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

Towards repeated clear-cutting of boreal forests - a tipping point for biodiversity?

Boreal forests are important carbon sinks and host a diverse array of species that provide important ecosystem functions. Boreal forests have a long history of intensive forestry, in which even-aged management with clear-cutting has been the dominant harvesting practice for the past 50-80 years. As a second cycle of clear-cutting is emerging, there is an urgent need to examine the effects of repeated clear-cutting events on biodiversity. Clear-cutting has led to reduced numbers of old and large trees, decreased volumes of dead wood of varied decay stages and diameters, and altered physical and chemical compositions of soils. The old-growth boreal forest has been fragmented and considerably reduced. Here, we review short- and long-term (≥50 years) effects of clear-cutting on boreal forest biodiversity in four key substrates: living trees, dead wood, ground and soil. We then assess landscape-level changes (habitat fragmentation and edge effects) on this biodiversity. There is evidence for long-term community changes after clear-cutting for several taxa: epiphytic lichens; saproxylic fungi, bryophytes and insects; epigeic bryophytes; and soil snails, bacteria, and ectomycorrhizal fungi. Long-term declines in species richness were found for saproxylic fungi, bryophytes and true flies. However, for the majority of taxa, long-term effects of clear-cutting are not well understood. On the landscape level, reduced connectivity to old-growth forests has negative effects on several species of fungi, lichens, bryophytes and insects, notably among Red-Listed species. Furthermore, altered microclimate near clear-cut edges negatively affects epiphytic lichens and epigeic arthropods, implying complex effects of habitat fragmentation. Repeated cycles of clear-cutting might pose even stronger pressures on boreal forest biodiversity due to continued fragmentation of old-growth forests and accumulation of extinction debts. Examining the broad effects of forestry on biodiversity across the boreal biome is crucial: (i) to increase our knowledge of long-term and landscape-level effects of former clear-cutting; and (ii) to gain a better understanding of how forestry will affect biodiversity and, subsequently, ecosystem functioning, with repeated cycles of clear-cutting.

The local-scale populations reveal cryptic processes occurring in the general population of Schizophyllum commune fungus

Population diversity of the species is principal for addressing questions concerning evolutionary processes and developing conservation strategies. Employing model organisms and sensitive DNA markers enables a comprehensive exploration of fungal functional systems and the intricate interplay between the genome and the environment. The cosmopolitan wood-decay fungus Schizophyllum commune is one of them, and widespread allows finding samples in almost all climatic zones, with various extreme environmental factors. The local-scale population research is infrequent because of their unlikely differentiation. Using sensitive genetic markers allows us to identify possible environmental causes leading to genetic differentiation. Our study aimed to determine the differentiation of S. commune local-scale populations with different topographic features and to identify cryptic environmental factors that affect the spread of the fungus's genetic material. The multi-stage study allowed us to establish the most homogeneous location 2 (Feof). Moderate R-values indicate the existence of obstacles to the free spread of the fungal genetic material. The flow direction, the left and right banks of the Dnipro River and altitude affect the spread of the S. commune fungus. These limiting environmental factors also could affect other fungal species with a similar lifestyle cycle. Samples Sc-141 and Sc-208 S. commune significantly influenced on structure of the populations within the research framework, and the movement of descendants occurred from north to south, with the active participation of large waterways (Dnipro River and tributaries).

Evolutionarily distinct lineages of a migratory bird of prey show divergent responses to climate change

Accurately predicting species' responses to anthropogenic climate change is hampered by limited knowledge of their spatiotemporal ecological and evolutionary dynamics. We combine landscape genomics, demographic reconstructions, and species distribution models to assess the eco-evolutionary responses to past climate fluctuations and to future climate of an Afro-Palaearctic migratory raptor, the lesser kestrel (Falco naumanni). We uncover two evolutionarily and ecologically distinct lineages (European and Asian), whose demographic history, evolutionary divergence, and historical distribution range were profoundly shaped by past climatic fluctuations. Using future climate projections, we find that the Asian lineage is at higher risk of range contraction, increased migration distance, climate maladaptation, and consequently greater extinction risk than the European lineage. Our results emphasise the importance of providing historical context as a baseline for understanding species' responses to contemporary climate change, and illustrate how incorporating intraspecific genetic variation improves the ecological realism of climate change vulnerability assessments.

