Data from: Population genetic consequences of habitat fragmentation in ectomycorrhizal fungi with different dispersal mechanisms: Implications from ice-aged relict forests across the Japanese archipelago

Recent human activities have caused extensive forest fragmentation, which
can profoundly affect the population genetic structure of soil microbes,
as has been well documented for plants and animals. However, such
information remains scarce for microbes, even for ectomycorrhizal (ECM)
fungi, which play key roles in the growth and survival of dominant forest
trees. To investigate the long-term effects of forest fragmentation on the
population genetic structure of ECM fungi, we examined ice-age relict
forests of Pinus pumila across nine alpine sites that have been isolated
for more than 10,000 years. We focused on two phylogenetically related ECM
fungi, Rhizopogon alpinus and Suillus spraguei, whose spores are dispersed
primarily by animals and wind, respectively. The genetic structure of
these fungi and their host trees was assessed via 28 microsatellite
markers, 14 of which were newly developed in this study. R. alpinus, an
animal-dispersed species, exhibited substantially greater genetic
differentiation among populations than its host tree P. pumila, which
disperses pollen via wind and seeds. In contrast, the wind-dispersed S.
spraguei presented little evidence of population differentiation.
Inbreeding levels were highest in P. pumila, intermediate in R. alpinus,
and negligible in S. spraguei. This study provides the first
direct evidence that forest fragmentation has contrasting effects on the
population genetic structure of eukaryotic microbes with different
dispersal mechanisms. The limited gene flow and elevated inbreeding
observed in R. alpinus indicate a heightened risk of
extinction—paralleling patterns observed in fragmented populations of
plants and animals—and highlight the need for targeted conservation
attention.