James Staley, Ph.D., suggests the phylogenomic species concept, which combines phylogenetic and genomic analyses, can be used to circumscribe species:
"Bacteriologists have not yet adopted a concept for a species. Bacterial and archaeal species are defined on the basis of phenotypic properties and whole-genome DNA-DNA hybridization. Each species must have unique phenotypic properties and exhibit more than 70% DNA hybridization among strains. This combination of phenotype and genotype, sometimes referred to as the polyphasic species definition, was a breakthrough in bacterial taxonomy and has served microbiologists very well by stabilizing the field and bringing uniformity to classifying species of Bacteria and Archaea.
The 1990s brought DNA, RNA, and protein sequencing to the fore, and they soon were adapted for use in phylogenetic analysis. The advantage of sequencing approaches from a taxonomic viewpoint is that sequences can be used to infer the evolution of lineages. The highly conserved 16S rRNA gene became the primary macromolecule for phylogeny because of its fidelity in deducing the relatedness of Bacteria and Archaea at taxonomic levels at and above the genus level. As a result, the entire second edition of Bergey's Manual of Systematic Bacteriology uses the phylogenetic approach for classifying Bacteria and Archaea (www.bergeys .org). Therefore, for the first time, there is a complete hierarchical taxonomy for the Bacteria and Archaea from the domain down to the genus. However, despite the wide acceptance of the phylogenetic approach for higher taxa, it has not yet been successfully applied at the species level."
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