Genome-wide differentiation corresponds to climatic niches in two species of lichen-forming fungi

Lichens can withstand fluctuating environmental conditions such as hydration-desiccation cycles. Many species distribute across climate zones, suggesting population-level adaptations to conditions such as freezing and drought. Here, we aim to understand how climate affects population genomic patterns in lichenized fungi. We analysed population structure along elevational gradients in closely related Umbilicaria phaea (North American; two gradients) and Umbilicaria pustulata (European; three gradients). All gradients showed clear genomic breaks splitting populations into low-elevation (Mediterranean zone) and high-elevation (cold temperate zone). A total of 3301 SNPs in U. phaea and 138 SNPs in U. pustulata were driven to fixation between the two ends of the gradients. The difference between the species is likely due to differences in recombination rate: the sexually reproducing U. phaea has a higher recombination rate than the primarily asexually reproducing U. pustulata. Cline analysis revealed allele frequency transitions along all gradients at approximately 0°C, coinciding with the transition between the Mediterranean and cold temperate zones, suggesting freezing is a strong driver of population differentiation. Genomic scans further confirmed temperature-related selection targets. Both species showed similar differentiation patterns overall, but different selected alleles indicate convergent adaptation to freezing. Our results enrich our knowledge of fungal genomic functions related to temperature and climate, fungal population genomics, and species responses to environmental heterogeneity.