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Unit Chapters
Genomics
Proteins & Proteomics
Evolution & Phylogenetics
Introduction
A Brief History of Classification
Cladistics and Classification
Applications of Molecular Phylogenetics
HIV and Forensic Uses of Phylogenetics
The Origin of Bats and Flight
Challenges
Coda: The Renaissance of Comparative Biology
Microbial Diversity
Emerging Infectious Diseases
HIV & AIDS
Genetics of Development
Cell Biology & Cancer
Human Evolution
Neurobiology
Biology of Sex & Gender
Biodiversity
Genetically Modified Organisms
A Brief History of Classification

Taxonomy, the practice of classifying biodiversity, has a venerable history. Although early natural historians did not recognize that the similarities and differences among organisms were consequences of evolutionary mechanisms, they still sought a means to organize biological diversity. In 1758 Carl Linn proposed a system that has dominated classification for centuries. Linnaeus gave each species two names, denoting genus and species (such as Homo sapiens). He then grouped genera into families, families into orders, orders into classes, classes into phyla, and phyla into kingdoms. Linn identified two kingdoms: Animalia (animals) and Plantae (plants). Biologists generally accepted the idea of evolution shortly after the publication of Darwin's The Origin of Species and, since Linnaeus' classification system, they have described an immense number of species. Despite these facts, taxonomy changed little until the 1960s.

The first major break from the Linnean model came from Thomas Whittaker. In 1969 Whittaker proposed a "five kingdom" system in which three kingdoms were added to the animals and plants: Monera (bacteria), Protista, and Fungi. Whittaker defined the kingdoms by a number of special characteristics. First, he specified whether the organisms possessed a true nucleus (eukaryotic) or not (prokaryotic). Because Monera are prokaryotic and virtually all are unicellar, they are distinct from the other four eukaryotic kingdoms. With few exceptions, the eukaryotic unicellular organisms were placed into the kingdom Protista.

The three multicellular eukaryotic kingdoms distinguish themselves by the general manner in which they acquire food. Plants are autotrophs and use photosynthetic systems to capture energy from sunlight. Animals are heterotrophs and acquire nutrients by ingesting plants or other animals, and then digesting those materials. Fungi are also heterotrophs but, unlike animals, they generally break down large organic molecules in their environment by secreting enzymes. Unicellular organisms use a variety of modes of nutrition. (See the Microbial Diversity unit.)

The five kingdoms system was certainly an advance over the previous system because it better captured the diversity of life. Three groups -- bacteria, fungi, and protists - did not fit well into either the animal or plant category. Moreover, each of these three groups appeared to possess diversity comparable to that of animals or plants. Thus, the designation of each as a kingdom seemed fitting.

In the years since Whittaker's system was developed, however, new evidence and new methods have shown that the five-kingdom system also fails to adequately capture what we now know about the diversity of life. Microbial biologists became aware of these limitations as they discovered unicellular organisms that appeared to be prokaryotic, but were extremely distinct in ultrastructure and other characteristics from the traditional bacteria. Some of these unusual prokaryotes lived in hot springs and other places where the temperatures were near, or even above, the boiling point of water (the thermophiles). Others, the extreme halophiles, were able to tolerate salt concentrations as high as five Molar, roughly ten times the concentration of seawater. (See the Microbial Diversity unit.) DNA sequence data also increasingly suggested that these prokaryotes were most unlike the traditional bacteria.

Figure 1. Five-kingdom vs. three-domain tree of life
The microbal evolutionist Carl Woese proposed a radical reorganization of the five kingdoms into three domains. (See the Microbial Diversity unit.) Starting in the 1980s Woese's scheme has been increasingly accepted by evolutionary biologists and is now the standard paradigm. In his classification system, Woese placed all four eukaryotic kingdoms into a single domain called Eukarya, also known as the eukaryotes. He then split the former kingdom of Monera into the Eubacteria (bacteria) and the Archaea (archaebacteria) domains. Woese then placed most of the "unusual" prokarytes in the Archaea, leaving traditional bacteria in the Eubacteria. The Woese classification represents a demotion of the animals and plants as individual kingdoms. This is consistent with recent discoveries of more diversity among microbes than between animals and plants.

Unlike Whittaker's five kingdoms system, Woese's three domains system organizes biodiversity by evolutionary relationships. After a discussion of the methodology of contemporary evolutionary classification, we will examine the methods Woese used and the justification for his system.
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