Response from Fenchel and Finlay
Curiously, we stand indicted of “perpetuating the myth of ubiquity” just when an unprecedented research effort is uncovering, for the first time, the true scale of ubiquitous microbial dispersal. Identical microbial genotypes (rRNA gene sequences) are being recorded worldwide, and outbreeding protists isolated from different continents will interbreed in the laboratory.
The neutral theory of molecular evolution predicts that organisms with huge population sizes (most microbial “species”) will display substantial genetic variation, and this is indeed the case. The fact that nominal species (phenotypically identical forms) fill out phylogenetic trees with deep roots reflects the fact that microbial phenotypes have remained identical over large stretches of geological time. They retain their identity through stabilizing selection, but the molecular clock ticks, so the rate of species turnover in microbes is very slow compared with that for mammals, for example.
We did emphasize that genetic variation occasionally generates some sort of geographic pattern, but the evidence that these patterns reflect something real is rather thin. The problem is that there are effectively no limits to neutral genetic variation, and the likelihood of finding a new sequence whenever a representative of a nominal species is isolated is very high. We therefore remain unconvinced by the limited evidence for microbial biogeographies. In particular, sampling bias, undersampling, and the absence of any a priori expectation of the likely number of sequences render any evaluation of the claims difficult.
The interesting thing about organisms is their phenotypic properties (not only morphology), and any useful species definition must be based on the fact that combinations of phenotypic properties usually come in discrete units. Gene sequencing has confirmed that such units are usually monophyletic. Molecular biology has contributed greatly to our understanding of microbial evolution—it has not, however, contributed much to the species concept.