has no distinct nucleus. Some researchers have divided Monera into Eubacteria, or "true" bacteria, and Archae-bacteria, which are bacteria-like organisms capable of living in extremely harsh and sometimes anaerobic (oxygen-lacking) environments, such as in acids, saltwater, or sewage.

Protista (or Protoctista) : protozoans, slime molds (which resemble fungi), and algae other than the blue-green variety. Made up of more than 250,000 species, this kingdom is distinguished by the fact that its members are single-cell organisms, like the Monera. These organisms, however, are eukaryotes, or cells with a nucleus as well as organelles (sections of the cell that perform specific functions).

Fungi : fungi, molds, mushrooms, yeasts, mildews, and smuts (a type of fungus that afflicts certain plants). Fungi are multicellular, consisting of specialized eukaryotic cells arranged in a filamentous form (that is, a long, thin series of cells attached either to one another or to a long, thin cylindrical cell). There are some 100,000 varieties of fungi.

Plantae : plants, of which there are upward of 250,000 species. Although plant is a common term, there is no universally accepted definition that includes all plants and excludes all nonplants. One of the most important characteristics of plants is the fact that they receive their nutrition almost purely through photosynthesis. Beyond the plant kingdom, this is true only of a few protests and bacteria. (For the most part, the three lower kingdoms obtain nutrition through absorption.) Other characteristics of plants include the fact that they are incapable of locomotion; have cells that contain a form of carbohydrate called cellulose, making their cell walls more or less rigid; are capable of nearly unlimited growth at certain localized regions (unlike most animals, which have set numbers of limbs and so forth); and have no sensory or nervous system.

Animalia : animals, of which there are more than 1,000,000 species. Like plants, animals are characterized by specialized eukaryotic cells, but also like plants, the comprehensive definition of animal is not as obvious as one might imagine. Mobility, or a means of locomotion, is not a defining characteristic, since sponges and corals are considered animals. The principal difference between animals and plants is at the cellular level: animals either lack cells walls entirely or have highly permeable walls, unlike the cellulose cell walls in plants. Another defining characteristic of animal is that they obtain nutrition by feeding on other organisms. Additionally, animals usually have more or less fixed morphological characteristics and possess a nervous system. The fact that most animals are mobile helps account for the large number of animal species compared with those of other kingdoms; over the course of evolutionary history, mobility brought about the introduction of animals to a wide range of environments, which required a wide range of adaptations.

Space does not permit a discussion of the various phyla, let alone the smaller divisions, inanything like the detail we have accorded to kingdoms. Furthermore, the distinctions among most phyla, apart from higher animals and some plants, makes for rather dry reading to a nonscientist. These divisions are discussed in furtherdetail, however, within the essays Species and Speciation. The latter essays also address the definition of species, a great and continuing challenge that faces taxonomists.

Taxonomy in Action

Two stories reported in National Geographic News online (see "Where to Learn More") in 2001 and 2002 illustrate the fact that scientific classification is an ongoing process, and that the world of taxonomy is frequently home to controversies and surprises. Lee R. Berger of the Geographic reported the first story, on December 17, 2001, under the heading "How Do You Miss a Whole Elephant Species?" As it turns out, there are not just two species of elephant, as had long been believed, but three.

In addition to the Asian elephant (Elephas maximus ) scientists had long recognized the African savanna elephant, or Loxodonta africana, as a second species. However, DNA testing (see Genetics and Genetic Engineering) in 2001 revealed a second African variety, Loxodonta cyclotisare or the African forest elephant, formerly believed to constitute merely a subspecies.

The news was not entirely new: as early as a century prior to the announcement of the "new" species, zoologists had begun to suspect that the forest elephant was a separate grouping distinguished by a number of characteristics. For example, the forest elephant is physically smaller, with males seldom measuring more than 8 ft. (2.5 m) at the shoulder, as compared to 13 ft. (4 m) for a large savanna male. Additionally, ivory samples confiscated from poachers or illegal hunters have revealed that the material in the tusks of the forest variety is pinker and harder than that of its savanna counterpart.

Recognition of the third elephant species followed years of argument as to whether the two African varieties are capable of interbreeding, which would indicate that they are not separate species. That debate was rendered moot by the DNA studies, which showed that the African forest and savanna elephants are less closely related genetically than are lions and tigers, or horses and zebras.

A "NEW" INSECT ORDER.

The identification of the forest elephant in 2001 was a major taxonomic event, inasmuch as the elephant itself is a large and commonly known creature. However, it was still a matter only of identifying a new species, whereas in 2002, for the first time in 87 years, taxonomists identified an entirely new insect order. Actually, the order consists of a single known species, but this one is so different from others that it must be grouped separately. Discovered in Namibia, in southwestern Africa, the creature was given the nickname "the gladiator" in honor of the Academy Award-winning 2000 film of that name.

Entomologist Oliver Zompro of the Max Planck Institute of Limnology in Plön, Germany, described the creature as "a cross between a stick insect, a mantid, and a grasshopper," according to the Geographic. Because its first body segment is the largest, it is distinguished from a stick insect, whereas it differs from a mantid inasmuch as it uses both fore and mid-legs to capture prey. And while it looks like a grasshopper, "the gladiator" cannot jump.

Measuring as much as 1.6 in. (4 cm) long, the insect, whose order is designated as Mantophasmatodea, is a carnivorous, nocturnal creature. Its discovery raised the number of known insect orders to 31, a discovery that Piotr Naskrecki, director of the Conservation International Invertebrate Diversity Initiative, compared to finding a mastodon or saber-toothed tiger. Colorado State University ecologist Diana Wall described the discovery as "tremendously exciting" and told the Geographic, "This new order could be a missing link to determining relationships between insects and other groups. … Every textbook discussing the orders of insects will now need to be rewritten."

WHERE TO LEARN MORE

Classification—The Dinosaur FAQ (Web site). <http://www.miketaylor.org.uk/dino/faq/index.html#4>.

The Germplasm Resources Information Network (GRIN), Agricultural Research Service (Web site). <http://www.ars-grin.gov/npgs/tax/>.

Goto, H. E. Animal Taxonomy. London: Arnold, 1982.

Lacey, Elizabeth A., and Robert Shetterley. What's the Difference?: A Guide to Some Familiar Animal Look-Alikes. New York: Clarion Books, 1993.

Margulis, Lynn, and Karlene V. Schwartz. Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth. New York: W. H. Freeman, 1988.

National Geographic News (Web site). <http://news.nationalgeographic.com/news/>.

O'Neil, Dennis. Classification of Living Things/Palomar College (Web site). <http://anthro.palomar.edu/animal/>.

Parker, Steve. Eyewitness Natural World. New York: Dorling Kindersley, 1994.

Simpson, George Gaylord. Principles of Animal Taxono my. New York: Columbia University Press, 1961.

Taxonomy Browser, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (Web site). <http://www.ncbi.nlm.nih.gov/Taxonomy/>.

The Tree of Life Web Project (Web site). <http://beta.tolweb.org/tree/>.

Tudge, Colin. The Variety of Life: A Survey and a Celebration of All the Creatures That Have Ever Lived. London: Oxford University Press, 2000.

Whyman, Kathryn. The Animal Kingdom: A Guide to Vertebrate Classification and Biodiversity. Austin, TX: Raintree Steck-Vaughn, 1999.

Willis, Paul. "Dinosaurs and Birds: The Story." Australian Broadcasting Corporation (Web site). <http://www.abc.net.au/science/slab/dinobird/story.htm>.

KEY TERMS

ALGORITHM:

A specific set of step-by-step procedures for computing answers toa mathematical problem.

ANALOGOUS FEATURES:

Morphological characteristics of two or more taxathat are superficially similar but not as a result of any common evolutionary origin. For example, birds, bats, and butterflies all have wings, but this is not because they are closely related. Compare with homologous features.

BINOMIAL NOMENCLATURE:

A system of nomenclature in biological taxonomy whereby each type of plant or animal is given a two-word name, with the first name identifying the genus and the second the species. Genus name is always capitalized and abbreviated after the firstuse, and species name is lowercased. Both are always shown in italics; thus, Homo sapiens and, later in the same document, H. sapiens.

BIOME:

A large ecosystem (community of interdependent organisms and their inorganic environment) characterized by its dominant life-forms. There are two basic varieties of biome: terrestrial, or land-based, and aquatic.

CLADISTICS:

A system of taxonomy that distinguishes taxonomic groups or entities (i.e., taxa) on the basis of shared derived characteristics, hypothesizing evolutionary relationships to arrange these in a tree like, branching hierarchy. Cladistics is one of several competing approaches to taxonomic study.

CLASS:

The third most general obligatory of the taxonomic classification ranks, after phylum but before order.

CLASSIFICATION:

A very broadterm, with application far beyond the biological sciences, that refers to the act of systematically arranging ideas or objects into categories according to specific criteria. A more specific term is taxonomy.

EUKARYOTE:

A cell that has a nucleus as well as organelles (sections of the cell that perform specific functions) bound bymembranes.

FAMILY:

The third most specific of the seven obligatory ranks in taxonomy, after order but before genus.

FUNGI:

One of the five kingdoms of living things, consisting of multicellulareukaryotic cells arranged in a filamentous form (that is, a long, thin series of cells attached either to one another or to a long, thin cylindrical cell.) Fungi include "true" fungi, molds, mushrooms, yeasts, mildews, and smuts (a type of fungus that afflicts certain plants).

