Landscape genomics of a forest fungus reveals high gene flow and signatures of climate adaptation. Fungen

Genome sequencing of spatially distributed individuals enable to study how local adaptation structures genetic variation. Phellopilus nigrolimitatus, a red-listed wood-inhabiting fungus associated with old growth coniferous forests, has undergone a decline in population sizes in the last century due to a decrease in suitable habitat. In order to assess the population genetic structure and investigate local adaptation in P. nigrolimitatus, we established a reference genome and genotyped using RAD sequencing 327 individuals sampled across 24 sites in Northern Europe. We revealed a shallow population genetic structure, indicating large historical population sizes and gene flow. In spite of weak sub-structuring, two genetic groups could be recognized, one western group distributed mainly in Norway and a second eastern group covering most of Finland, Poland and Russia. This sub-structuring could reflect co-immigration with the main host, Norway spruce (Picea abies), into northern Europe after the last glaciation. We found evidence of reduced genetic diversity in southwestern Finland, a region that has a long history of intensive forestry and urbanization. Numerous loci were significantly associated with one or more environmental factors, indicating adaptation to specific environments. These loci clustered into two groups with distinct associations to temperature and precipitation. Acquiring similar knowledge for more fungal species will undoubtedly be useful to assess the consequences of the combined effect of habitat fragmentation and climate change on fungi strongly bound to old-growth forests.