Fossilized stromatolites, coral-like mats of filamentous microorganisms, suggest that prokaryotes have existed on the earth for at least 3 billion years (figure 10.14). Other data based on isotopic analysis of rocks suggest that prokaryotes
existed on this planet 3.5 billion years ago. Because of the relatively few sizes and shapes of bacteria, however, such fossilized remains do little to help identify or understand these ancient organisms. It thus remains difficult to place the diverse types of prokaryotes into their proper place in the evolution of living beings.
Historically, prokaryotes have been grouped according to phenotypic attributes such as size and shape, staining characteristics, and metabolic capabilities. Using this system, a species can loosely be defined as group of organisms that share many properties and differ significantly from other groups. While the use of phenotypic characteristics is a convenient approach to
prokaryotic taxonomy, there are several drawbacks. For example, observable differences may be due to only a few gene products, and a single mutation resulting in a nonfunctional enzyme can dramatically alter that phenotypic property. In addition, organisms that are phenotypically similar may, in fact, be only distantly related. Conversely, those that appear dissimilar may be closely related.
Newer molecular approaches circumvent some of the problems associated with phenotypic classification schemes while also giving greater insights into evolutionary relatedness of microorganisms. The more similar the nucleotide sequences, the more closely related are two organisms. Differences in DNA sequences can also be used to determine the point in time at which two organisms diverged from a common ancestor. This is because random mutations cause sequences to change over time. Thus, the more time that has elapsed since two organisms diverged, the greater the difference in the sequences of their DNA. Prokaryotes, however, can transfer DNA to other species, a process called horizontal or lateral gene transfer, which can complicate insights provided by some types of DNA sequence comparison. ■ phenotype, p. 192
Some of the methods used to classify prokaryotes by determining their relatedness are summarized in table 10.6.
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