GENUS:

The second most specific of the obligatory ranks in taxonomy, after family but before species.

HOMOLOGOUS FEATURES:

Morphological characteristics of two or more taxa that indicate a common evolutionaryorigin, even though the organisms may differ in terms of other morphological features. An example is the pentadactyl limb, common to many birds and most mammals (e.g., the human's four fingers and thumb), which indicates a common ancestor. Compare with analogous features.

KINGDOM:

The highest or most general ranking in the obligatory taxonomic system. In the system used in this book, there are five kingdoms: Monera, Protista, Fungi, Plantae, and Animalia.

MONERA:

One of the five kingdoms of living things, consisting of single-cell prokaryotes, including bacteria, blue-greenalgae, and spirochetes (spiral-shapedundulating bacteria that may cause such diseases as syphilis).

MORPHOLOGY:

Structure or form, or the study thereof.

NOMENCLATURE:

The act or process of naming, or a system of names—particularly one used in a specific science or discipline. See also binomial nomenclature.

NUMERICAL TAXONOMY:

Anapproach to taxonomy in which specific morphological characteristics of an organism are measured and assigned numerical value, so that similarities between two types of organism can be compared mathematically by means of an algorithm. Numerical taxonomy also is called phenetics.

OBLIGATORY TAXONOMY (OROBLIGATORY HIERARCHY):

The seven taxonomic ranks by which all species must be identified, whether or not they also are identified according to nonobligatory categories, such as subphylum, cohort, or tribe. These ranks are kingdom, phylum, class, order, family, genus, and species.

ORDER:

The middle of the seven obligatory ranks in taxonomy, more specific than class but more general than family.

PHENETICS:

Another name for numerical taxonomy.

PHOTOSYNTHESIS:

The biological conversion of light energy (that is, electromagnetic energy) from the Sun to chemical energy in plants. In this process carbondioxide and water are converted to sugars.

PHYLOGENY:

The evolutionary history of organisms, particularly as that history refers to the relationships between life-forms, and the broad lines of descent that unite them.

PHYLUM:

The second most general of the obligatory taxonomic classificationranks, after kingdom and before class.

PROKARYOTE:

A cell without a nucleus.

PROTISTA (OR PROTOCTISTA):

One of the five kingdoms of living things, consisting of single-cell eukaryotes. Protista include protozoans, slime molds (which resemble fungi), and algae otherthan the blue-green variety.

SPECIES:

The most specific of the seven obligatory ranks in taxonomy.

SYSTEMATICS:

The science of classifying and studying organisms with regard to their natural relationships.

TAXON:

A taxonomic group or entity.

TAXONOMY:

The area of the biological sciences devoted to the identification, nomenclature, and classification of organisms according to apparent common characteristics. The word taxonomy also can be used more generally to refer to the study of classification or to methods of classification (e.g., "the taxonomy of Dickens's characters.")

Taxonomy

Definition of species

Nomenclature

Identification

Classification

Evolution and classification

Modern trends

Methods of classification

The kingdoms of organisms

Resources

Taxonomy is the field of biology which deals with the nomenclature, identification, and classification of organisms. There are over one million known species on Earth and probably several million more not yet identified. Taxonomists are responsible for identifying, naming, and classifying all these different species. Systematics is a discipline of biology that explicitly examines the natural variation and relationships of organisms, and which includes the field of taxonomy. Systematics also deals with the relationships of different groups of organisms, as most systematicists strive to construct natural classification systems reflecting evolutionary relationships. Many biologists use the terms taxonomy and systematics interchangeably.

Definition of species

Before taxonomists can identify, name, and classify organisms, they need to agree on a definition of the concept of species. The definition of species is not as simple as it may seem, and has been debated by biologists and philosophers alike for many years.

Most modern biologists agree that species, unlike higher taxa (genus, family, order, and so on), are authentic taxonomic units. In other words, species really do exist in nature, and are not merely artificial human constructs. Some of the most persuasive evidence in support of this is the close correspondence between the species identified by western taxonomists and those identified in the “folk taxonomy” of relatively isolated non-western societies. For example, Ernst Mayr, a noted bird taxonomist, identified 137 species of birds in his field work in the mountains of New Guinea; the folk taxonomy of the native New Guineans identifies 136 species. Similar correlations occur with plants. For example, an extensive interdisciplinary study of the native people and plants of the Chiapas highlands of Mexico showed a very close correspondence between species identified by western botanists and those identified by Chiapas natives.

Many modern biologists, particularly zoologists, define species according to the “biological species concept,” a definition that has been forcibly advocated by Ernst Mayr. According to this definition, a species is a group of organisms reproductively isolated from other organisms. In other words, a species is a group of organisms that interbreed and produce fertile off spring only with one another.

Some microbiologists and botanists are dissatisfied with the biological species concept. Microbiologists have noted that single-celled organisms do not reproduce sexually in nature (although they may undergo genetic recombination), yet they can still be segregated into discrete natural groups considered species. Botanists have noted that many species of related plants can hybridize with one another in nature. For example, the different species in the subgenus Leucobalanus (white oak) can hybridize and produce fertile offspring. Thus, rigorous application of the biological species concept would require that all of these separate species of oak be considered a single species, even though they have very different morphologies.

Most biologists basically accept the biological species concept, but argue that it is really an idealized concept, since only rarely is an actual test for reproductive compatibility performed. Thus, in practice, nearly all biologists think of species as morphologically distinct groups of organisms.

Nomenclature

nomenclature (from the Latin term nomenclatura, indicating the procedure of assigning names) is the naming of organisms. For many centuries, naturalists used Latinized names to refer to different species of plants and animals in their scientific writings. Following the lead of the Swedish naturalist Carl von Linné (1707-1778) (Carolus Linnaeus) in the mid-1700s, scientists began using a binomial (two word) Latinized name for all species. The first word is the genus name and the second word is the specific epithet, also called the trivial name.

Modern taxonomists have devised formal rules of nomenclature so that scientists throughout the world can more easily communicate with one another. For example, biologists use the term Acer to refer to a genus of trees commonly called maple in England and America, èrable in France, acre in Spain, and Ahorn in Germany. The rules of nomenclature in botany and zoology were established by different governing bodies, and are very similar, though not identical. In both systems the genus, species, and subspecies are italicized.

In the modern scientific literature, the complete name for a species has three parts: the genus, a name which is usually Latinized, is written in italics, and begins with a capital letter; the specific epithet, a name which is usually Latinized, is written in italics, but begins with a lowercase letter; and the author, the name of the person who gave the organism its Latinized name, which is capitalized and written in normal typeface. For example, the sugar maple is named Acer saccharinum L., where Acer is the genus, saccharinum is the specific epithet, and L. stands for Linneaus, who first named the species.

If subsequent studies indicate that a plant species should be transferred to a new genus, the original author’s name is given in parenthesis and this is followed by the name of the botanist who changed the name. For example, a shrub known as inkberry is named Ilex glabra (L.) Gray, indicating that Linneaus first named this plant, but Gray gave it its current name. For animals, the convention is different, in that a renamed species only lists the first author’s name, but places it in parentheses. For example, the red squirrel is named Tamiasciurus hudsonicus (Banks), indicating that a biologist named Banks was the original author, but someone else gave it its current name. The year of publication of the original description of the species is often included with the name of the original describer.

In addition to being given a genus name, specific epithet, author and year of publication, all species are assigned broader taxonomic categories. Thus, related genera are placed in the same family; related families are placed in the same order; related orders are placed in the same class; related classes are placed in the same phylum (botanists prefer the term division over phylum ); and related phyla are placed in the same kingdom. Occasionally, additional groups are added to this classification scheme, such as subphylum, subclass, or suborder.

For example, human beings (Homo sapiens L.) are placed into the following taxonomic categories:

Kingdom-Animalia, Phylum-Chordata, Subphylum Vertebrata, Class-Mammalia, Order-Primata, Family-Hominoidea, Genus-Homo, Species-sapiens L.

Identification

taxonomic identification is the recognition of the identity or essential character of an organism. Taxonomists often present organized written descriptions of the characteristics of similar species so that other biologists can identify unknown organisms. These organized descriptions are referred to as taxonomic keys. A taxonomic key is often published with pictures of the species it describes. However, written descriptions are usually preferred over pictures, since pictures cannot convey the natural variation in the morphology of a species, nor the small, yet characteristic, morphological features of a species. In addition, matching an unidentified organism to one picture in a book of hundreds or thousands of pictures can be very time-consuming.

The dichotomous key is the best and most-used format for taxonomic keys. A dichotomous key sequentially presents pairs of alternative morphological features (dichotomies) and requires the user to decide which alternative best describes the unknown organism. A very simple hypothetical key for identifying four species of flowering plants illustrates the dichotomous key:

a. Flowers white; stem woody

b. Sepals present; bark deep-furrowed—species A

bb. Sepals absent; bark not deep-furrowed—species B

aa. Flowers not white; stem herbaceous

c. Flowers blue; flowers with five petals—species C

cc. Flowers red; flowers with three petals—species D

The first dichotomy asks the user to choose between a and aa. If alternative a is chosen, the user must choose between b and bb. If alternative aa is chosen, the user must choose between c and cc.

Taxonomic keys often require knowledge of the morphology of the taxa in question and consequently rely upon technical terminology. In the above example, it is assumed the user knows that sepals constitute the leaf-like, outermost whorl of a flower.

