Inger Skrede

• Fonseca, Jose Mauricio Salamanca; Sanchez, Adriana; Corrales, Adriana; Kauserud, Håvard; Thoen, Ella & Krabberød, Anders K. [Show all 7 contributors for this article] (2025). Beyond seasonal and host factors: ecosystem dynamics drive palm-associated root fungal communities at a local scale. Plant and Soil. ISSN 0032-079X. 514, p. 1027–1041. doi: 10.1007/s11104-025-07438-y. Full text in Research Archive Show summary

  Background and Aims The increase of extreme weather events due to climate change may alter ecosystem dynamics. In the tropics, little is known about how ecosystems and species will respond to droughts or floods. Identifying the most important biotic and abiotic factors in ecosystems at the local level is key to developing better forest management practices and understanding the effects of climate change on the fungal community. Methods We conducted a random sampling of adult individuals from several palm species across three adjacent ecosystems with different hydrological conditions, during rainy and dry seasons. Using next-generation sequencing, we identified fungal communities and determined the influence of soil physicochemical properties, as well as host and seasonal variables, on the relative abundance of the root- and rhizosphere-associated fungal communities. Results The composition of the fungal communities was similar between the seasonally flooded forest and the terra-firme forest, while the palm swamp diverged due to differences in soil physicochemical properties. Seasonal analyses revealed significant differences in the relative abundance of several taxa, mainly associated with the seasonally flooded forest. However, no influence of palm species on fungal abundance was detected at any taxonomic level. Conclusion This study highlights the importance of studying ecosystems at the local scale and considering ecosystem dynamics into the study of fungal communities and other microorganisms. Such an approach is crucial for improving predictions under climate change scenarios and understanding the consequences of altering these dynamics in vulnerable, often understudied ecosystems.

• Thoen, Ella; Krabberød, Anders K.; Nogerius, Veera Tuovinen; Skrede, Inger; Rosling, Anna & Kauserud, Håvard (2025). Short‐ and long‐read metabarcoding of Archaeorhizomycetes reveals high phylogenetic diversity structured by vegetation and climate. New Phytologist. ISSN 0028-646X. 249 (2026)(1), p. 418–432. doi: 10.1111/nph.70682. Full text in Research Archive Show summary

  Summary Archaeorhizomycetes is a class of globally widespread soil‐dwelling fungi, originally proposed to be associated with plant roots, but their ecology and nutritional mode are not clearly defined. To increase the knowledge about Archaeorhizomycetes' ecology and biogeography, we investigate how they are distributed along major environmental gradients, as well as different soil compartments. To assess their abundance and diversity, we use both short‐ and long‐read metabarcoding with class‐specific primers for the long reads. The short‐read sequences revealed that Archaeorhizomycetes is proportionally abundant and a dominant fungal class in alpine vegetation types, as well as boreal spruce and pine forests. The long‐read sequences revealed high phylogenetic diversity of Archaeorhizomycetes, with 120 OTUs grouping into 13 clades with potentially differing ecologies and biogeographic distributions. Vegetation types and climate primarily structure the Archaeorhizomycetes community, while community composition was similar in litter, soil, and roots. However, Archaeorhizomycetes were significantly more abundant in soil and plant roots than litter, supporting the idea that Archaeorhizomycetes depend on the presence of plant roots. Our study illustrates that targeted group‐specific amplification coupled with long‐read sequencing is a powerful approach for exploring the diversity and ecology of specific fungal groups.

• Lü, Dabao Sun; Methlie, Ine-Susanne Hopland; Sønstebø, Jørn Henrik; Andersen, Anneli; Peris, David & Maurice, Sundy Ursula MaryJanne [Show all 8 contributors for this article] (2025). Postglacial History of a Widespread Wood-Decaying Fungus in Europe Suggests Migration out of Multiple Refugia Followed by Admixture. Molecular Ecology. ISSN 0962-1083. 34(22), p. 1–14. doi: 10.1111/mec.70053. Full text in Research Archive Show summary

  While postglacial migration patterns have been well-studied in plants and animals in Europe, the same is not true for microorganisms such as fungi, and it remains unclear whether fungi have followed the same postglacial migration trajectories. In this study, we infer the postglacial history of the widespread wood-decay fungus Trichaptum abietinum in Europe. We investigate whether this fungus resided in multiple glacial refugia, as observed in many plants and animals, and how it migrated following the retreat of the ice. Population genomic analyses of T. abietinum suggest at least two glacial refugia in Europe: a southern refugium extending from Portugal to the Caucasus (potentially formed by several earlier distinct refugia), an eastern refugium and a potential third western refugium. Expansion from these refugia followed by migration and secondary contact has led to a complex genomic pattern of what we call the Mediterranean, Boreal, Atlantic and Central European admixed groups. From the southern and potential western refugia there have likely been northwards expansions resulting in the Mediterranean and Atlantic groups, while the Boreal group probably expanded westwards from the eastern refugium. A contact zone is present in Central Europe, where the Mediterranean and Boreal groups are admixing. In these admixed individuals, the second half of their largest scaffold is entirely inherited from the Boreal group, indicating either strong selection or genomic incompatibilities. In Scandinavia, the Atlantic and Boreal groups are in close contact but with limited admixture. Tajima's D and analyses of linkage disequilibrium decay support a recent history of contraction and expansion of this fungus in Europe. We conclude that the postglacial migration patterns in T. abietinum resemble those observed in several plants and animals, suggesting multiple glacial refugia followed by admixture during northward and westward expansions.

