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.

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.

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.