Although some organisms form genotypic and phenotypic clusters tight enough that we might want to call them “species”, there is no single process causing such clusters to form, and for some datasets taken to delimit species, a purely random birth-death explanation cannot be rejected. Although polyphyletic groupings are not acceptable as taxonomic species, and some form of “metapopulation lineage” requirement might be universally applicable, lineage concepts provide no principled way to distinguish “species” from “varieties” on the one hand and “genera” on the other, and hold up poorly in the face of promiscuous inter-taxon (“lateral”) gene transfer. None of these problems is unique to prokaryotes but microbiologists have often written as if they were, and indeed there may be differences in degree, prokaryotes to eukaryotes. Sensible microbiologists now preoccupy themselves with studying speciation, while finessing any definition of ‘species’.
The Prokaryotic Species Problem is Even Worse
Ford Doolittle & Olga Zhaxybayeva