Population genomics of a forest fungus reveals high gene flow and climate adaptation signatures

Genome sequencing of spatially distributed individuals sheds light on how
evolution structures genetic variation. Populations of Phellopilus
nigrolimitatus, a red-listed wood-inhabiting fungus associated with
old-growth coniferous forests, have decreased in size over the last
century due to a loss of suitable habitats. We assessed the population
genetic structure and investigated local adaptation in P. nigrolimitatus,
by establishing a reference genome and genotyping 327 individuals sampled
from 24 locations in Northern Europe by RAD sequencing. We revealed a
shallow population genetic structure, indicating large historical
population sizes and high levels of gene flow. Despite this weak
sub-structuring, two genetic groups were recognized; a western group
distributed mostly in Norway and an eastern group covering most of
Finland, Poland and Russia. This sub-structuring may reflect
co-immigration with the main host, Norway spruce (Picea abies), into
Northern Europe after the last ice age. We found evidence of low levels of
genetic diversity in southwestern Finland, which has a long history of
intensive forestry and urbanization. Numerous loci were significantly
associated with one or more environmental factors, indicating adaptation
to specific environments. These loci clustered into two groups with
different associations with temperature and precipitation. Overall, our
findings indicate that the current population genetic structure of P.
nigrolimitatus results from a combination of gene flow, genetic drift and
selection. The acquisition of similar knowledge especially over broad
geographic scales, linking signatures of adaptive genetic variation to
evolutionary processes and environmental variation, for other fungal
species will undoubtedly be useful for assessment of the combined effects
of habitat fragmentation and climate change on fungi strongly bound to
old-growth forests. --