Illuminating ecology and distribution of the rare fungus Phellinidium pouzarii in the Bavarian Forest National Park

Due to their cryptic lifestyle, hidden diversity and a lack of ecological knowledge, conservation of wood-inhabiting fungi continues to be a niche interest. Molecular methods are able to provide deeper insights into the ecology of rare fungal species. We investigated the occurrence of the rare wood-inhabiting fungus Phellinidium pouzarii across the Bavarian Forest National Park in Germany using a fruit body survey, amplicon sequencing and qPCR. Additionally, we sequenced the genome of P. pouzarii and characterized the chemical substances responsible for its distinctive scent. Our approach gave matching results between amplicon sequencing and qPCRs, however, we found no evidence that P. pouzarii is more abundant in the National Park than we can assume based on fruit body inventories, underlining the species' critically endangered status. Genomics revealed P. pouzarii's repertoire of ligninolytic enzymes, pointing towards a white rot lifestyle. Two main components of P. pouzarii's distinct odour we identified (2-phenylethanol, methyl p-anisate) are known to act as insect attractants and/or to possess antimicrobial properties.

Whole-genome sequencing reveals fine-scale environment-associated divergence near the range limits of a temperate reef fish

Environmental variation is increasingly recognized as an important driver of diversity in marine species despite the lack of physical barriers to dispersal and the presence of pelagic stages in many taxa. A robust understanding of the genomic and ecological processes involved in structuring populations is lacking for most marine species, often hindering management and conservation action. Cunner (Tautogolabrus adspersus) is a temperate reef fish with both pelagic early life-history stages and strong site-associated homing as adults; the species is also of interest for use as a cleaner fish in salmonid aquaculture in Atlantic Canada. We aimed to characterize genomic and geographic differentiation of cunner in the Northwest Atlantic. To achieve this, a chromosome-level genome assembly for cunner was produced and used to characterize spatial population structure throughout Atlantic Canada using whole-genome sequencing. The genome assembly spanned 0.72 Gbp and 24 chromosomes; whole-genome sequencing of 803 individuals from 20 locations from Newfoundland to New Jersey identified approximately 11 million genetic variants. Principal component analysis revealed four regional Atlantic Canadian groups. Pairwise FST and selection scans revealed signals of differentiation and selection at discrete genomic regions, including adjacent peaks on chromosome 10 across multiple pairwise comparisons (i.e. FST 0.5-0.75). Redundancy analysis suggested association of environmental variables related to benthic temperature and oxygen range with genomic structure. Results suggest regional scale diversity in this temperate reef fish and can directly inform the collection and translocation of cunner for aquaculture applications and the conservation of wild populations throughout the Northwest Atlantic.

Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics With an Emphasis on Coltricia

To elucidate the genomic traits of ecological diversification in the Hymenochaetales, we sequenced 15 new genomes, with attention to ectomycorrhizal (EcM) Coltricia species. Together with published data, 32 genomes, including 31 Hymenochaetales and one outgroup, were comparatively analyzed in total. Compared with those of parasitic and saprophytic members, EcM species have significantly reduced number of plant cell wall degrading enzyme genes, and expanded transposable elements, genome sizes, small secreted proteins, and secreted proteases. EcM species still retain some of secreted carbohydrate-active enzymes (CAZymes) and have lost the key secreted CAZymes to degrade lignin and cellulose, while possess a strong capacity to degrade a microbial cell wall containing chitin and peptidoglycan. There were no significant differences in secreted CAZymes between fungi growing on gymnosperms and angiosperms, suggesting that the secreted CAZymes in the Hymenochaetales evolved before differentiation of host trees into gymnosperms and angiosperms. Nevertheless, parasitic and saprophytic species of the Hymenochaetales are very similar in many genome features, which reflect their close phylogenetic relationships both being white rot fungi. Phylogenomic and molecular clock analyses showed that the EcM genus Coltricia formed a clade located at the base of the Hymenochaetaceae and divergence time later than saprophytic species. And Coltricia remains one to two genes of AA2 family. These indicate that the ancestors of Coltricia appear to have originated from saprophytic ancestor with the ability to cause a white rot. This study provides new genomic data for EcM species and insights into the ecological diversification within the Hymenochaetales based on comparative genomics and phylogenomics analyses.