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The area of study focusing on the development of a classification system, or taxonomy, for plants based on their evolutionary relationships (phylogeny). The assumption is that if classification reflects phylogeny, reference to the classification will help researchers focus their work in a more accurate manner. The task is to make phylogeny reconstruction as accurate as possible. The basic unit of classification is generally accepted to be the species, but how a species should be recognized has been intensely debated. See Plant kingdom, Plant phylogeny
The earliest classifications of plants were those of the Greek philosophers such as Aristotle (384–322 B.C.) and Theophrastus (372–287 B.C.). The latter is often called the father of botany largely because he listed the names of over 500 species, some of which are still used as scientific names today. In the next 1600 years little progress occurred in plant taxonomy. It was not until the fifteenth century that there was renewed interest in botany, much of which was propelled by the medical use of plants. In 1753 Carolus Linnaeus, a Swedish botanist, published his Species Plantarum, a classification of all plants known to Europeans at that time. Linnaeus's system was based on the arrangement and numbers of parts in flowers, and was intended to be used strictly for identification (a system now referred to as an artificial classification as opposed to a natural classification, based on how closely related the species are).
In Species Plantarum, Linnaeus made popular a system of binomial nomenclature developed by the French botanist Gaspard Bauhin (1560–1624), which is still in use. Each species has a two-part name, the first being the genus and the second being the species epithet. For example, Rosa alba (italicized because it is Latin) is the scientific name of one species of rose; the genus is Rosa and the species epithet is alba, meaning white (it is not a requirement that scientific names be similar to common names or have real meaning, although such relevance is often the case). The genus name Rosa is shared by all species of roses, reflecting that they are thought to be more closely related to each other than to species in any other group.
Today, we understand that the best classification system is one that reflects the patterns of the evolutionary processes that produced these plants. The rules of botanical nomenclature (and those of zoology as well, although they are not identical) are part of an internationally accepted Code that is revised (minimally) at an international congress every 5 years. See Plant evolution
Use of common names in science and horticulture is not practical. Scientific names are internationally agreed upon so that a consistent taxonomic name is used everywhere for a given organism. In addition to genus and species, plants are classified by belonging to a family; related families are grouped into orders, and these are typically grouped into a number of yet higher and more encompassing categories. In general, higher categories are composed of many members of lower types—for example, a family may contain 350 genera, but some may be composed of a single genus with perhaps a single species if that species is distantly related to all others.
Many botanists use a number of intermediate categories between the level of genus and family, such as subfamilies, tribes, and subtribes, as well as some between species and genus, such as subgenera and sections, but none of these categories is formally mandated. They are useful nonetheless to reflect intermediate levels of relatedness, particularly in large families (composed of several hundreds or even thousands of species). Below the level of species, some botanists use the concept of subspecies (which is generally taken to mean a geographically distinct form of a species) and variety (which is often a genetic form or genotype, for example a white-flowered form of a typically blue-flowered species, or a form that is ecologically distinct).
The basic idea that plant classification should reflect evolutionary (genetic) relationships has been well accepted for some time, but the degree to which this could be assessed by the various means available differed. It has only recently become possible to assess genetic patterns of relatedness directly by analyzing DNA sequences. In the 1990s, DNA technology became much more efficient and less costly, resulting in a dramatic upsurge in the availability of DNA sequence data for various genes from each of the three genetic compartments present in plants (nuclear, mitochondrial, and plastid or chloroplast). In 1998 a number of botanists collectively proposed the first DNA-based classification of a major group of organisms, the angiosperms or flowering plants. For the first time, a classification was directly founded on assessments of the degree of relatedness made with objective, computerized methods of phylogeny reconstruction. Other data, such as chemistry and morphology, were also incorporated into these analyses, but by far the largest percentage of information came from DNA sequences—that is, relatedness was determined mostly on the basis of similarities in plants' genetic codes. The advantages of such a classification were immediately obvious: (1) it was not based on intuition about which category of information best reflected natural relationships; (2) it ended competition between systems based on differing emphases; (3) the analysis could be repeated by other researchers using either the same or different data (other genes or categories of information); and (4) it could be updated as new data emerged, particularly from studies of how chromosomes are organized and how morphology and other traits are determined by the genes that code for them. See Deoxyribonucleic acid (DNA)
At the same time that DNA data became more widely available as the basis for establishing a classification, a more explicit methodology for turning the results of a phylogenetic analysis into a formal classification became popular. This methodology, called cladistics, allowed a large number of botanists to share ideas of how the various taxonomic categories could be better defined. Although there remain a number of dissenting opinions about some minor matters of classification, it is now impossible for scientists to propose alternative ideas based solely on opinion. See Phylogeny, Taxonomy