Three distinct forms of Pneumocystis coexist in individuals of two species of deer mice (genus Peromyscus).

As emerging zoonoses represent a significant public health threat, understanding how pathogens' host ranges evolve is critical to protect human and wildlife health. Closely related hosts infected with host-specific pathogens provide valuable opportunities for clear inferences of host range evolution, as they allow for the examination of early diversification patterns in their resident pathogens. Pneumocystis, an obligate lung symbiont that is believed to be ubiquitous in mammals, exemplifies such a model. To explore the early stages of divergence in Pneumocystis, we collected geographically dispersed samples from two sister species of deer mice: Peromyscus leucopus (white-footed mice) and Peromyscus gossypinus (cotton mice). We sequenced two nuclear and two mitochondrial loci of Pneumocystis sampled from the lungs of these mice. These sequences revealed three distinct Pneumocystis taxa, two of which were found to cross-infect both host species and were often found coexisting within the same individual. Genetic diversity and phylogenetic analysis suggest that the three Pneumocystis taxa represent separate species. Further analysis of the mitochondrial large subunit rRNA gene from the most common taxon of these three revealed that host geographic origins influenced Pneumocystis genetic structure more than host species identity. Nevertheless, the results also suggest an overall interconnectedness of the symbiont metapopulation.