• Kauserud, Håvard; Sanchez, Pedro Maria Martin; Estensmo, Eva Lena Fjeld; Botnen, Synnøve Smebye; Morgado, Luis & Maurice, Sundy Ursula MaryJanne [Show all 8 contributors for this article] (2025). Yeasts Prefer Daycares and Molds Prefer Private Homes. Microbial Ecology. ISSN 0095-3628. 88(1). doi: 10.1007/s00248-025-02505-4. Full text in Research Archive Show summary

  Worldwide, people spend most of their time indoors; in their homes, workplaces, schools, and daycares. Indoor fungi can cause negative health effects due to the production of toxins or volatiles that trigger the immune system of the occupants. To what degree indoor fungi (mycobiomes) differ between buildings with different usage is poorly known. Here, we compare the indoor mycobiomes in 123 children’s daycare centers and 214 private homes throughout Norway, as revealed by metabarcoding of DNA extracted from dust samples collected by community scientists. Although the fungal richness per se was similar in dust samples from daycares and homes, the fungal community composition differed. Yeast fungi, distributed mainly across the orders Saccharomycetales, Filobasidiales, and Tremellales, were proportionally more abundant in the daycares, while filamentous fungi, including spore-producing molds such as Aspergillus, Penicillum, and Cladosporium, were relatively more abundant in homes. Number of occupants, which is considerably higher in daycares, correlated significantly with the fungal community shift. We hypothesize that the density of occupants and their age distribution drive the systematic difference of yeasts and filamentous fungi in the two building types.

• Lunde, Lisa Fagerli; Birkemoe, Tone; Sverdrup-Thygeson, Anne; Asplund, Johan; Halvorsen, Rune & Kjønaas, O. Janne [Show all 11 contributors for this article] (2025). Towards repeated clear-cutting of boreal forests – a tipping point for biodiversity? Biological Reviews. ISSN 1464-7931. 100(3), p. 1181–1205. doi: 10.1111/brv.13180. Full text in Research Archive Show summary

  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.

• Asplund, Johan; Nordén, Jenni; Kjønaas, O. Janne; Madsen, Rieke Lo; Lunde, Lisa Fagerli & Birkemoe, Tone [Show all 18 contributors for this article] (2024). Long term effects of forest management on forest structure and dead wood in mature boreal forests. Forest Ecology and Management. ISSN 0378-1127. 572. doi: 10.1016/j.foreco.2024.122315. Full text in Research Archive Show summary

  The history of forestry in Fennoscandia spans five centuries, with clear-cutting being the dominant practice since the mid-20th century. This has led to a significant transformation of the forest landscape. In this study we investigated long-term effects of clear-cutting on forest structure and dead wood volumes. We established twelve pairs of spruce forest sites in southeastern Norway, each pair constituting of a mature, previously clear-cut stand and its near-natural counterpart with similar edaphic factors. The near-natural stands had 2.8 times higher volumes of dead wood and a larger proportion of dead wood in late stages of decay. The near-natural stands had on average 36.8 ± 9.1 m3 ha− 1 of downed dead wood and 24.1 ± 6.2 m3 ha− 1 of standing dead wood. Corresponding numbers for the previously clear-cut stands were 10.2 ± 2.8 m3 ha− 1 and 11.9 ± 3.7 m3 ha− 1 . Forests with lower volumes of dead wood often also had lower connectivity of old spruce forests, which potentially have further negative effects on biodiversity. Furthermore, near-natural stands displayed greater tree size heterogeneity, resulting in a wider variation in light conditions. While no difference was observed in living tree volume, we found only weak evidence for higher basal area in the previously clear-cut stands, which had a higher stem density with more slender stems and shorter crowns. Our findings suggest that managed forests do not develop structures typical of near-natural forests before they become mature for logging. We stress the importance of a thorough site selection for studies of management effects, as forest management history may be confounded with productivity and other edaphic factors. Experimental designs like ours are vital for testing how differences in structure and deadwood volumes, driven by forest management, translate into variations in biodiversity, carbon sequestration and ecosystem functioning in future studies Coarse woody debris Clear-cutting forestry Norway spruce Structural heterogeneity

• Simpson, Hunter J.; Andrew, Carrie; Skrede, Inger; Kauserud, Håvard & Schilling, Jonathan S. (2024). Global field collection data confirm an affinity of brown rot fungi for coniferous habitats and substrates. New Phytologist. ISSN 0028-646X. 242(6). doi: 10.1111/nph.19723. Full text in Research Archive Show summary

  Unlike ‘white rot’ (WR) wood-decomposing fungi that remove lignin to access cellulosic sugars, ‘brown rot’ (BR) fungi selectively extract sugars and leave lignin behind. The relative frequency and distribution of these fungal types (decay modes) have not been thoroughly assessed at a global scale; thus, the fate of one-third of Earth's aboveground carbon, wood lignin, remains unclear. Using c. 1.5 million fungal sporocarp and c. 30 million tree records from publicly accessible databases, we mapped and compared decay mode and tree type (conifer vs angiosperm) distributions. Additionally, we mined fungal record metadata to assess substrate specificity per decay mode. The global average for BR fungi proportion (BR/(BR + WR records)) was 13% and geographic variation was positively correlated (R2 = 0.45) with conifer trees proportion (conifer/(conifer + angiosperm records)). Most BR species (61%) were conifer, rather than angiosperm (22%), specialists. The reverse was true for WR (conifer: 19%; angiosperm: 62%). Global BR proportion patterns were predicted with greater accuracy using the relative distributions of individual tree species (R2 = 0.82), rather than tree type. Fungal decay mode distributions can be explained by tree type and, more importantly, tree species distributions, which our data suggest is due to strong substrate specificities.

• Harder, Christoffer Bugge; Miyuachi, Shingo; Virágh, Máté; Kuo, Alan; Thoen, Ella & Andreopoulos, Bill [Show all 28 contributors for this article] (2024). Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations. Cell Genomics. 4(7), p. 1–16. doi: 10.1016/j.xgen.2024.100586. Full text in Research Archive Show summary

  Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2–8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.

