The Pleistocene glacial cycles shaped the historical demography and phylogeography of a pine fungal endophyte

The fungal endophyte Lophodermium nitens is an obligate symbiont of soft pines inhabiting only two pine species in Mexico with a broad distribution of geographically isolated populations. A previous study for the hosts indicated a main east–west subdivision with recurrent gene flow within these regions and demographic expansion of populations. We took these patterns as null hypotheses to test for the demography and phylogeographical patterns of the fungus, given the obligatory relationship of the endophyte to the host and its reduced capacity for long-distance dispersal. For this purpose, we employed two nuclear DNA loci, fragments of the actin and chitin synthase I genes. Both loci showed high genetic variation, consisting of private single-copy alleles, as well as few ones at high frequency that were shared among almost all populations. In order to distinguish between shared polymorphism due to incomplete lineage sorting and gene flow posterior to population divergence, we applied the coalescent-based Isolation–Migration (IM) model. We found patterns of gene flow and isolation similar to those of the hosts as well as signs of population expansion. Mean migration time and divergence time estimates fell within the Pleistocene, previous to Last Glacial Maximum. The results presented here for L. nitens emphasize the potential use of endophytic fungi to deepen the knowledge of historical patterns and processes of their host plants.