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Abstract Studying the signatures of evolution can help to understand genetic processes. Here, we demonstrate how the existence of balancing selection can be used to identify the breeding systems of fungi from genomic data. The breeding systems of fungi are controlled by self-incompatibility loci that determine mating types between potential mating partners, resulting in strong balancing selection at the loci. Within the fungal phylum Basidiomycota, two such self-incompatibility loci, namely HD MAT locus and P/R MAT locus, control mating types of gametes. Loss of function at one or both MAT loci results in different breeding systems and relaxes the MAT locus from balancing selection. By investigating the signatures of balancing selection at MAT loci, one can infer a species’ breeding system without culture-based studies. Nevertheless, the extreme sequence divergence among MAT alleles imposes challenges for retrieving full variants from both alleles when using the conventional read-mapping method. Therefore, we employed a combination of read-mapping and local de novo assembly to construct haplotypes of HD MAT alleles from genomes in suilloid fungi (genera Suillus and Rhizopogon). Genealogy and pairwise divergence of HD MAT alleles showed that the origins of mating types predate the split between these two closely related genera. High sequence divergence, trans-specific polymorphism, and the deeply diverging genealogy confirm the long-term functionality and multiallelic status of HD MAT locus in suilloid fungi. This work highlights a genomics approach to studying breeding systems regardless of the culturability of organisms based on the interplay between evolution and genetics. 

Aim Ectomycorrhizal fungi (ECMF) are partners in a globally distributed tree symbiosis implicated in most major ecosystem functions. However, resilience of ECMF to future climates is uncertain. We forecast these changes over the extent of North American Pinaceae forests. Location About 68 sites from North American Pinaceae forests ranging from Florida to Ontario in the east and southern California to Alaska in the west. Taxon Ectomycorrhizal fungi (Asco‐ and Basidiomycetes). Methods We characterized ECMF communities at each site using molecular methods and modelled climatic drivers of diversity and community composition with general additive, generalized dissimilarity models and Threshold Indicator Taxa ANalysis (TITAN). Next, we projected our models across the extent of North American Pinaceae forests and forecast ECMF responses to climate changes in these forests over the next 50 years. Results We predict median declines in ECMF species richness as high as 26% in Pinaceae forests throughout a climate zone comprising more than 3.5 million square kilometres of North America (an area twice that of Alaska state). Mitigation of greenhouse gas emissions can reduce these declines, but not prevent them. The existence of multiple diversity optima along climate gradients suggest regionally divergent trajectories for North American ECMF, which is corroborated by corresponding ECMF community thresholds identified in TITAN models. Warming of forests along the boreal–temperate ecotone results in projected ECMF species loss and declines in the relative abundance of long‐distance foraging ECMF species, whereas warming of eastern temperate forests has the opposite effect. Main Conclusions Our results reveal potentially unavoidable ECMF species‐losses over the next 50 years, which is likely to have profound (if yet unclear) effects on ECMF‐associated biogeochemical cycles.