• Kauserud, Håvard; Justad, Tor Arne; Vindenes, Yngvild; Methlie, Ine-Susanne Hopland; Sønstebø, Jørn Henrik & Skrede, Inger [Show all 7 contributors for this article] (2024). Limited evidence of local adaptation of growth and decomposition rates in the widespread wood-decay fungus Fomitopsis pinicola. Fungal ecology. ISSN 1754-5048. 70. doi: 10.1016/j.funeco.2024.101353. Full text in Research Archive
• Lü, Dabao Sun; Peris, David; Sønstebø, Jørn Henrik; James, Timothy Y.; Rieseberg, Loren H. & Maurice, Sundy [Show all 9 contributors for this article] (2024). Reticulate evolution and rapid development of reproductive barriers upon secondary contact in a forest fungus. Current Biology. ISSN 0960-9822. 34(19), p. 4513–4525. doi: 10.1016/j.cub.2024.08.046. Full text in Research Archive Show summary

  Reproductive barriers between sister species of the mushroom-forming fungi tend to be stronger in sympatry, leading to speculation on whether they are being reinforced by selection against hybrids. We have used population genomic analyses together with in vitro crosses of a global sample of the wood decay fungus Trichaptum abietinum to investigate reproductive barriers within this species complex and the processes that have shaped them. Our phylogeographic analyses show that T. abietinum is delimited into six major genetic groups: one in Asia, two in Europe, and three in North America. The groups present in Europe are interfertile and admixed, whereas our crosses show that the North American groups are reproductively isolated. In Asia, a more complex pattern appears, with partial intersterility between subgroups that likely originated independently and more recently than the reproductive barriers in North America. We found pre-mating barriers in T. abietinum to be moderately correlated with genomic divergence, whereas mean growth reduction of the mated hybrids showed a strong correlation with increasing genomic divergence. Genome-wide association analyses identified candidate genes with programmed cell death annotations, which are known to be involved in intersterility in distantly related fungi, although their link here remains unproven. Our demographic modeling and phylogenetic network analyses fit a scenario where reproductive barriers in Trichaptum abietinum could have been reinforced upon secondary contact between groups that diverged in allopatry during the Pleistocene glacial cycles. Our combination of experimental and genomic approaches demonstrates how T. abietinum is a tractable system for studying speciation mechanisms.

• Krabberød, Anders Kristian; Stokke, Embla Elen; Thoen, Ella; Skrede, Inger & Kauserud, Håvard (2024). The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies. Molecular Ecology Resources. ISSN 1755-098X. doi: 10.1111/1755-0998.14031. Full text in Research Archive Show summary

  Current rDNA reference sequence databases are tailored towards shorter DNA markers, such as parts of the 16/18S marker or the internally transcribed spacer (ITS) region. However, due to advances in long-read DNA sequencing technologies, longer stretches of the rDNA operon are increasingly used in environmental sequencing studies to increase the phylogenetic resolution. There is, therefore, a growing need for longer rDNA reference sequences. Here, we present the ribosomal operon database (ROD), which includes eukaryotic full-length rDNA operons fished from publicly available genome assemblies. Full-length operons were detected in 34.1% of the 34,701 examined eukaryotic genome assemblies from NCBI. In most cases (53.1%), more than one operon variant was detected, which can be due to intragenomic operon copy variability, allelic variation in non-haploid genomes, or technical errors from the sequencing and assembly process. The highest copy number found was 5947 in Zea mays. In total, 453,697 unique operons were detected, with 69,480 operon variant clusters remaining after intragenomic clustering at 99% sequence identity. The operon length varied extensively across eukaryotes, ranging from 4136 to 16,463 bp, which will lead to considerable polymerase chain reaction (PCR) bias during amplification of the entire operon. Clustering the full-length operons revealed that the different parts (i.e., 18S, 28S, and the hypervariable regions V4 and V9 of 18S) provide divergent taxonomic resolution, with 18S, the V4 and V9 regions being the most conserved. The ROD will be updated regularly to provide an increasing number of full-length rDNA operons to the scientific community.

• Kinneberg, Vilde Bruhn; Lü, Dabao Sun; Peris, David; Ravinet, Mark & Skrede, Inger (2023). Introgression between highly divergent fungal sister species. Journal of Evolutionary Biology. ISSN 1010-061X. 36(8), p. 1133–1149. doi: 10.1111/jeb.14190. Full text in Research Archive Show summary

  Abstract To understand how species evolve and adapt to changing environments, it is important to study gene flow and introgression due to their influence on speciation and radiation events. Here, we apply a novel experimental system for investigating these mechanisms using natural populations. The system is based on two fungal sister species with morphological and ecological similarities occurring in overlapping habitats. We examined introgression between these species by conducting whole genome sequencing of individuals from populations in North America and Europe. We assessed genome-wide nucleotide divergence and performed crossing experiments to study reproductive barriers. We further used ABBA–BABA statistics together with a network analysis to investigate introgression, and conducted demographic modelling to gain insight into divergence times and introgression events. The results revealed that the species are highly divergent and incompatible in vitro. Despite this, small regions of introgression were scattered throughout the genomes and one introgression event likely involves a ghost population (extant or extinct). This study demonstrates that introgression can be found among divergent species and that population histories can be studied without collections of all the populations involved. Moreover, the experimental system is shown to be a useful tool for research on reproductive isolation in natural populations. Abstract We studied population histories with demographic modelling and found introgression between highly divergent fungal sister species, involving a ghost population.

