Analyzing and comparing the sequences of ribosomal RNA (rRNA) has revolutionized the classification of organisms. Ribosomal RNA is viewed as an evolutionary chronometer. A comparison of the nucleotide sequences of rRNA in two different organisms appears to provide a relative measure of the time elapsed since the organisms diverged from a common ancestor. This is because rRNA, which is present in all organisms, performs a critical and functionally constant task, limiting the number of mutations that can happen in certain regions without affecting the viability of an organism. Over time, however, at least some changes will occur.
In the 1970s, Carl Woese and his colleagues determined the sequence of 16S ribosomal RNA of more than 400 organisms, discovering characteristic sequences, called signature sequences, that are almost always found in particular groups. Based on these sequences as well as other properties, they proposed the three-domain system of classification, which is now believed to reflect the primary lines of evolutionary descent. Since that time, the genes encoding the 16S rRNA of thousands of prokaryotes have been sequenced. To study the phylogeny of eukaryotes, 18S rRNA is used, which is analogous in function to the 16S prokaryotic structure. In either case, it is generally the rDNA, which encodes the rRNA, that is sequenced.
Long after organisms have diverged so much that they appear to be unrelated by nucleic acid hybridization, portions of their rDNAs are still similar. Changes in these highly conserved regions occur very slowly over time and are thus useful for determining even distant relationships of diverse organisms. At the same time, certain regions of rDNAs are relatively variable. Comparing these sequences can be used to determine more recent divergence. Thus, depending on the region compared, the sequence of rDNA can be used to assess distant as well as close relationships between organisms.
Determining the base sequence of 16S rDNA is the most accurate and reliable procedure yet available for identifying evolutionary relationships of organisms. It is better than DNA hybridization, because it is far more quantitative. Organisms in which DNA hybridization can barely be detected are related, but how closely is not certain. Comparing the sequence of their 16S ribosomal RNA genes can give an accurate estimate. Some organisms that appear to be quite different based on their phe-notypic characteristics are actually related. For example, the mycoplasmas, cell wall-deficient bacteria, are related to mem bers of the genus Clostridium, anaerobic spore-forming rods. As another example, some photosynthetic bacteria are included in a group with many nonphotosynthetic species.
A genomic analysis such as sequencing of 16S ribosomal RNA (or its DNA counterpart) enables one to more accurately construct a phylogenetic tree. These trees are somewhat like a family tree, tracing the evolutionary heritage of organisms. Each line, or branch, of the tree represents the evolutionary distance between two species (figure 10.18). Individual species are represented as nodes. An external node, one that includes a species name, represents an organism that still exists. In contrast, an internal node, a branch point, represents an ancestor to today's organisms. Ancient prokaryotes, those that branch at an early point in evolution, are sometimes called deeply branching to reflect their position in the phylogenetic tree.
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