Interestingly, taxonomic keys often use the sexual organs of animals (genitalia), plants (flowers, fruits, and cones), and fungi (spore-bearing structures), because these differ significantly among closely related species. This indicates that sexual organs of animals, plants, and fungi tend to evolve rapidly and divergently, presumably because they are subjected to great evolutionary selection pressures. Differences in reproductive structures also indicate that mating may not be successful, and that two organisms may be reproductively isolated–that is, different species.

Classification

taxonomic classification is the grouping together of different organisms into different taxa (taxonomic categories), such as family, genus, and species. In the time of Linneaus (mid-1700s), taxonomists and naturalists did not generally acknowledge that all species have evolutionary affinities to other species. Thus, early classification systems were artificial, in that they did not represent the lines of evolutionary descent. Most early taxonomists classified species according to their overall similarity because they thought this revealed the divine origin of nature.

Evolution and classification

The theory of organic evolution, developed by Charles Darwin in the mid-1800s, revolutionized taxonomy. In Origin of Species, Darwin proposed that “community of descent—the one known cause of close similarity in organic beings” be used as the basis for taxonomic classification systems. Ever since Darwin, taxonomists have tried to represent phylogeny (lines of evolutionary descent) in their classification systems. Thus, modern taxonomists who study plants or animals do not merely name and catalog species, they also try to construct evolutionary trees showing the relationships of different species.

The early evolutionary taxonomists relied on morphological features to classify organisms. Many early animal taxonomists found similarities in the embryos of related organisms and proposed that these similarities indicate evolutionary affinities. For example, early in development, all animals exist as a ball of cells, referred to as a blastula. The blastula of higher animals, called the coelomates, forms an invagination, called a blastopore, which later develops into the digestive cavity. Early taxonomists further divided coelomate animals into two large taxonomic groups, the protosomes, in which the blastopore opening develops into the mouth, and the deuterostomes, in which the blastopore opening develops into the anus. In contrast to the coelomates, the blastula of lower animals does not form a blastopore and these animals are called the acoelomates. When acoelomate animals are fully grown, they lack true digestive systems.

Thus, the early evolutionary taxonomists concluded humans are more closely related to segmented worms than to flatworms, since humans and segmented worms both have coelomate embryos, whereas flat worms have an acoelomate embryo. In addition, humans are more closely related to sea urchins than to segmented worms, since humans and sea urchins are both coelomate deuterostomes whereas round worms are coelomate protostomes.

Modern trends

Modern biologists accept many of the conclusions of the early evolutionary taxonomists, such as the relationships of the major animal phyla, as determined by the comparative morphology of their embryos. However, these early classification systems all had a weakness in that they were based, at least in part, on the intuition of taxonomists. Thus, all early classification systems had a strong element of subjectivity.

In the 1950s, R. R. Sokal and P. H. A. Sneath advocated the use of numerical taxonomy to remove the subjectivity of classification. In their method, all relevant characters (morphological features) of a group of organisms are numerically coded and the overall similarity is calculated by use of a mathematical algorithm. Initially, many traditional taxonomists rejected numerical taxonomy, since its results sometimes contradicted their own decade-long studies of comparative morphology. However, nearly all modern taxonomists currently use numerical methods in taxonomy, although there is often very contentious debate about which particular algorithms should be used.

In recent years, advances in molecular biology have had a profound impact on the field of taxonomy. In particular, biologists can now clone and sequence the DNA (deoxyribonucleic acid) in the genes of many different organisms and compare these DNA sequences to estimate relationships and construct classification systems. The use of such molecular data in taxonomy has several advantages. First, classification schemes for groups such as the fungi, whose phylogeny has long confounded the many taxonomists who rely upon more traditional morphological characters, can now be determined more easily. Second, organisms typically have many thousands of different genes, so there is a potential database of characters which is virtually unlimited in size. Third, since changes in DNA form the basis for all other evolutionary changes, such as changes in morphology, comparison of gene sequences allows study of evolution at its most basal level. Comparative studies of morphology will continue to play an important role in taxonomy, but gene sequences are becoming more widely used as gene sequencing becomes easier.

Methods of classification

Most modern taxonomists agree that classification systems should reflect evolutionary relationships. Thus, they agree that one should distinguish between homologous features and analogous features in constructing a classification system.

Homologous features have a common evolutionary origin, although they may differ in superficial morphology. For example, the arms of a human, fins of a whale, and front legs of a dog are all homologous. The underlying skeletal system of these appendages is similar and these three species had a common mammalian ancestor having appendages with similar skeletal structure.

Analogous features are superficially similar, but the similarity is not a result of common evolutionary origin. For example, the wings of a bird, bat, and butterfly are all analogous. Although they all have a similar superficial morphology and function, their underlying structure is very different. In other words, birds, bats, and butterflies did not share a common ancestor that had wings with a common design. The wings of birds, bats, and butterflies are similar merely because the laws of physics places certain restrictions on the shape of an appendage that can support flight.

Although taxonomists agree on the distinction between analogous and homologous features, they sometimes disagree about which specific method should be used to classify species. The three most commonly used methods are phenetics, cladistics, and evolutionary taxonomy. Some taxonomists use a combination of several of these different methods.

Phenetics

Phenetics, also known as numerical taxonomy, was proposed by Sokal and Sneath in the 1950s. Although very few modern taxonomists currently use phenetics, Sokal and Sneath’s methods clearly revolutionized taxonomy by introducing computer-based numerical algorithms, now an essential tool of all modern taxonomists.

Phenetics classifies organisms based on their overall similarity. First, many different characteristics of a group of organisms are measured. These measurements are then used to calculate similarity coefficients between all pairs of organisms. The similarity coefficient is a number between 0 and 1, where 1 indicates absolute identity, and 0 indicates absolute dissimilarity. Finally, the similarity coefficients are used to develop a classification system.

Critics of phenetic classification have argued that it tends to classify unrelated organisms together, because it is based on overall morphological similarity, and does not distinguish between analogous and homologous features. Pheneticists have responded that they ignore the distinction between analogous and homologous features because analogous features are usually numerically overwhelmed by the larger number of homologous features. Most evolutionary biologists would consider this response questionable, at best.

Cladistics

Cladistics is a method that classifies organisms based on the order in which different evolutionary lines branch off from one another. It was first proposed in the 1950s by Willi Hennig, a German entomologist. Subsequently, many other scientists have made Hennig’s original method more practicable by developing various cladistic numerical algorithms, some of which are very sophisticated. Cladistics is currently the most widely used method of classification.

One might reasonably ask: how can cladistics possibly determine the branching points of different evolutionary lines, given that we never have a complete fossil record and often have only living species for constructing a classification system? The answer is that cladistics relies upon the fact that all new species evolve by descent with modification. In other words, cladistics determines the evolutionary branching order on the basis of shared derived characteristics. It does not use shared primitive characteristics as a basis for classification, since these may be lost or modified through the course of evolution. To establish which characters are primitive and which are derived, cladistic classification generally relies upon one or more outgroups, species hypothesized to be primitive ancestors of all the organisms under study.

An example illustrates the distinction between shared derived and shared primitive characteristics in cladistic classification. The common mammalian ancestor of humans, cats, and seals had five digits on each hand and foot. Thus, the presence of five digits is a shared primitive characteristic and cladistics does not segregate humans and cats, which have five digits on their hands and feet, from seals, which have flippers instead of distinct digits. Instead, cladistics classifies seals and cats in the order Carnivora, based on certain shared derived characteristics of the Carnivora, and humans in the order Primata, based on other derived characteristics of the Primates.

It is important to note that a cladistic classification is not based on the amount of evolutionary change after the branching off of an evolutionary line. For example, although chimps and orangutans appear more similar to one another then either does to humans, cladistic classification places humans and chimps together since they share a more recent common ancestor than chimps and orangutans. Such a classification may seem counterintuitive; however, cladistic taxonomists would argue that such classifications should be considered the starting point for subsequent comparative studies. Such comparative studies might seek to discover why human morphology evolved so rapidly, relative to that of chimps and orangutans.

Some botanists have noted a limitation of cladistics, in that it does not recognize the role of interspecific hybridization in the evolution of new species. In interspecific hybridization, two different species mate and produce offspring that constitute a new species. Certain derived features of the parent species revert to primitive features in the new hybrid species. Hybrid species appear to be more common among plants than animals, but taxonomists who study any group of organisms clearly need to account for the possibility of interspecific hybridization in the evolution of new species.

W. H. Wagner, a noted plant taxonomist, has shown that interspecific hybridization has had a particularly important role in the evolution of ferns. He has advocated the development of a new methodology he calls reticulistics, to account for the evolution of hybrid species. In reticulate phylogeny, one evolutionary line can split to form two new species or two evolutionary lines can join together to form one new species. Unfortunately, there are not yet any numerical algorithms that can be used to reconstruct a reticulate phylogeny.

Evolutionary taxonomy

Evolutionary taxonomy can be considered a mixture of phenetics and cladistics. It classifies organisms partly according to their evolutionary branching pattern and partly according to the overall morphological similarity. Evolutionary taxonomy is basically the method used by the early evolutionary taxonomists and is also called classical taxonomy.

The major limitation of evolutionary taxonomy is that it requires a highly arbitrary judgment about how much information to use for overall similarity and how much information about branching pattern to use. This judgment is always highly subjective, and makes evolutionary taxonomy a very poor method of classification, albeit one that survives in the hands of certain older taxonomists.