• Skrede, Inger; Løken, Solveig Bua; Mathiesen, Cecilie & Schumacher, Trond Kristian (2023). Additions to the knowledge of the genus Helvella in Europe. New records and de novo description of five species from the Nordic region. Fungal Systematics and Evolution. 11, p. 71–84. doi: 10.3114/fuse.2023.11.06. Full text in Research Archive Show summary

  Helvella is a species-rich genus, forming a large variation of astounding ascocarps in many different habitats. During the last decade, molecular markers and morphological characters have been combined to delimit and identify cryptic species in this genus. We report on a list of 54 species of Helvella s.s. in the Nordic region and describe five new species, i.e. H. bresadolae , H. convexa , H. japonica , H. nordlandica and H. oroarctica . The morphological and molecular characteristics of the new species and the emended / hypocrateriformis, / fibrosa-macropus, and / fallaxpezizoides lineages of Helvella s.s. are shortly commented upon. Further we include a discussion of the distribution of species in the Nordic region based on a large set of studied collections. The ecological versatility and variable geographic patterns of these species indicate that cryptic species may have contrasting ecology in their local habitats.

• Sanchez, Pedro Maria Martin; Nunez, Maria; Estensmo, Eva Lena Fjeld; Skrede, Inger & Kauserud, Håvard (2022). Comparison of Methods to Identify and Monitor Mold Damages in Buildings. Applied Sciences. 12(18). doi: 10.3390/app12189372. Full text in Research Archive Show summary

  Molds thrive in indoor environments, challenging the stability of building materials and occupants’ health. Diverse sampling and analytical techniques can be applied in the microbiology of buildings, with specific benefits and drawbacks. We evaluated the use of two methods, the microscopy of visible mold growth (hereinafter “mold” samples) (tape lifts) and the DNA metabarcoding of mold and dust samples (swabs), for mapping mold-damage indicator fungi in residential buildings in Oslo. Overall, both methods provided consistent results for the mold samples, where nearly 80% of the microscopy-identified taxa were confirmed by DNA analyses. Aspergillus was the most abundant genus colonizing all materials, while some taxa were associated with certain substrates: Acremonium with gypsum board, Chaetomium with chipboard, Stachybotrys with gypsum board and wood, and Trichoderma with wood. Based on the DNA data, the community composition was clearly different between the mold and the dust, with a much higher alpha diversity in the dust. Most genera identified in the mold were also detected with a low abundance in the dust from the same apartments. Their spatial distribution indicated some local spread from the mold growth to other areas, but there was no clear correlation between the relative abundances and the distance to the damages. To study mold damages, different microbiological analyses (microscopy, cultivation, DNA, and chemistry) should be combined with a thorough inspection of buildings. The interpretation of such datasets requires the collaboration of skilled mycologists and building consultants.

• Sønstebø, Jørn Henrik; Trucchi, Emiliano; Nordén, Jenni; Skrede, Inger; Miettinen, Otto & Haridas, Sajeet [Show all 11 contributors for this article] (2022). Population genomics of a forest fungus reveals high gene flow and climate adaptation signatures. Molecular Ecology. ISSN 0962-1083. 31(7), p. 1963–1979. doi: 10.1111/mec.16369. Full text in Research Archive Show summary

  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 substructuring, two genetic groups were recognized; a western group distributed mostly in Norway and an eastern group covering most of Finland, Poland and Russia. This substructuring may reflect coimmigration 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. demography, forest fragmentation, genotype-environment associations, local adaptation, Picea abies, post-glacial colonization, wood decay fungi

• Estensmo, Eva Lena Fjeld; Botnen, Synnøve Smebye; Maurice, Sundy; Sanchez, Pedro Maria Martin; Morgado, Luis & Engh, Ingeborg Bjorvand [Show all 9 contributors for this article] (2022). The Indoor Mycobiomes of Daycare Centers Are Affected by Occupancy and Climate. Applied and Environmental Microbiology. ISSN 0099-2240. 88(6). doi: 10.1128/aem.02113-21. Full text in Research Archive Show summary

  With an alarming increase in chronic diseases like childhood asthma and allergies, there is an increased focus on the exposure of young children to indoor biological and chemical air pollutants. Our study of 125 daycares throughout Norway demonstrates that the indoor mycobiome not only reflects cooccurring outdoor fungi but also includes a high abundance of yeast and mold fungi with an affinity for indoor environments.

• Cowan, Andrew J.; Skrede, Inger & Moody, Suzy Clare (2022). Cytochrome P450 Complement May Contribute to Niche Adaptation in Serpula Wood-Decay Fungi. Journal of fungi (JoF). 8(3). doi: 10.3390/jof8030283. Full text in Research Archive Show summary

  Serpula wood-decay fungi occupy a diverse range of natural and man-made ecological niches. Serpula himantioides is a forest-floor generalist with global coverage and strong antagonistic ability, while closely related species Serpula lacrymans contains specialist sister strains with widely differing ecologies. Serpula lacrymans var. shastensis is a forest-floor specialist in terms of resource preference and geographic coverage, while Serpula lacrymans var. lacrymans has successfully invaded the built environment and occupies a building-timber niche. To increase understanding of the cellular machinery required for niche adaptation, a detailed study of the P450 complement of these three strains was undertaken. Cytochrome P450 monooxygenases are present in all fungi and typically seen in high numbers in wood decay species, with putative roles in breakdown of plant extractives and lignocellulose metabolism. Investigating the genomes of these related yet ecologically diverse fungi revealed a high level of concordance in P450 complement, but with key differences in P450 family representation and expression during growth on wood, suggesting P450 proteins may play a role in niche adaptation. Gene expansion of certain key P450 families was noted, further supporting an important role for these proteins during wood decay. The generalist species S. himantioides was found to have the most P450 genes with the greatest family diversity and the highest number of P450 protein families expressed during wood decay.

