Ecological Niche Differentiation Parallels Genomic Divergence of Three Thelephora Ectomycorrhizal Fungi.

Ecological speciation via divergent selection despite gene flow remains poorly documented in fungi. We integrated niche modeling and comparative genomics to examine ecological and genomic divergence among three ectomycorrhizal Thelephora species. T. ganbajun is restricted to mid-elevation Yunnan with climatically stable environments; T. aurantiotincta occupies lower elevations with pronounced temperature seasonality; and T. terrestris displays the broadest distribution, tolerating extreme temperature fluctuations and low precipitation. Phylogenomic analysis recovered the three species as distinct lineages, with T. terrestris diverging at 21.16 Mya and T. ganbajun and T. aurantiotincta splitting at 14.97 Mya. Gene flow analysis revealed unidirectional introgression: T. terrestris donated to both other species, and T. aurantiotincta donated to T. ganbajun, with negligible reverse migration. T. terrestris possesses the largest genome (40.73 Mb) with recent LTR retrotransposon expansion and amplified cytochrome P450 and lignocellulose-active CAZymes. T. ganbajun shows expanded copper transport and cell wall remodeling genes, while T. aurantiotincta exhibits expansion of fatty acid metabolism genes. These results document pronounced niche differentiation, genomic divergence, and directional historical gene flow among closely related species, providing an ecological and genomic basis for examining ecological speciation in fungi.