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Chapter 3 : Defining Microbial Diversity—the Species Concept for Prokaryotic and Eukaryotic Microorganisms
Species are the basis of the taxonomic scheme. They are the universally accepted lowest taxonomic cluster of living organisms; among many uses, they are considered to be the units for measuring biodiversity and evolution. This chapter discusses this unit from a "prokaryotologist" point of view, as prokaryotes may be endowed with the widest diversity among the living organisms. Additionally, microscopic eukaryotes are circumscribed in species whose conception is dependent on the nature of the group they are assigned to and the analysis techniques that taxonomists use to classify them. The currently practiced species concept in microbiology corresponds partially to several concepts designed for eukaryotes. It is phenetic in that the basis for the understanding of the taxon's coherency and internal diversity is based on the numerical analysis of independently covarying characters, which are not necessarily universally present in the taxon. It is phylogenetic in that the members of these units have to show a common pattern of ancestry, i.e., they must be monophyletic. Finally, it is based on a genotypic (genomic) cluster definition in the way that genome comparisons, although indirect, give objective numerical frontiers to the unit circumscription, and guarantee the close genealogical relationship of the strains included in a cluster.
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- Restriction Fragment Length Polymorphism