• Peris, David; Lü, Dabao Sun; Kinneberg, Vilde Bruhn; Methlie, Ine-Susanne Hopland; Dahl, Malin Stapnes & James, Timothy Y. [Show all 8 contributors for this article] (2022). Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection. PLoS Genetics. ISSN 1553-7390. 18(3). doi: 10.1371/journal.pgen.1010097. Full text in Research Archive Show summary

  Balancing selection, an evolutionary force that retains genetic diversity, has been detected in multiple genes and organisms, such as the sexual mating loci in fungi. However, to quantify the strength of balancing selection and define the mating-related genes require a large number of strains. In tetrapolar basidiomycete fungi, sexual type is determined by two unlinked loci, MATA and MATB. Genes in both loci define mating type identity, control successful mating and completion of the life cycle. These loci are usually highly diverse. Previous studies have speculated, based on culture crosses, that species of the non-model genus Trichaptum (Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with multiple alleles. Here, we sequenced a hundred and eighty strains of three Trichaptum species. We characterized the chromosomal location of MATA and MATB, the molecular structure of MAT regions and their allelic richness. The sequencing effort was sufficient to molecularly characterize multiple MAT alleles segregating before the speciation event of Trichaptum species. Analyses suggested that long-term balancing selection has generated trans-species polymorphisms. Mating sequences were classified in different allelic classes based on an amino acid identity (AAI) threshold supported by phylogenetics. 17,550 mating types were predicted based on the allelic classes. In vitro crosses allowed us to support the degree of allelic divergence needed for successful mating. Even with the high amount of divergence, key amino acids in functional domains are conserved. We conclude that the genetic diversity of mating loci in Trichaptum is due to long-term balancing selection, with limited recombination and duplication activity. The large number of sequenced strains highlighted the importance of sequencing multiple individuals from different species to detect the mating-related genes, the mechanisms generating diversity and the evolutionary forces maintaining them.

• Andreasen, Mathias; Skrede, Inger; Jaklitsch, Walter; Voglmayr, Hermann & Nordén, Björn (2021). Multi-locus phylogenetic analysis of lophiostomatoid fungi motivates a broad concept of Lophiostoma and reveals nine new species. Persoonia. ISSN 0031-5850. 46, p. 240–271. doi: 10.3767/persoonia.2021.46.09. Full text in Research Archive Show summary

  Recent studies on the fungal families Lophiostomataceae and Lophiotremataceae (Pleosporales) have provided varying phylogenetic and taxonomic results concerning constituent genera and species. By adding DNA sequences of 24 new strains of Lophiostomataceae and nine new strains of Lophiotremataceae to a sequence data matrix from international databases, we provide a new understanding of the relationships within these families. Multigene analysis of the four molecular markers ITS, LSU, TEF1-α, and RPB2 reveals that the genera within Lophiotremataceae are phylogenetically well supported. Lophiostoma myriocarpum is recognised as a species of Lophiotrema in contrast to earlier concepts. In Lophiostomataceae, we resurrect a broad generic concept of the genus Lophiostoma and reduce 14 genera to synonymy: Alpestrisphaeria, Biappendiculispora, Capulatispora, Coelodictyosporium, Guttulispora, Lophiohelichrysum, Lophiopoacea, Neopaucispora, Neotrematosphaeria, Platystomum, Pseudocapulatispora, Pseudolophiostoma, Pseudoplatystomum, and Sigarispora. Nine new species are described based on molecular data and in most cases supported by morphological characters: Antealophiotrema populicola, Atrocalyx nordicus, Lophiostoma carpini, Lophiostoma dictyosporium, Lophiostoma erumpens, Lophiostoma fusisporum, Lophiostoma jotunheimenense, Lophiostoma plantaginis, and Lophiostoma submuriforme. Lophiostoma caespitosum and Lophiotrema myriocarpum are lecto- and epitypified to stabilise their species concepts. High intraspecific variability of several morphological traits is common within Lophiostomataceae Lophiostomataceae Lophiotremataceae molecular phylogeny new taxa Pleosporales taxonomy

• Estensmo, Eva Lena Fjeld; Maurice, Sundy Ursula Mary Jane; Morgado, Luis; Martin-Sanchez, Pedro Maria; Skrede, Inger & Kauserud, Håvard (2021). The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species. Molecular Ecology Resources. ISSN 1755-098X. doi: 10.1111/1755-0998.13329. Full text in Research Archive Show summary

  DNA metabarcoding has become a powerful approach for analysing complex communities from environmental samples, but there are still methodological challenges limiting its full potential. While conserved DNA markers, like 16S and 18S, often are not able to discriminate among closely related species, other more variable markers – like the fungal ITS region, may include considerable intraspecific variation, which can lead to oversplitting of species during DNA metabarcoding analyses. Here we assessed the effects of intraspecific sequence variation in DNA metabarcoding by analysing local populations of eleven fungal species. We investigated the allelic diversity of ITS2 haplotypes using both Sanger sequencing and high throughput sequencing (HTS) coupled with error correction with the software dada2. All the eleven species, except one, included some level of intraspecific variation in the ITS2 region. Overall, we observed a high correspondence between haplotypes generated by Sanger sequencing and HTS, with the exception of a few additional haplotypes detected using either approach. These extra haplotypes, typically occurring in low frequencies, were probably due to PCR and sequencing errors or intragenomic variation in the rDNA region. The presence of intraspecific (and possibly intragenomic) variation in ITS2 suggest that haplotypes (or ASVs) should not be used as basic units in ITS‐based fungal community analyses, but an extra clustering step is needed to approach species‐level resolution.