The kingdoms of organisms

In the past, biologists classified all organisms into the plant kingdom or animal kingdom. Fungi were placed into the plant kingdom and single-celled organisms were rather arbitrarily placed into one kingdom or the other. Very few biologists currently use this simple two kingdom system. In recent years, biologists have proposed a great variety of classification systems, based on as many as 13 separate kingdoms of organisms. The five kingdom system, based on proposals by ecologist Robert Whittaker in 1959 and 1969, is widely used as a framework for discussing the diversity of life in most modern biology textbooks.

Five kingdom system

According to the five kingdom system designated by L. Margulis and K. V. Schwartz, all organisms are classified into one of five kingdoms: Monera, single-celled prokaryotes (bacteria); Protista, single-celled eukaryotes (algae, water molds and various other protozoans); Fungi, multicellular eukaryotic organisms which decompose organic matter (molds and mushrooms); Plantae, multicellular eukaryotic photosynthetic organisms (seed plants, mosses, ferns, and fern allies); and Animalia, multicellular eukaryotic organisms which eat other organisms (animals).

Clearly, the five kingdom system does not segregate organisms according to their evolutionary ancestry. The Monera and Protista are single-celled organisms only distinguished by their intracellular organization. The Animalia, Fungi, and Plantae are distinguished by their mode of nutrition, an ecological, not a phylogenetic, characteristic. Plants are considered producers, in that they use photosynthesis to make complex organic molecules from simple precursors and sunlight. Fungi are considered decomposers, in that they break down the dead cells of other organisms. Animals are considered consumers, in that they primarily eat other organisms, such as plants, fungi, or other animals.

KEY TERMS

Algorithm —Method for solving a numerical problem consisting of a series of mathematical steps.

Analogous features —Characteristics of organisms that are superficially similar, but have different evolutionary origins.

Chimera —Organism or part of an organism consisting of two or more genetically distinct types of cells.

Eukaryote —A cell whose genetic material is carried on chromosomes inside a nucleus encased in a membrane. Eukaryotic cells also have organelles that perform specific metabolic tasks and are supported by a cytoskeleton which runs through the cytoplasm, giving the cell form and shape.

Homologous features —Characteristics of organisms that have a common evolutionary origin, but are not necessarily similar in form.

Monophyletic —Group including all species or other taxa descended from a single common ancestor.

Outgroup —Primitive ancestor of all organisms being classified by cladistics, used to identify primitive and derived characteristics.

Phylogeny —Evolutionary history or lineage of an organism or group of related organisms.

Prokaryote —Cell without a nucleus, considered more primitive than a eukaryote.

Taxon (plural, taxa ) —Taxonomic group, such as species, genus, or family.

Taxonomic key —Descriptions of the characteristics of species or other taxa organized in a manner to assist in identification of unknown organisms.

More recently, a six kingdom model has been widely, although not universally, accepted. In this system, the former kingdom Monera is divided into two kingdoms: Eubacteria and Archaebacteria. The eubacteria (or true bacteria) are more common species of bacteria. Free-living decomposing bacteria, pathogenic (or disease causing) bacteria, and photosynthe-sizing cyanobacteria belong to this group. Some familiar members of Eubacteria, then, would be the bacteria found on human skin that can cause acne, or the bacteria found in a compost pile, which facilitate decomposition of organic material.

The Archaebacteria (or ancient bacteria) are quite different. Members of this group of bacteria live in very hostile environments. Examples are those living in extremely warm environments (called thermophiles) and bacteria living in extremely salty environments (called halopohiles). Archaebacteria are believed to be representative “living ancestors” of bacteria that inhabited Earth eons ago. The Archaebacteria are so fundamentally different from other bacteria that the new taxonomy reflects this difference by assigning them their own kingdom. Archaebacteria are believed to be the most primitive organisms found on earth.

Alternative systems

Many cladistic taxonomists have criticized Whittakers five kingdom classification system because it is not based on the branching pattern of evolutionary lineages. Cladistic classification systems seek to place organisms into monophyletic taxa. A monophyletic taxon is one that includes all species descended from a single common ancestor. For example, since biologists believe different groups of multicellular animals evolved from different single-celled eukaryotic ancestors, the kingdom Animalia is clearly not a monophyletic group.

Several cladistic taxonomists advocate a classification system that groups all organisms into three apparently monophyletic kingdoms, the Eukaryota, Eubacteria, and Archaebacteria (alternatively called Eukarya, Bacteria, and Archaea). The Eukaryota kingdom includes eukaryotic organisms, and all organisms in the Plantae, Animalia, Fungi, and Protista kingdoms. The kingdoms Eubacteria and Archaebacteria both consist of single-celled prokaryotes, all of which Whittaker placed into the Monera kingdom. The Archaebacteria (ancient bacteria ) were originally considered more primitive than the Eubacteria. The Archaebacteria includes the methanogens (methane-producing bacteria), halophiles (salt-loving bacteria), and thermophiles (heat-loving bacteria), all rather unusual prokaryotes which live in very unusual habitats.

Many cladistic taxonomists are currently studying the relationships of the Eubacteria, Archaebacteria, and Eukaryota, and have proposed different classification schemes based on comparisons of different gene sequences of these organisms. Ironically, although Archaebacteria acquired their name because they were considered primitive to Eubacteria, many taxonomists now believe that Archaebacteria are in fact more modern and more closely related to the Eukaryota than are the Eubacteria. Some taxonomists have proposed a fourth kingdom called the Eocytes, a group of hyperthermophilic bacteria which other biologists include within the Archaebacteria. One of the most intriguing recent studies found that Eukaryota have some genes that are most like those in Archaebacteria and other genes most like those in Eubacteria. This suggests that the Eukaryota may have evolved as a chimera of some primitive Eubacterium and Archaebacterium.

Taxonomists who are intrigued by this controversy are encouraged in knowing there are many undiscovered species of bacteria, perhaps millions, and only a very small portion of Eubacterial, Archaebacterial, and Eukaryotal DNA sequences have been studied to date.

See also Adaptation.

Resources

BOOKS

Gould, S. J. The Pandas Thumb. New York, W.W. Norton, 1980.

Kapoor, V.C. Principles and Practices of Animal Taxonomy.2nd ed. Enfield, New Hampshire: Science Publishers, 2001.

PERIODICALS

Lewis, R. “A New Place for Fungi?” Bioscience. 44 (1994): 389-391.

Peter A. Ensminger

Taxonomy

Taxonomy is the field of biology which deals with the nomenclature, identification, and classification of organisms. There are over one million known species on Earth and probably several million more not yet identified. Taxonomists are responsible for identifying, naming, and classifying all these different species. Systematics is a discipline of biology that explicitly examines the natural variation and relationships of organisms, and which includes the field of taxonomy. Systematics also deals with the relationships of different groups of organisms, as most systematicists strive to construct natural classification systems reflecting evolutionary relationships. Many biologists use the terms taxonomy and systematics interchangeably.

Definition of species

Before taxonomists can identify, name, and classify organisms, they need to agree on a definition of the concept of species. The definition of species is not as simple as it may seem, and has been debated by biologists and philosophers alike for many years.

Most modern biologists agree that species, unlike higher taxa (genus, family, order, and so on), are authentic taxonomic units. In other words, species really do exist in nature, and are not merely artificial human constructs. Some of the most persuasive evidence in support of this is the close correspondence between the species identified by western taxonomists and those identified in the "folk taxonomy" of relatively isolated non-western societies. For example, Ernst Mayr, a noted bird taxonomist, identified 137 species of birds in his field work in the mountains of New Guinea; the folk taxonomy of the native New Guineans identifies 136 species. Similar correlations occur with plants. For example, an extensive interdisciplinary study of the native people and plants of the Chiapas highlands of Mexico showed a very close correspondence between species identified by western botanists and those identified by Chiapas natives.

Many modern biologists, particularly zoologists, define species according to the "biological species concept," a definition that has been forcibly advocated by Ernst Mayr. According to this definition, a species is a group of organisms reproductively isolated from other organisms. In other words, a species is a group of organisms that interbreed and produce fertile offspring only with one another.

Some microbiologists and botanists are dissatisfied with the biological species concept. Microbiologists have noted that single-celled organisms do not reproduce sexually in nature (although they may undergo genetic recombination), yet they can still be segregated into discrete natural groups considered species. Botanists have noted that many species of related plants can hybridize with one another in nature. For example, the different species in the sub-genus Leucobalanus (white oak) can hybridize and produce fertile offspring. Thus, rigorous application of the biological species concept would require that all of these separate species of oak be considered a single species, even though they have very different morphologies.

Most biologists basically accept the biological species concept, but argue that it is really an idealized concept, since only rarely is an actual test for reproductive compatibility performed. Thus, in practice, nearly all biologists think of species as morphologically distinct groups of organisms.

Nomenclature

Nomenclature (from the Latin term nomenclatura, indicating the procedure of assigning names) is the naming of organisms. For many centuries, naturalists used Latinized names to refer to different species of plants and animals in their scientific writings. Following the lead of the Swedish naturalist Carl von Linné (1707-1778) (Carolus Linnaeus) in the mid-1700s, scientists began using a binomial (two word) Latinized name for all species. The first word is the genus name and the second word is the specific epithet, also called the trivial name.

Modern taxonomists have devised formal rules of nomenclature so that scientists throughout the world can more easily communicate with one another. For example, biologists use the term Acer to refer to a genus of trees commonly called maple in England and America, érable in France, acre in Spain, and Ahorn in Germany. The rules of nomenclature in botany and zoology were established by different governing bodies, and are very similar, though not identical. In both systems the genus, species, and subspecies are italicized.

