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necessarily equivalent. Rapidly evolving macromolecules are mainly useful for measuring
short evolutionary distances, while slowly evolving molecules record the relationships between
very divergent species. The size and relative degree of conservation (rate of mutational
change) in any particular macromolecule studied will largely determine the range and accuracy
of phylogenetic inference.
Comparison of strictly homologous features is as crucial to molecular phylogenetic studies as
it is to morphological systematics. Structural and functional homology is an absolute
requirement for inference of organismal phylogenies from molecular phylogenies. Universal
distribution, and the presence of highly conserved, as well as more variable sites, are
particularly useful features in informational macromolecules. These properties permit
unambiguous comparison of highly divergent sequences, and inference of relationships
between both closely and distantly related organisms. The absence of lateral (interspecies)
transfer of the genes being studied is another necessary requirement for the inference of
phylogenies from molecular sequence data. Genes borne on extrachromosomal elements
(e.g. plasmids), which can be transferred within and between species, are inappropriate for
inferring organismal phylogenetic relationships.
Historically, both direct and indirect methods have been used to estimate macromolecular
sequence similarity (Schleifer and Stackebrandt, 1983). Direct methods involve the comparison
of the actual amino acid or nucleic acid sequences. Indirect approaches include immunological
techniques, which detect the antigenic similarity of proteins, or nucleic acid hybridization
techniques, which measure the similarity of sequences based on the relative stability of nucleic
acid heteroduplexes. These approaches yield data in the form of pairwise similarity values.
Studies of Baumann et ai. (1983), focussing on the evolutionary relationships of
well-characterized marine eubacteria, demonstrate that good agreement can be obtained
between a variety of these indirect techniques. One disadvantage of these indirect approaches,
however, is that it is necessary to repeat the entire array of pairwise comparisons whenever
a new organism is analyzed.
Analyses of restriction fragment length polymorphisms (RFLPs) is another method for
measuring macromolecular similarities. In RFLP analysis, DNA from different organisms is
necessarily equivalent. Rapidly evolving macromolecules are mainly useful for measuring
short evolutionary distances, while slowly evolving molecules record the relationships between
very divergent species. The size and relative degree of conservation (rate of mutational
change) in any particular macromolecule studied will largely determine the range and accuracy
of phylogenetic inference.
Comparison of strictly homologous features is as crucial to molecular phylogenetic studies as
it is to morphological systematics. Structural and functional homology is an absolute
requirement for inference of organismal phylogenies from molecular phylogenies. Universal
distribution, and the presence of highly conserved, as well as more variable sites, are
particularly useful features in informational macromolecules. These properties permit
unambiguous comparison of highly divergent sequences, and inference of relationships
between both closely and distantly related organisms. The absence of lateral (interspecies)
transfer of the genes being studied is another necessary requirement for the inference of
phylogenies from molecular sequence data. Genes borne on extrachromosomal elements
(e.g. plasmids), which can be transferred within and between species, are inappropriate for
inferring organismal phylogenetic relationships.
Historically, both direct and indirect methods have been used to estimate macromolecular
sequence similarity (Schleifer and Stackebrandt, 1983). Direct methods involve the comparison
of the actual amino acid or nucleic acid sequences. Indirect approaches include immunological
techniques, which detect the antigenic similarity of proteins, or nucleic acid hybridization
techniques, which measure the similarity of sequences based on the relative stability of nucleic
acid heteroduplexes. These approaches yield data in the form of pairwise similarity values.
Studies of Baumann et ai. (1983), focussing on the evolutionary relationships of
well-characterized marine eubacteria, demonstrate that good agreement can be obtained
between a variety of these indirect techniques. One disadvantage of these indirect approaches,
however, is that it is necessary to repeat the entire array of pairwise comparisons whenever
a new organism is analyzed.
Analyses of restriction fragment length polymorphisms (RFLPs) is another method for
measuring macromolecular similarities. In RFLP analysis, DNA from different organisms is