• Skrede, Inger; Murat, Claude; Hess, Jaqueline; Maurice, Sundy Ursula Mary Jane; Sønstebø, Jørn Henrik & Kohler, Annegret [Show all 11 contributors for this article] (2021). Contrasting demographic histories revealed in two invasive populations of the dry rot fungus Serpula lacrymans. Molecular Ecology. ISSN 0962-1083. 30(12), p. 2772–2789. doi: 10.1111/mec.15934. Full text in Research Archive Show summary

  Globalization and international trade have impacted organisms around the world leading to a considerable number of species establishing in new geographic areas. Many organisms have taken advantage of human-made environments, including buildings. One such species is the dry rot fungus Serpula lacrymans, which is the most aggressive wood-decay fungus in indoor environments in temperate regions. Using population genomic analyses of 36 full genome sequenced isolates, we demonstrated that European and Japanese isolates are highly divergent and the populations split 3000–19,000 generations ago, probably predating human influence. Approximately 250 generations ago, the European population went through a tight bottleneck, probably corresponding to the fungus colonization of the built environment in Europe. The demographic history of these populations, probably lead to low adaptive potential. Only two loci under selection were identified using a Fst outlier approach, and selective sweep analyses identified three loci with extended haplotype homozygosity. The selective sweep analyses found signals in genes possibly related to decay of various substrates in Japan and in genes involved DNA replication and protein modification in Europe. Our results suggest that the dry rot fungus independently established in indoor environments in Europe and Japan and that invasive species can potentially establish large populations in new habitats based on a few colonizing individuals.

• Martin-Sanchez, Pedro Maria; Estensmo, Eva Lena Fjeld; Morgado, Luis; Maurice, Sundy Ursula Mary Jane; Engh, Ingeborg Bjorvand & Skrede, Inger [Show all 7 contributors for this article] (2021). Analysing indoor mycobiomes through a large‐scale citizen science study in Norway. Molecular Ecology. ISSN 0962-1083. 30, p. 2689–2705. doi: 10.1111/mec.15916. Full text in Research Archive Show summary

  In the built environment, fungi can cause important deterioration of building materials and adverse health effects on occupants. Increased knowledge about indoor mycobiomes from different regions of the world, and their main environmental determinants, will enable improved indoor air quality management and identification of health risks. This is the first citizen science study about indoor mycobiomes at a large geographical scale in Europe, including 271 houses from Norway and 807 dust samples from three house compartments: outside of the building, living room and bathroom. The fungal community composition determined by DNA metabarcoding was clearly different between indoor and outdoor samples, but there were no significant differences between the two indoor compartments. The 32 selected variables, related to the outdoor environment, building features and occupant characteristics, accounted for 15% of the overall variation in community composition, with the house compartment as the key factor (7.6%). Next, the climate was the main driver of the dust mycobiomes (4.2%), while building and occupant variables had significant but minor influences (1.4% and 1.1%, respectively). The house‐dust mycobiomes were dominated by ascomycetes (⁓70%) with Capnodiales and Eurotiales as the most abundant orders. Compared to the outdoor samples, the indoor mycobiomes showed higher species richness, which is probably due to the mixture of fungi from outdoor and indoor sources. The main indoor indicator fungi belonged to two ecological groups with allergenic potential: xerophilic molds and skin‐associated yeasts. Our results suggest that citizen science is a successful approach for unraveling the built microbiome at large geographical scales.

• Estensmo, Eva Lena F.; Morgado, Luis; Maurice, Sundy; Sanchez, Pedro Maria Martin; Engh, Ingeborg B. & Mattsson, Johan [Show all 8 contributors for this article] (2021). Spatiotemporal variation of the indoor mycobiome in daycare centers. Microbiome. 9(1), p. 1–12. doi: 10.1186/s40168-021-01167-x. Full text in Research Archive Show summary

  Background Children spend considerable time in daycare centers in parts of the world and are exposed to the indoor micro- and mycobiomes of these facilities. The level of exposure to microorganisms varies within and between buildings, depending on occupancy, climate, and season. In order to evaluate indoor air quality, and the effect of usage and seasonality, we investigated the spatiotemporal variation in the indoor mycobiomes of two daycare centers. We collected dust samples from different rooms throughout a year and analyzed their mycobiomes using DNA metabarcoding. Results The fungal community composition in rooms with limited occupancy (auxiliary rooms) was similar to the outdoor samples, and clearly different from the rooms with higher occupancy (main rooms). The main rooms had higher abundance of Ascomycota, while the auxiliary rooms contained comparably more Basidiomycota. We observed a strong seasonal pattern in the mycobiome composition, mainly structured by the outdoor climate. Most markedly, basidiomycetes of the orders Agaricales and Polyporales, mainly reflecting typical outdoor fungi, were more abundant during summer and fall. In contrast, ascomycetes of the orders Saccharomycetales and Capnodiales were dominant during winter and spring. Conclusions Our findings provide clear evidences that the indoor mycobiomes in daycare centers are structured by occupancy as well as outdoor seasonality. We conclude that the temporal variability should be accounted for in indoor mycobiome studies and in the evaluation of indoor air quality of buildings.

• Skrede, Inger (2021). Diversity and distribution of ligninolytic fungi. Advances in Botanical Research. ISSN 0065-2296. 99, p. 1–36. doi: 10.1016/bs.abr.2021.05.004. Full text in Research Archive Show summary

  Ligninolytic fungi is a large and heterogeneous group of species, mainly from the two phyla Ascomycota and Basidiomycota. They are the main players in the decomposition of wooden materials worldwide. In this chapter, the diversity and distribution of ligninolytic fungal species is presented. Attention is given to how the species diversity can be detected, as fungi are mainly living within their substrate and consequently may be difficult to observe. I present the current knowledge on how the species diversity originates, and the discovery of cryptic ligninolytic fungal species. I also focus on the distribution of ligninolytic fungi, both on how individuals are locally distributed on a single substrate of dead wood and on how species are distributed at larger scales. Across larger scales fungi are affected by the size and environmental conditions in local forests and large-scale climatic variables. The chapter ends with a discussion about conservation, with some perspectives for future research directions.

