ABSTRACT
Genome size determinations based on large restriction fragment analysis have been more informative, but the paucity of data precludes useful phylogenetic analysis. The discovery of enzymes that specifically cut both strands of DNA at a specific nucleotide sequence led the way to a variety of new methods for phylogenetic analysis. The ideal alignment of two or more sequences for phylogenetic analysis results in comparing characters that are derived from common ancestral nucleotides. The methods used to classify subsurface bacteria have included a mixture of phenetic and phylogenetic techniques. Historically bacteria have been classified primarily by a combination of shared phenotypic traits. Habitat and natural history have been useful in clustering bacteria and in some cases has been at least partially congruent with phylogeny. Genome restriction endonuclease patterns are only useful in grouping very closely related bacteria. A rapid advance in the sequencing of proteins and nucleic acids has been primarily responsible for the development of phylogenetic methods for classifying bacteria.
