Systematics is the part of comparative biology that tracks the diversity of organisms with regard to specified relationships among those organisms. It is the branch of biology responsible for recognizing, comparing, classifying, and naming the millions of different sorts of organism that exist. Taxonomy is the theory and practice of describing the diversity of organisms and the arrangement of these organisms into classifications.
Widely accepted as the most basic of natural taxa is the species. However, there is still some argument over what
exactly a species is. A major problem stems from variation observed among individual organisms, and the species question is largely one of how biologists attempt to classify individual organisms, all of which differ to a greater or lesser extent when compared with one another, into discrete groups or taxa. There is a range of definitions that largely reflects the various theories of the origin of diversity. When biological classification was first developed, organisms were considered each to have a fundamental design and the task of the taxonomist was to discover the essential features of these "types." Even after the publication of Darwin's theory of biological evolution, this concept did not change.
It was only with the emergence of a reliable theory of inheritance, and the development of the disciplines of genetics and population biology, that biologists began to develop rational explanations for the origin of diversity and then apply this knowledge to the species concept. The initial step forward was the recognition of geographical variation, first as "varieties," then as subspecies. This led to the concept of the species as a group of populations that reflected both common ancestry and adaptation to local conditions. In turn, this view was developed into the biological species concept, which defined the species as "groups of interbreeding natural populations that are isolated from other such groups." This species concept is perhaps the most widely accepted today, but it applies only to sexually reproducing species.
After the recognition of species, the next step in taxonomy is to classify the relationship of these species. A number of methods have been developed by which phylogenetic relationships can be estimated. Of these, cladistic analysis is now widely acknowledged as the best. Cladistic analysis rests upon three basic assumptions: features shared by organisms (termed homologies or apomorphies) form a hierarchic pattern; this pattern can be expressed as a branching diagram (cladogram); and each branching point symbolizes the features held in common by all the species arising from that node. Cladograms are the most efficient method for representing information about organisms, hence are the most predictive of unknown properties of those organisms.
Once a cladogram of taxa has been established, the next stage is to formally recognize and name the species and higher taxa. Names are assigned to these taxa according to a system based upon that first developed by the Swedish naturalist Linnaeus in the mid-18th century. Species are grouped into genera, and these in turn are grouped into families, orders, classes, phyla, and kingdoms. The ultimate goal of this nomenclature is to produce a universal system of unambiguous names for all recognized taxa. Animals, plants, and bacteria each have a separate set of rules or codes, which are applied voluntarily by taxonomists and are designed to promote stability and consistency in taxonomic nomenclature, and thus to biological science in general. Traditionally, lifeform have been grouped into two kingdoms, Animalia (including the insects) and Plantae, but in the last few decades this view has been questioned by experts, with other kingdoms being recognized. Recent work using analyses of ribosomal RNA sequences has shown that the total genetic diversity of the traditionally well-known groups such as fungi, plants, and animals is only a tiny proportion of the genetic diversity shown by microorganisms. The term "domain" has now replaced "kingdom," with the higher organisms (fungi, plants, and animals) being grouped in the domain Eukarya and a variety of microorganisms being included in two further domains, Archaea and Bacteria.
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