• Thoen, Ella; Harder, Christoffer Bugge; Kauserud, Håvard; Botnen, Synnøve Smebye; Vik, Unni & Taylor, Andy F.S. [Show all 8 contributors for this article] (2020). In vitro evidence of root colonization suggests ecological versatility in the genus Mycena. New Phytologist. ISSN 0028-646X. 227, p. 601–612. doi: 10.1111/nph.16545. Full text in Research Archive Show summary

  - The root‐associated habit has evolved on numerous occasions in different fungal lineages, suggesting a strong evolutionary pressure for saprotrophic fungi to switch to symbiotic associations with plants. Species within the ubiquitous, saprotrophic genus Mycena are frequently major components in molecular studies of root‐associated fungal communities, suggesting that an evaluation of their trophic status is warranted. Here, we report on interactions between a range of Mycena species and the plant Betula pendula. - In all, 17 Mycena species were inoculated onto B. pendula seedlings. Physical interactions between hyphae and fine roots were examined using differential staining and fluorescence microscopy. Physiological interactions were investigated using 14C and 32P to show potential transfer between symbionts. - All Mycena species associated closely with fine roots, showing hyphal penetration into the roots, which in some cases were intracellular. Seven species formed mantle‐like structures around root tips, but none formed a Hartig net. Mycena pura and Mycena galopus both enhanced seedling growth, with M. pura showing significant transfer of 32P to the seedlings. - Our results support the view that several Mycena species can associate closely with plant roots and some may potentially occupy a transitional state between saprotrophy and biotrophy.

• Seierstad, Kristian S.; Fossdal, Renate Myking; Miettinen, Otto; Carlsen, Tor; Skrede, Inger & Kauserud, Håvard (2020). Contrasting genetic structuring in the closely related basidiomycetes Trichaptum abietinum and Trichaptum fuscoviolaceum (Hymenochaetales). Fungal Biology. ISSN 1878-6146. 125(4), p. 269–275. doi: 10.1016/j.funbio.2020.11.001. Full text in Research Archive Show summary

  Trichaptum abietinum and Trichaptum fuscoviolaceum (Hymenochaetales, Basidiomycota) are closely related saprotrophic fungi, widely distributed on coniferous wood in temperate regions worldwide. Three intersterility groups have previously been detected in T. abietinum, while no prezygotic barriers have been proven within T. fuscoviolaceum. The aim of this study was to reveal the phylogeography and genetic relationship between these two closely related species and to explore whether the previously observed intersterility groups in T. abietinum are reflected in the genetic data. We assembled worldwide fruit body collections of both species (N = 314) and generated DNA sequences from three nuclear (ITS2, LSU, IGS) and one mitochondrial rDNA region (mtLSU). The two species are genetically well separated in all analyses. In correspondence with observations from earlier mating studies, our results revealed that T. fuscoviolaceum is genetically more uniform than T. abietinum. Multiple genetic sub-groups exist in T. abietinum that may correspond to the previously observed intersterility groups. However, there is low consistency across the investigated loci in delimiting the different sub-groups, except for a consistent North American group. As for many other widespread fungi, a complex phylogeographic pattern is found in T. abietinum which may have been formed by geographic, as well as multiple genetic intersterility barriers.

• Hess, Jaqueline; Balasundaram, Sudhagar V.; Bakkemo, Reneè Isabel; Drula, Elodie; Henrissat, Bernard & Högberg, Nils [Show all 8 contributors for this article] (2020). Niche differentiation and evolution of the wood decay machinery in the invasive fungus Serpula lacrymans. The ISME Journal. ISSN 1751-7362. p. 1–13. doi: 10.1038/s41396-020-00799-5. Full text in Research Archive Show summary

  Abstract Ecological niche breadth and the mechanisms facilitating its evolution are fundamental to understanding adaptation to changing environments, persistence of generalist and specialist lineages and the formation of new species. Woody substrates are structurally complex resources utilized by organisms with specialized decay machinery. Wood-decaying fungi represent ideal model systems to study evolution of niche breadth, as they vary greatly in their host range and preferred decay stage of the substrate. In order to dissect the genetic basis for niche specialization in the invasive brown rot fungus Serpula lacrymans , we used phenotyping and integrative analysis of phylogenomic and transcriptomic data to compare this species to wild relatives in the Serpulaceae with a range of specialist to generalist decay strategies. Our results indicate specialist species have rewired regulatory networks active during wood decay towards decreased reliance on enzymatic machinery, and therefore nitrogen-intensive decay components. This shift was likely accompanied with adaptation to a narrow tree line habitat and switch to a pioneer decomposer strategy, both requiring rapid colonization of a nitrogen-limited substrate. Among substrate specialists with narrow niches, we also found evidence for pathways facilitating reversal to generalism, highlighting how evolution may move along different axes of niche space.

• Skrede, Inger; Gonzalvo, Luis Ballester; Mathiesen, Cecilie & Schumacher, Trond (2020). The genera Helvella and Dissingia (Ascomycota: Pezizomycetes) in Europe – Notes on species from Spain. Fungal Systematics and Evolution. 6(1), p. 65–93. doi: 10.3114/fuse.2020.06.05. Full text in Research Archive Show summary

  Phylogenetic analyses of 115 newly collected Helvella specimens from Spain using three genetic markers [heat shock protein 90 ( hsp ), RNA polymerase II second largest subunit ( rpb2 ) and the nuclear large subunit ribosomal DNA (LSU)] confirm the assignment of the Spanish collections to one Dissingia and 30 Helvella species. The analyses were supplemented with an additional sample of 65 Spanish and extralimital Helvella specimens from the fungaria of Oslo (O), Trondheim (TRH), Copenhagen (C), Uppsala (UPS), Stockholm (S) and Venice (MCVE). Nine species are described as new, i.e. Helvella fuscolacunosa, H. hispanica, H. iberica, H. inexpectata, H. neopallescens, H. phlebophoroides, H. poculiformis , H. retinervis , and H. terricola . We present photographs of a selection of fresh specimens and provide descriptions of all species of this diverse South European Mediterranean element of the genera in Europe.