In the modern scientific literature, the complete name for a species has three parts: the genus, a name which is usually Latinized, is written in italics, and begins with a capital letter; the specific epithet, a name which is usually Latinized, is written in italics, but begins with a lowercase letter; and the author, the name of the person who gave the organism its Latinized name, which is capitalized and written in normal typeface. For example, the sugar maple is named Acer saccharinum L., where Acer is the genus, saccharinum is the specific epithet, and L. stands for Linneaus, who first named the species.

If subsequent studies indicate that a plant species should be transferred to a new genus, the original author's name is given in parenthesis and this is followed by the name of the botanist who changed the name. For example, a shrub known as inkberry is named Ilex glabra (L.) Gray, indicating that Linneaus first named this plant, but Gray gave it its current name. For animals, the convention is different, in that a renamed species only lists the first author's name, but places it in parentheses. For example, the red squirrel is named Tamiasciurus hudsonicus (Banks), indicating that a biologist named Banks was the original author, but someone else gave it its current name. The year of publication of the original description of the species is often included with the name of the original describer.

In addition to being given a genus name, specific epithet, author and year of publication, all species are assigned broader taxonomic categories. Thus, related genera are placed in the same family; related families are placed in the same order; related orders are placed in the same class; related classes are placed in the same phylum (botanists prefer the term division over phylum); and related phyla are placed in the same kingdom. Occasionally, additional groups are added to this classification scheme, such as subphylum, subclass, or suborder.

For example, human beings (Homo sapiens L.) are placed into the following taxonomic categories:

Kingdom-Animalia, Phylum-Chordata, Subphylum-Vertebrata, Class-Mammalia, Order-Primata, Family-Hominoidea, Genus-Homo, Species-sapiens L.

Identification

Taxonomic identification is the recognition of the identity or essential character of an organism. Taxonomists often present organized written descriptions of the characteristics of similar species so that other biologists can identify unknown organisms. These organized descriptions are referred to as taxonomic keys. A taxonomic key is often published with pictures of the species it describes. However, written descriptions are usually preferred over pictures, since pictures cannot convey the natural variation in the morphology of a species, nor the small, yet characteristic, morphological features of a species. In addition, matching an unidentified organism to one picture in a book of hundreds or thousands of pictures can be very time-consuming.

The dichotomous key is the best and most-used format for taxonomic keys. A dichotomous key sequentially presents pairs of alternative morphological features (dichotomies) and requires the user to decide which alternative best describes the unknown organism. A very simple hypothetical key for identifying four species of flowering plants illustrates the dichotomous key:

a. Flowers white; stem woody

b. Sepals present; bark deep-furrowed—species A

bb. Sepals absent; bark not deep-furrowed—species B

aa. Flowers not white; stem herbaceous

c. Flowers blue; flowers with five petals—species C

cc. Flowers red; flowers with three petals—species D

The first dichotomy asks the user to choose between a and aa. If alternative a is chosen, the user must choose between b and bb. If alternative aa is chosen, the user must choose between c and cc.

Taxonomic keys often require knowledge of the morphology of the taxa in question and consequently rely upon technical terminology. In the above example, it is assumed the user knows that sepals constitute the leaf-like, outermost whorl of a flower .

Interestingly, taxonomic keys often use the sexual organs of animals (genitalia), plants (flowers, fruits , and cones), and fungi (spore-bearing structures), because these differ significantly among closely related species. This indicates that sexual organs of animals, plants, and fungi tend to evolve rapidly and divergently, presumably because they are subjected to great evolutionary selection pressures. Differences in reproductive structures also indicate that mating may not be successful, and that two organisms may be reproductively isolated—that is, different species.

Classification

Taxonomic classification is the grouping together of different organisms into different taxa (taxonomic categories), such as family, genus, and species. In the time of Linneaus (mid-1700s), taxonomists and naturalists did not generally acknowledge that all species have evolutionary affinities to other species. Thus, early classification systems were artificial, in that they did not represent the lines of evolutionary descent. Most early taxonomists classified species according to their overall similarity because they thought this revealed the divine origin of nature.

Evolution and classification

The theory of organic evolution , developed by Charles Darwin in the mid-1800s, revolutionized taxonomy. In Origin of Species, Darwin proposed that "community of descent—the one known cause of close similarity in organic beings" be used as the basis for taxonomic classification systems. Ever since Darwin, taxonomists have tried to represent phylogeny (lines of evolutionary descent) in their classification systems. Thus, modern taxonomists who study plants or animals do not merely name and catalog species, they also try to construct evolutionary trees showing the relationships of different species.

The early evolutionary taxonomists relied on morphological features to classify organisms. Many early animal taxonomists found similarities in the embryos of related organisms and proposed that these similarities indicate evolutionary affinities. For example, early in development, all animals exist as a ball of cells, referred to as a blastula. The blastula of higher animals, called the coelomates, forms an invagination, called a blastopore, which later develops into the digestive cavity. Early taxonomists further divided coelomate animals into two large taxonomic groups, the protosomes, in which the blastopore opening develops into the mouth, and the deuterostomes, in which the blastopore opening develops into the anus. In contrast to the coelomates, the blastula of lower animals does not form a blastopore and these animals are called the acoelomates. When acoelomate animals are fully grown, they lack true digestive systems.

Thus, the early evolutionary taxonomists concluded humans are more closely related to segmented worms than to flatworms , since humans and segmented worms both have coelomate embryos, whereas flat worms have an acoelomate embryo. In addition, humans are more closely related to sea urchins than to segmented worms, since humans and sea urchins are both coelomate deuterostomes whereas round worms are coelomate protostomes.

Modern trends

Modern biologists accept many of the conclusions of the early evolutionary taxonomists, such as the relationships of the major animal phyla, as determined by the comparative morphology of their embryos. However, these early classification systems all had a weakness in that they were based, at least in part, on the intuition of taxonomists. Thus, all early classification systems had a strong element of subjectivity.

In the 1950s, R. R. Sokal and P. H. A. Sneath advocated the use of numerical taxonomy to remove the subjectivity of classification. In their method, all relevant characters (morphological features) of a group of organisms are numerically coded and the overall similarity is calculated by use of a mathematical algorithm . Initially, many traditional taxonomists rejected numerical taxonomy, since its results sometimes contradicted their own decade-long studies of comparative morphology. However, nearly all modern taxonomists currently use numerical methods in taxonomy, although there is often very contentious debate about which particular algorithms should be used.

In recent years, advances in molecular biology have had a profound impact on the field of taxonomy. In particular, biologists can now clone and sequence the DNA (deoxyribonucleic acid) in the genes of many different organisms and compare these DNA sequences to estimate relationships and construct classification systems. The use of such molecular data in taxonomy has several advantages. First, classification schemes for groups such as the fungi, whose phylogeny has long confounded the many taxonomists who rely upon more traditional morphological characters, can now be determined more easily. Second, organisms typically have many thousands of different genes, so there is a potential database of characters which is virtually unlimited in size. Third, since changes in DNA form the basis for all other evolutionary changes, such as changes in morphology, comparison of gene sequences allows study of evolution at its most basal level. Comparative studies of morphology will continue to play an important role in taxonomy, but gene sequences are becoming more widely used as gene sequencing becomes easier.

Methods of classification

Most modern taxonomists agree that classification systems should reflect evolutionary relationships. Thus, they agree that one should distinguish between homologous features and analogous features in constructing a classification system.

Homologous features have a common evolutionary origin, although they may differ in superficial morphology. For example, the arms of a human, fins of a whale, and front legs of a dog are all homologous. The underlying skeletal system of these appendages is similar and these three species had a common mammalian ancestor having appendages with similar skeletal structure.

Analogous features are superficially similar, but the similarity is not a result of common evolutionary origin. For example, the wings of a bird, bat, and butterfly are all analogous. Although they all have a similar superficial morphology and function, their underlying structure is very different. In other words, birds, bats , and butterflies did not share a common ancestor that had wings with a common design. The wings of birds, bats, and butterflies are similar merely because the laws of physics places certain restrictions on the shape of an appendage that can support flight.

Although taxonomists agree on the distinction between analogous and homologous features, they sometimes disagree about which specific method should be used to classify species. The three most commonly used methods are phenetics, cladistics, and evolutionary taxonomy. Some taxonomists use a combination of several of these different methods.

Phenetics

Phenetics, also known as numerical taxonomy, was proposed by Sokal and Sneath in the 1950s. Although very few modern taxonomists currently use phenetics, Sokal and Sneath's methods clearly revolutionized taxonomy by introducing computer-based numerical algorithms, now an essential tool of all modern taxonomists.

Phenetics classifies organisms based on their overall similarity. First, many different characteristics of a group of organisms are measured. These measurements are then used to calculate similarity coefficients between all pairs of organisms. The similarity coefficient is a number between 0 and 1, where 1 indicates absolute identity, and 0 indicates absolute dissimilarity. Finally, the similarity coefficients are used to develop a classification system.

Critics of phenetic classification have argued that it tends to classify unrelated organisms together, because it is based on overall morphological similarity, and does not distinguish between analogous and homologous features. Pheneticists have responded that they ignore the distinction between analogous and homologous features because analogous features are usually numerically over-whelmed by the larger number of homologous features. Most evolutionary biologists would consider this response questionable, at best.

