Pneumocystis genetic variability: cryptic biological species or clonal near-clades? PLoS Pathog

Abstract: An abundant literature dealing with the population genet-ics and taxonomy of Giardia duo-denalis, Cryptosporidium spp., Pneu-mocystis spp., and Cryptococcus spp., pathogens of high medical and veterinary relevance, has been produced in recent years. We have analyzed these data in the light of new population genetic concepts dealing with predominant clonal evolution (PCE) recently proposed by us. In spite of the considerable phylogenetic diversity that exists among these pathogens, we have found striking similarities among them. The two main PCE features described by us, namely highly significant linkage disequilibrium and near-clading (stable phyloge-netic clustering clouded by occa-sional recombination), are clearly observed in Cryptococcus and Giar-dia, and more limited indication of them is also present in Cryptospo-ridium and Pneumocystis. Moreover, in several cases, these features still obtain when the near-clades that subdivide the species are analyzed separately (‘‘Russian doll pattern’’). Lastly, several sets of data under-mine the notion that certain mi-crobes form clonal lineages simply owing to a lack of opportunity to outcross due to low transmission rates leading to lack of multiclonal infections (‘‘starving sex hypothe-sis’’). We propose that the diver-gent taxonomic and population genetic inferences advanced by various authors about these path-ogens may not correspond to true evolutionary differences and could be, rather, the reflection of idiosyn-cratic practices among compart-mentalized scientific communities. The PCE model provides an oppor-tunity to revise the taxonomy and applied research dealing with these pathogens and others, such as viruses, bacteria, parasitic protozoa, and fungi