Genetic diversity and evolution of <italic>Pneumocystis</italic> fungi infecting wild Southeast Asian murid rodents.

<italic>Pneumocystis</italic> organisms are airborne-transmitted fungal parasites that infect the lungs of numerous mammalian species with strong host specificity. In this study, we investigated the genetic diversity and host specificity of <italic>Pneumocystis</italic> organisms infecting Southeast Asian murid rodents through PCR amplification of two mitochondrial genes and tested the co-phylogeny hypothesis among these fungi and their rodent hosts. <italic>Pneumocystis</italic> DNA was detected in 215 of 445 wild rodents belonging to 18 Southeast Asian murid species. Three of the <italic>Pneumocystis</italic> lineages retrieved in our phylogenetic trees correspond to known <italic>Pneumocystis</italic> species, but some of the remaining lineages may correspond to new undescribed species. Most of these <italic>Pneumocystis</italic> species infect several rodent species or genera and some sequence types are shared among several host species and genera. These results indicated a weaker host specificity of <italic>Pneumocystis</italic> species infecting rodents than previously thought. Our co-phylogenetic analyses revealed a complex evolutionary history among <italic>Pneumocystis</italic> and their rodent hosts. Even if a significant global signal of co-speciation has been detected, co-speciation alone is not sufficient to explain the observed co-phylogenetic pattern and several host switches are inferred. These findings conflict with the traditional view of a prolonged process of co-evolution and co-speciation of <italic>Pneumocystis</italic> and their hosts. [ABSTRACT FROM AUTHOR]