Cladistics

Cladistics is a method that classifies organisms based on the order in which different evolutionary lines branch off from one another. It was first proposed in the 1950s by Willi Hennig, a German entomologist. Subsequently, many other scientists have made Hennig's original method more practicable by developing various cladistic numerical algorithms, some of which are very sophisticated. Cladistics is currently the most widely used method of classification.

One might reasonably ask: how can cladistics possibly determine the branching points of different evolutionary lines, given that we never have a complete fossil record and often have only living species for constructing a classification system? The answer is that cladistics relies upon the fact that all new species evolve by descent with modification. In other words, cladistics determines the evolutionary branching order on the basis of shared derived characteristics. It does not use shared primitive characteristics as a basis for classification, since these may be lost or modified through the course of evolution. To establish which characters are primitive and which are derived, cladistic classification generally relies upon one or more outgroups, species hypothesized to be primitive ancestors of all the organisms under study.

An example illustrates the distinction between shared derived and shared primitive characteristics in cladistic classification. The common mammalian ancestor of humans, cats , and seals had five digits on each hand and foot. Thus, the presence of five digits is a shared primitive characteristic and cladistics does not segregate humans and cats, which have five digits on their hands and feet, from seals, which have flippers instead of distinct digits. Instead, cladistics classifies seals and cats in the order Carnivora, based on certain shared derived characteristics of the Carnivora, and humans in the order Primata, based on other derived characteristics of the Primates .

It is important to note that a cladistic classification is not based on the amount of evolutionary change after the branching off of an evolutionary line. For example, although chimps and orangutans appear more similar to one another then either does to humans, cladistic classification places humans and chimps together since they share a more recent common ancestor than chimps and orangutans. Such a classification may seem counterintuitive; however, cladistic taxonomists would argue that such classifications should be considered the starting point for subsequent comparative studies. Such comparative studies might seek to discover why human morphology evolved so rapidly, relative to that of chimps and orangutans.

Some botanists have noted a limitation of cladistics, in that it does not recognize the role of interspecific hybridization in the evolution of new species. In interspecific hybridization, two different species mate and produce offspring that constitute a new species. Certain derived features of the parent species revert to primitive features in the new hybrid species. Hybrid species appear to be more common among plants than animals, but taxonomists who study any group of organisms clearly need to account for the possibility of interspecific hybridization in the evolution of new species.

W. H. Wagner, a noted plant taxonomist, has shown that interspecific hybridization has had a particularly important role in the evolution of ferns . He has advocated the development of a new methodology he calls reticulistics, to account for the evolution of hybrid species. In reticulate phylogeny, one evolutionary line can split to form two new species or two evolutionary lines can join together to form one new species. Unfortunately, there are not yet any numerical algorithms that can be used to reconstruct a reticulate phylogeny.

Evolutionary taxonomy

Evolutionary taxonomy can be considered a mixture of phenetics and cladistics. It classifies organisms partly according to their evolutionary branching pattern and partly according to the overall morphological similarity. Evolutionary taxonomy is basically the method used by the early evolutionary taxonomists and is also called classical taxonomy.

The major limitation of evolutionary taxonomy is that it requires a highly arbitrary judgment about how much information to use for overall similarity and how much information about branching pattern to use. This judgment is always highly subjective, and makes evolutionary taxonomy a very poor method of classification, albeit one that survives in the hands of certain older taxonomists.

The kingdoms of organisms

In the past, biologists classified all organisms into the plant kingdom or animal kingdom. Fungi were placed into the plant kingdom and single-celled organisms were rather arbitrarily placed into one kingdom or the other. Very few biologists currently use this simple two kingdom system. In recent years, biologists have proposed a great variety of classification systems, based on as many as 13 separate kingdoms of organisms. The five kingdom system, based on proposals by ecologist Robert Whittaker in 1959 and 1969, is widely used as a framework for discussing the diversity of life in most modern biology textbooks.

Five kingdom system

According to the five kingdom system designated by L. Margulis and K. V. Schwartz, all organisms are classified into one of five kingdoms: Monera, single-celled prokaryotes (bacteria ); Protista , single-celled eukaryotes (algae , water molds and various other protozoans); Fungi, multicellular eukaryotic organisms which decompose organic matter (molds and mushrooms ); Plantae, multicellular eukaryotic photosynthetic organisms (seed plants, mosses, ferns, and fern allies); and Animalia, multicellular eukaryotic organisms which eat other organisms (animals).

Clearly, the five kingdom system does not segregate organisms according to their evolutionary ancestry. The Monera and Protista are single-celled organisms only distinguished by their intracellular organization. The Animalia, Fungi, and Plantae are distinguished by their mode of nutrition , an ecological, not a phylogenetic, characteristic. Plants are considered producers, in that they use photosynthesis to make complex organic molecules from simple precursors and sunlight. Fungi are considered decomposers, in that they break down the dead cells of other organisms. Animals are considered consumers, in that they primarily eat other organisms, such as plants, fungi, or other animals.

More recently, a six kingdom model has been widely, although not universally, accepted. In this system, the former kingdom Monera is divided into two kingdoms: Eubacteria and Archaebacteria . The eubacteria (or true bacteria) are more common species of bacteria. Free-living decomposing bacteria, pathogenic (or disease causing) bacteria, and photosynthesizing cyanobacteria belong to this group. Some familiar members of Eubacteria, then, would be the bacteria found on human skin that can cause acne , or the bacteria found in a compost pile, which facilitate decomposition of organic material.

The Archaebacteria (or ancient bacteria) are quite different. Members of this group of bacteria live in very hostile environments. Examples are those living in extremely warm environments (called thermophiles) and bacteria living in extremely salty environments (called halopohiles). Archaebacteria are believed to be representative "living ancestors" of bacteria that inhabited the earth eons ago. The Archaebacteria are so fundamentally different from other bacteria that the new taxonomy reflects this difference by assigning them their own kingdom. Archaebacteria are believed to be the most primitive organisms found on earth.

Alternative systems

Many cladistic taxonomists have criticized Whittakers five kingdom classification system because it is not based on the branching pattern of evolutionary lineages. Cladistic classification systems seek to place organisms into monophyletic taxa. A monophyletic taxon is one that includes all species descended from a single common ancestor. For example, since biologists believe different groups of multicellular animals evolved from different single-celled eukaryotic ancestors, the kingdom Animalia is clearly not a monophyletic group.

Several cladistic taxonomists advocate a classification system that groups all organisms into three apparently monophyletic kingdoms, the Eukaryota, Eubacteria, and Archaebacteria (alternatively called Eukarya, Bacteria, and Archaea). The Eukaryota kingdom includes eukaryotic organisms, and all organisms in the Plantae, Animalia, Fungi, and Protista kingdoms. The kingdoms Eubacteria and Archaebacteria both consist of single-celled prokaryotes, all of which Whittaker placed into the Monera kingdom. The Archaebacteria (ancient bacteria) were originally considered more primitive than the Eubacteria. The Archaebacteria includes the methanogens (methane-producing bacteria), halophiles (salt-loving bacteria), and thermophiles (heat-loving bacteria), all rather unusual prokaryotes which live in very unusual habitats.

Many cladistic taxonomists are currently studying the relationships of the Eubacteria, Archaebacteria, and Eukaryota, and have proposed different classification schemes based on comparisons of different gene sequences of these organisms. Ironically, although Archaebacteria acquired their name because they were considered primitive to Eubacteria, many taxonomists now believe that Archaebacteria are in fact more modern and more closely related to the Eukaryota than are the Eubacteria. Some taxonomists have proposed a fourth kingdom called the Eocytes, a group of hyperthermophilic bacteria which other biologists include within the Archaebacteria. One of the most intriguing recent studies found that Eukaryota have some genes that are most like those in Archaebacteria and other genes most like those in Eubacteria. This suggests that the Eukaryota may have evolved as a chimera of some primitive Eubacterium and Archaebacterium.

Taxonomists who are intrigued by this controversy are encouraged in knowing there are many undiscovered species of bacteria, perhaps millions, and only a very small portion of Eubacterial, Archaebacterial, and Eukaryotal DNA sequences have been studied to date.

See also Adaptation.

Resources

books

Gould, S. J. The Pandas Thumb. New York, W.W. Norton, 1980. Luria, S.E., S.J. Gould, and S. Singer. A View of Life. Redwood City, CA: Benjamin-Cummings, 1989.

Margulis, L., and K.V. Schwartz. Five Kingdoms. New York: W.H. Freeman, 1988.

Mayr, E. Principles of Animal Taxonomy. New York: Columbia University Press, 1997.

periodicals

Lewis, R. "A New Place for Fungi?" Bioscience 44 (1994): 389-391.

Peter A. Ensminger

KEY TERMS

Algorithm

—Method for solving a numerical problem consisting of a series of mathematical steps.

Analogous features

—Characteristics of organisms that are superficially similar, but have different evolutionary origins.

Chimera

—Organism or part of an organism consisting of two or more genetically distinct types of cells.

Eukaryote

—A cell whose genetic material is carried on chromosomes inside a nucleus encased in a membrane. Eukaryotic cells also have organelles that perform specific metabolic tasks and are supported by a cytoskeleton which runs through the cytoplasm, giving the cell form and shape.

Homologous features

—Characteristics of organisms that have a common evolutionary origin, but are not necessarily similar in form.

Monophyletic

—Group including all species or other taxa descended from a single common ancestor.

