Résumé
Background. Delineating microbial populations, discovering ecologically relevant phe¬notypes, and identifying migrants and admixed individuals has long proved notoriously difficult, thereby limiting our understanding the evolutionary forces at play during the diversification of microbial species. However, recent advances in sequencing and com¬putational methods have enabled an unbiased approach whereby incipient species and the genetic correlates of speciation can be identified by examining patterns of genomic variation within and between lineages. Results. We present here a population genomic study of a phylogenetic species in the Neurospora discreta species complex, based on the resequencing of full genomes (ca. 37Mb) for 52 fungal isolates from 9 sites in three continents. Population structure analy¬ses revealed two distinct lineages in Southeast Asia, three lineages in North America/ Europe with a broad longitudinal and latitudinal range, and limited admixture between lineages. Genome scans for selective sweeps and comparisons of the genomic land¬scapes of diversity and recombination provided no support for a role of linked selection on genomic heterogeneity in levels of divergence between lineages. However, demo¬graphic inference indicated that the observed genomic heterogeneity in divergence was generated by varying rates of gene flow between lineages following a period of isolation. Conclusion. Many putative gene transfer events between phylogenetically divergent fungal lineages have been discovered, and our work highlights the quantitative impor¬tance of genetic exchanges between more closely related taxa to the evolution of fungal genomes. Our study also supports the role of allopatric isolation as a driver of diversi¬fication in saprobic microbes.