Data from: Habitat fragmentation strongly restricts gene flow in endangered ectomycorrhizal fungal populations: Evidence from Rhizopogon togasawarius, specific to Pseudotsuga japonica, across the entire distribution range

Habitat fragmentation reduces gene flow, causing genetic differentiation
and diversity loss in endangered species through genetic drift and
inbreeding. However, the impact of habitat fragmentation on
ectomycorrhizal (ECM) fungi remains unexplored, despite their critical
roles in forest ecosystems. Here, we investigated the population genetic
structure and the demographic history of Rhizopogon togasawarius, the ECM
fungus specifically colonizing the host tree Pseudotsuga japonica, across
its entire distribution range (>200 km). These two species are
designated as endangered species on the IUCN Red List since they are found
only in small, fragmented forests in Japan. We analyzed 236 R.
togasawarius individuals from five remaining populations across the Kii
Peninsula and the Shikoku Island, separated by a sea channel. Simple
sequence repeat (SSR) analyses using 20 loci revealed strong genetic
differentiation among populations (FST = 0.255), even significant in the
nearest population pair separated by a distance of only 8 km (FST =
0.075), indicating extremely limited gene flow between populations.
DIYABC-RF analyses implied that population divergence occurred
approximately 6000 generations ago between the two regions, and nearly
1500 generations ago between the nearest populations within Shikoku
Island, related to past climate events. Because of prolonged genetic
isolation, significant inbreeding was confirmed in four of five
populations, where effective population sizes became very small
(Ne = 9.0–58.0). Although evaluation of extinction risks for
microorganisms is challenging, our conservation genetic results indicated
that habitat fragmentation increases extinction risk through population
genetic mechanisms, and therefore should not be overlooked in biodiversity
conservation efforts.