Outgroup

—Primitive ancestor of all organisms being classified by cladistics, used to identify primitive and derived characteristics.

Phylogeny

—Evolutionary history or lineage of an organism or group of related organisms.

Prokaryote

—Cell without a nucleus, considered more primitive than a eukaryote.

Taxon (plural, taxa)

—Taxonomic group, such as species, genus, or family.

Taxonomic key

—Descriptions of the characteristics of species or other taxa organized in a manner to assist in identification of unknown organisms.

Taxonomy

Narrowly defined, plant taxonomy is that aspect of the study of plants having to do with taxa—that is, the naming of plant names (nomenclature) and the determination of the hierarchical relationships used to identify them or understand their relationships (identification and classification). More broadly defined, plant taxonomy includes areas of investigation from a variety of disciplines, including classification, nomenclature, phylogeny reconstruction, and investigation of evolutionary processes. Under this broader definition, the goal of taxonomy is to use comparative data to assess relationships between plants, define taxonomic boundaries between species and other ranks, provide means of identifying and communicating about the organisms, and understanding the patterns (and even the processes) in the evolution of the plants. Seen in this way, plant taxonomy overlaps and grades into the disciplines of plant systematics, phylogenetics , and evolution.

Distinguishing, classifying, and naming plant taxa is basic to any study of nature and for making use of plants. To have the name of a plant (or taxon) is the prerequisite to get further information about it. Taxonomy, therefore, is inevitably necessary for all further studies of plants in order to understand their structures, life histories, and distributions, as well as for making use of them for the benefit of humans (i.e., applied botany, comprising pharmacy [medicinal plants], crops and food production [agriculture],

forestry, production of plant raw material [fibers, gum, etc.], horticulture [ornamental plants], and conservation).

Taxonomy, therefore, is one of the oldest branches within the life sciences. But taxonomy is a synthetic science, as it uses and relies on data from all other fields of botany, including that from structural botany (cytology and anatomy, palynology and ultrastructure), morphology (including embryology), genetics (heredity), physiology , phytochemistry, ecology (habitats), and phytogeography (distribution of taxa).

Plant Systems: Artificial and Natural

Variation among plants is not continuous—that is, there are discontinuities separating one type of plant from another. We distinguish different individuals of the same kind, and we distinguish different kinds of oaks, roses, dandelions, violets, and so on. Variations among taxa are of different quantity and quality, and as a result, they can be arranged in a hierarchical system. Those plants being almost alike and interbreeding belong to the same species. All similar species together form a genus, similar genera are put together as a family, and so forth. The tasks of taxonomy, therefore, are to describe the plants thoroughly (phytography) and to compare them in order to discover natural groups, and to classify (classification) and name them (nomenclature).

Other questions examined in evolutionary botany and phylogenetics include: How did the differences between taxa come about? And what are the reasons for their mutual hierarchical connections? To some authors, all these studies together are called (biological) systematics, and taxonomy is restricted to dealing only with classification.

The Swedish botanist Carolus Linnaeus (1707-1778) was an excellent analytical observer, and his talent for methodical recording, concise summarizing, and systematic thinking enabled him to produce a synthesis, the Linnaean System, which was in use for almost one hundred years. It was easy to handle because it was mainly based on very few numerical flower characters (number of stamens and styles). A system using only one or very few characters is considered an artificial one, and the Linnaean System for the most part did not reflect natural (evolutionary) relationships.

Botanists who followed Linnaeus elaborated a natural system of classification, considering all organs of the plant. Important contributors included the Frenchmen M. Adanson, A. L. de Jussieu, and Jean Baptiste de Lamarck; their Swiss colleagues A. P. and Augustin de Candolle; the Scot Robert Brown; the Austrian S. Endlicher; and the Britons G. Bentham and J. D. Hooker. Their system was based on comparative morphology, a discipline arising in the beginning of the nineteenth century. It made use of the concept of homology and of crucial discoveries like the alternation of generations by the German W. Hofmeister. Their "natural system"—though subsequently modified in many ways—essentially persisted up to modern times, although it aimed at reflecting the natural order they believed to have been established by God the Creator rather than attempting to reveal evolutionary relationships.

Biological Kinship: Phylogenetic, Phenetic, and Evolutionary Systems

A revolution in biology was the discovery of evolution and its mechanisms by the English naturalists Charles Darwin and A. R. Wallace in the middle of the nineteenth century, presenting common descent and gradual changes in geological time scale as an explanation for the taxonomic hierarchy already established. No essential changes of the previous morphologically based system, therefore, proved necessary. However, the acceptance of evolution as a unifying concept in biology turned the attention of taxonomists to questions of ancestry and descent.

Toward the end of the nineteenth century, the connections among taxa were more carefully studied in order to answer the questions: Which are the older (i.e., more primitive) characters and taxa, and which are the younger and more advanced ones? How did specific adaptations evolve? A typical and important question concerned the evolution of pollination mechanisms. Are unisexual wind-pollinated flowers primitive (original) or advanced (derived, secondary) or vice versa?

The first attempts to answer these questions were by A. Engler and R. V. Wettstein and followers in the late nineteenth century. They considered the Fagales (beech and birch families), Juglandaceae (hickories), and Salicaceae (wil-lows and cottonwoods) as the most primitive angiosperms because of their small, wind-pollinated, unisexual flowers arranged in catkins , thus forming a presumptive link between the more ancestral gymnosperms (including conifers like pines, spruces, firs, cedars, etc.) and the angiosperms , which often have showy, insect-pollinated, hermaphroditic flowers. However, subsequent research in the early part of the twentieth century, especially by C. E. Bessey, showed that the phylogenetic relations are just the other way around: angiosperms appear to be primarily hermaphroditic and insect-pollinated, these traits being responsible for one of their major advantages (more effective pollination) in contrast to gymnosperms . The catkin-bearing families are judged to have evolved later, adapting to habitats in which wind pollination is advantageous.

In the beginning of the twentieth century, the new field of genetics strongly improved our understanding of evolution. Many phylogenists, however, were skeptical because of the large number of empirically ill-based, speculative phylogenetic trees produced at the turn of the century. Toward the middle of the twentieth century, taxonomy at the specific and infraspecific (below species) levels was changed into the New Systematics, Biosystematics, and Experimental Systematics, strongly accelerated by knowledge from genetics, population genetics, breeding systems, cytogenetics, karyology (chromosome number), and ecology in combination with traditional data from morphology, embryology, anatomy, and distribution.

Despite these stimulating and largely successful efforts to combine understanding of evolutionary processes with the needs and challenges of taxonomy, the study of phylogeny (trees of evolutionary descent) and of systematics above the species level (macrosystematics) was not markedly improved because no data were available for establishing scientifically sound hypotheses. A pragmatic method was developed, therefore, that tried to overcome the difficulty of having classification based on phylogeny, but these were often burdened with intuitive and speculative hypotheses. Phenetic systems were designed in the late 1950s to resolve these problems.

Phenetics

Phenetics is a strictly empirical method. It avoids evaluating character states as ancestral versus derived and thus avoids any phylogenetic hypotheses. All characters are treated as equal (unweighted). The use of newly developed mathematical methods and of electronic data processing allowed calculation of large amounts of character data and classification based exclusively on overall similarity. The resulting phenetic system does not attempt to reveal kinship (relationships based on descent). As it is not biased by phylogenetic judgements, it can be considered, in some way, a multipurpose system allowing a maximum of predictability. Convergences (i.e., similarities caused by evolutionary adaptation to the same environmental factors), however, may not become apparent in a phenetic system.

Not all workers were satisfied with phenetics, however, and starting in the late 1960s the method called cladistics was developed for handling taxonomic characters and exploring relationships between taxa. Cladistics, which was strongly opposed to phenetics, developed rapidly and successfully.

Cladistics

Using and developing the ideas and concepts of the German entomologist Willi Hennig, cladistics is an effective tool for studying and describing phylogenetic relationships and reconstructing a truly phylogenetic system. It constructs conceptually strict phylogenetic branching patterns by evaluating character states as ancestral (plesiomorphic) or derived (apomorphic). The basic assumption is that speciation takes place mainly by bifurcation: one ancestral species splits into two sister species, which are to be treated as having equal taxonomic rank, both characterized by newly developed (apomorphic) characters.

The big advantage of cladistics is the use of clear assumptions and procedures, in contrast to intuitive phylogenetic trees devised by earlier generations of phylogenetic taxonomists. An important conceptual change is the more restrictive definition of monophyly, meaning a group containing all descendants of a certain taxon. But if, say, one or more descendants are excluded, the remaining group forms a paraphyletic group because it does not contain all descendants from the common ancestor. In pre-cladistic phylogenetic systems, however, a paraphyletic group has been accepted as being monophyletic because all its members share a common ancestor. This, however, has not been accepted by cladistic practitioners.

These simple concepts, seemingly formalistic and of no empirical value, have, however, major effects on defining phylogenetic taxa and constructing a phylogeny-based system. Through this type of work, the understanding of relationships in the plant kingdom has recently undergone a major revision.

