Taxonomy

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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.