There is much evidence, accumulated for many decades and including modern molecular investigations, that all plants in the strict sense (the so-called Embryophyta, the bryophytes and the vascular plants) are offspring of the green algae (Chlorophyta s.l.) because they share a combination of common features that would have been unlikely to have evolved several times independently. Both together form a single big branch (clade ) of the phylogenetic tree and, therefore, are united into one monophyletic taxon, the Chlorobionta. This big and highly heterogenous taxon, comprising unicellular algae together with all the land plants, has the same rank in the phylo-genetic system as the red algae, comprising a number of seaweeds only. In a cladistic sense, you cannot unite the green algae with the red algae (and other algal groups) to form the taxon algae. Such a group, which mixes organisms from different branches, is called a polyphyletic group.

see also Algae; Bessey, Charles; Candolle, Augustin de; Family; Flora; Herbaria; Hooker, Joseph Dalton; Identification of Plants; Linnaeus, Carolus; Phylogeny; Species; Systematics, Molecular; Systematics, Plant; Taxonomic Keys; Taxonomist.

Manfred A. Fischer

Bibliography

Greuter, W., et al., eds. International Code of Botanical Nomenclature. Berlin: Regnum Veg, 1988.

Stuessy, T. F. Plant Taxonomy. New York: Columbia University Press. 1990.

INTERNATIONAL CODE OF BOTANICAL NOMENCLATURE (ICBN)

In order to standardize terminology and promote effective communication among plant scientists, plant taxonomists have agreed to a set of formal guidelines to be used when naming plants. Known as the International Code of Botanical Nomenclature (ICBN), these guidelines were adopted in 1867 and serve as the official reference rules with which nomenclatural decisions about plants must be made. The Code is updated and modified periodically by an international committee on plant nomenclature and serves as the basis for all naming of plant ranks from infraspecific taxa (variety, subspecies, etc.) to species and to taxa of higher ranks (genus, family, order, etc.). There is also a separate code for the naming of cultivated plants, which has nomenclatural conventions very similar to that of the ICBN.

At its founding, the ICBN agreed that plant nomenclature would officially begin with the work by Linnaeus, Species Plan-tarum, published in 1753. To avoid unnecessary duplication of names for the same species or to stabilize the way plant names are applied to the various taxonomic hierarchies, a system of date priority was also instituted, so that the earliest correctly published name for a taxon must be used if the plants concerned are found to be the same. Taxonomic publications describing new species or proposing new genera, families, or other formal ranks are expected to follow the rules included in the ICBN. If these requirements are not met, the name proposed by the botanist may be rejected.

Taxonomy, History of

Taxonomy, the field of biological classification, attempts to group types of organisms in meaningful ways. Modern taxonomy is based on similarities among organisms that reflect descent from recent shared ancestors, rather than similar solutions to environmental challenges. For example, a bird's wing and a human's arm reflect common descent from a vertebrate ancestor, whereas a bird's wing and an insect's wing are derived from different structures and therefore not characteristics on which modern classification might be based.

Taxonomic designations increasingly rely on deoxyribonucleic acid (DNA) sequence similarities. Because DNA mutates at a known rate, the more alike the DNA sequences are for two types of organisms, the more recently they diverged from a shared ancestor. By considering such data on pairs of species, biologists can construct evolutionary tree diagrams that depict how existing organisms are related to one another. In this way, taxonomy in the modern sense reflects evolution.

Early Classification Schemes

Humans have probably always classified life. Thousands of years ago, people designated plants, animals, and fungi by whether they were tasty and safe to eat, of medicinal value, or were foul-tasting or even poisonous. An early taxonomist was Greek philosopher Aristotle (384–322 B.C.), who organized five hundred types of animals according to habitat and body form. His designations were rather subjective: he considered animals that gave birth to live young and had lungs as the pinnacle of living perfection.

By the sixteenth century, explorers had discovered so many new species that Aristotle's plan could no longer suffice. Newer schemes continued to be based on what people could see, but the characteristics considered were often more mystical than scientific. For example, an early-sixteenth-century botanical classification assigns a high ranking to the plantain, because "more than any other plant, it bears witness to God's omnipotence." John Ray (1627–1705) was an English naturalist who classified more than twenty thousand types of plants and animals. His highly descriptive method distinguished animals by their hoofs, nails, claws, teeth, and toes. Yet the inability to see microscopic distinctions and reliance on superficial similarities led him to group together algae, lichens, fungi, and corals. A lichen is a compound organism that consists of an alga and a fungus, but a coral is an animal.

Carolus Linnaeus (1707–1778) is the best-known taxonomist. Heavily influenced by John Ray, Linnaeus compared, contrasted, and meticulously listed types of organisms from his earliest childhood. He started his first botanical listing at age eight, which evolved into a series of publications called Systema Naturare, reaching twenty-five hundred pages by its tenth edition. Linnaeus distinguished plants by their sexual parts. He is most noted for introducing the binomial name for a species, which includes an organism's genus and "specific epithet," an adjective that describes the species in some way. The human animal, according to Linnaeus's scheme, is Homo sapiens, sapiens meaning "wise." French anatomist Georges Cuvier (1769–1832) and others contributed broader levels of taxonomic classification: family, order, class, phylum or division, and kingdom. The full taxonomic classification of humans is: Animalia (kingdom), Chordata (phylum), Mammalia (class), Primates (order), Hominidae (family), Homo (genus), sapiens (specific epithet).

Beyond Plants and Animals

As biologists catalogued more of life's diversity, classification as plant or animal was no longer sufficient. For a while, biologists assigned to the plant kingdom anything that couldn't move, such as the fungi. These organisms are not plants because they do not photosynthesize, among other distinctions. Then the invention of the microscope revealed an entirely hidden, but vastly populated, world. In 1866, German naturalist Ernst Haeckel (1834–1919) proposed a third kingdom, Protista, to include one-celled organisms. But Protista according to this early definition lumped together some very different types of organisms. In 1937, French marine biologist Edouard Chatton made an enormous contribution to biology by introducing the terms prokaryote and eukaryote. The prokaryotes lack nuclei; eukaryotes have nuclei as well as other organelles , and include unicellular and multicellular life. The prokaryotes include bacteria, cyanobacteria, and the fairly recently recognized archaea.

By 1959, it became clear that three kingdoms weren't enough. For a decade, several four-kingdom schemes reigned. One approach split single-celled life into prokaryotes and eukaryotes; another separated fungi from plants. Both changes were included in Cornell University ecologist Robert Whittaker's five-kingdom system. He introduced it in 1969 and it prevailed for many years. Whittaker's scheme recognized the Monera (prokaryotes), Protista (unicellular eukaryotes), Fungi, Plantae, and Animalia.

Enter the Archaea

Classification of life reflects the tools that scientists have to observe organisms and to compare their characteristics. With the ability to distinguish nucleic acid sequences in the 1970s came a new way to deduce evolutionary relationships and classify organisms on this basis. Carl Woese, a microbiologist at the University of Illinois, analyzed the ribosomal ribonucleic acid (rRNA) genes of various microbes, reasoning that these genes are so vital that they would be similar in sequence among different types of organisms. (That is, any major deviation would be lethal.) Comparing the differences in sequence, therefore, might be useful in establishing evolutionary relationships. He quickly learned that prokaryotes and eukaryotes have very distinctive rRNA gene sequences.

After examining the rRNA genes of all of the microbes in his colleagues' labs, Woese turned to an organism in a more natural habitat, Methanobacter thermoautotrophica, a methane-emitting microbe found in a nearby lake. Its rRNA genes were markedly different in sequence from the prokaryotic "signature." Woese found others like it. This new class of microbes also had different lipid molecules in their membranes than other bacteria. Eventually, when the list had grown, Woese published his work. In 1977 he introduced the archaebacteria and suggested that a new and broader taxonomic level, called the domain, embrace them.

Early use of the term "archaebacteria" led to much initial confusion, because these organisms are quite different from bacteria, although they are also small and lack nuclei. Because the first archaea that Woese worked with were found in what are termed extreme environments—high heat, salt, or pressure—the idea arose that this was one of their key characteristics. Since then, however, biologists have found archaea in many habitats, including rice paddies, swamps, and throughout the oceans. To identify them, biologists just had to know what to look for.

The three domains of life are the Archaea, the Prokarya, and the Eukarya. Both the Archaea and the Prokarya consist of unicellular organisms that are prokaryotic cells. The Eukarya includes the eukaryotes (protista, plants, fungi, and animals). This invention of domains to supercede kingdoms solved a problem that the identification of archaea brought to Whittaker's five-kingdom scheme. At first, the archaea were considered a sixth kingdom. The dilemma was that the differences between archaea and any of the other five kingdoms were greater than the differences among those other kingdoms. The three-domain organization has gained acceptance as distinctions among the groups have accumulated. Today scientists know that archaea lack nuclei and organelles like the bacteria, their cell walls are distinctive, and their mechanisms of DNA replication and protein synthesis are more like those of eukaryotes than other prokaryotes. The genome sequences of a few archaea have confirmed what Woese proposed a quarter century ago: that they share some characteristics with bacteria and eukaryotes, but are very much a distinct type of organism. On a more philosophical note, the addition of domains to biological classification indicates that taxonomy is very much a dynamic discipline.

see also Animalia; Archaea; Eubacteria; Extreme Communities; Fungi; Linnaeus, Carolus; Plant

Ricki Lewis

Bibliography

Mayr, Ernst. "Two Empires or Three?" Proceedings of the National Academy of Science 95 (1998): 9720–9723.

Wade, Nicholas. "Rethinking the Universal Ancestor: A New 'Tree of Life.'" New York Times (June 4, 2000): F1.

Woese, Carl R., and George E. Fox. "Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms." Proceedings of the National Academy of Science 74 (1977): 5088–5090.