• Hansen, Karen; Schumacher, Trond; Skrede, Inger; Huhtinen, Seppo & Wang, Xianghua (2019). Pindara revisited – evolution and generic limits in Helvellaceae. Persoonia. ISSN 0031-5850. 42, p. 186–204. doi: 10.3767/persoonia.2019.42.07. Full text in Research Archive Show summary

  The Helvellaceae encompasses taxa that produce some of the most elaborate apothecial forms, as well as hypogeous ascomata, in the class Pezizomycetes (Ascomycota). While the circumscription of the Helvellaceae is clarified, evolutionary relationships and generic limits within the family are debatable. A robust phylogeny of the Helvellaceae, using an increased number of molecular characters from the LSU rDNA, RPB2 and EF-1α gene regions (4 299 bp) and a wide representative sampling, is presented here. Helvella s.lat. was shown to be polyphyletic, because Helvella aestivalis formed a distant monophyletic group with hypogeous species of Balsamia and Barssia. All other species of Helvella formed a large group with the enigmatic Pindara (/Helvella) terrestris nested within it. The ear-shaped Wynnella constitutes an independent lineage and is recognised with the earlier name Midotis. The clade of the hypogeous Balsamia and Barssia, and H. aestivalis is coherent in the three-gene phylogeny, and considering the lack of phenotypic characters to distinguish Barssia from Balsamia we combine species of Barssia, along with H. aestivalis, in Balsamia. The closed/tuberiform, sparassoid H. astieri is shown to be a synonym of H. lactea; it is merely an incidental folded form of the saddle-shaped H. lactea. Pindara is a sister group to a restricted Helvella, i.e., excluding the /leucomelaena lineage, on a notably long branch. We recognise Pindara as a separate genus and erect a new genus Dissingia for the /leucomelaena lineage, viz. H. confusa, H. crassitunicata, H. leucomelaena and H. oblongispora. Dissingia is supported by asci that arise from simple septa; all other species of Helvellaceae have asci that arise from croziers, with one exception being the /alpina-corium lineage of Helvella s. str. This suggests ascus development from croziers is the ancestral state for the Helvellaceae and that ascus development from simple septa has evolved at least twice in the family. Our phylogeny does not determine the evolutionary relationships within Helvella s.str., but it is most parsimonious to infer that the ancestor of the helvelloids produced subsessile or shortly stipitate, cup-shaped apothecia. This shape has been maintained in some lineages of Helvella s.str. The type species of Underwoodia, Underwoodia columnaris, is a sister lineage to the rest of the Helvellaceae.

• Skrede, Inger; Solbakken, Monica Hongrø; Hess, Jaqueline; Fossdal, Carl Gunnar; Hegnar, Olav Aaseth & Alfredsen, Gry (2019). Wood Modification by Furfuryl Alcohol Resulted in a Delayed Decomposition Response in Rhodonia (Postia) placenta. Applied and Environmental Microbiology. ISSN 0099-2240. 85(14), p. 1–21. doi: 10.1128/AEM.00338-19. Full text in Research Archive Show summary

  The aim of this study was to investigate differential expression profiles of the brown rot fungus Rhodonia placenta (previously Postia placenta) harvested at several time points when grown on radiata pine (Pinus radiata) and radiata pine with three different levels of modification by furfuryl alcohol, an environmentally benign commercial wood protection system. The entire gene expression pattern of a decay fungus was followed in untreated and modified wood from initial to advanced stages of decay. The results support the current model of a two-step decay mechanism, with the expression of genes related to initial oxidative depolymerization, followed by an accumulation of transcripts of genes related to the hydrolysis of cell wall polysaccharides. When the wood decay process is finished, the fungus goes into starvation mode after five weeks when grown on unmodified radiata pine wood. The pattern of repression of oxidative processes and oxalic acid synthesis found in radiata pine at later stages of decay is not mirrored for the high-furfurylation treatment. The high treatment level provided a more unpredictable expression pattern throughout the incubation period. Furfurylation does not seem to directly influence the expression of core plant cell wall-hydrolyzing enzymes, as a delayed and prolonged, but similar, pattern was observed in the radiata pine and the modified experiments. This indicates that the fungus starts a common decay process in the modified wood but proceeds at a slower pace as access to the plant cell wall polysaccharides is restricted. This is further supported by the downregulation of hydrolytic enzymes for the high treatment level at the last harvest point (mass loss, 14%). Moreover, the mass loss does not increase during the last weeks. Collectively, this indicates a potential threshold for lower mass loss for the high-furfurylation treatment. IMPORTANCE Fungi are important decomposers of woody biomass in natural habitats. Investigation of the mechanisms employed by decay fungi in their attempt to degrade wood is important for both the basic scientific understanding of ecology and carbon cycling in nature and for applied uses of woody materials. For wooden building materials, long service life and carbon storage are essential, but decay fungi are responsible for massive losses of wood in service. Thus, the optimization of durable wood products for the future is of major importance. In this study, we have investigated the fungal genetic response to furfurylated wood, a commercial environmentally benign wood modification approach that improves the service life of wood in outdoor applications. Our results show that there is a delayed wood decay by the fungus as a response to furfurylated wood, and new knowledge about the mechanisms behind the delay is provided.

• Thoen, Ella; Aas, Anders Bjørnsgard; Vik, Unni; Brysting, Anne Krag; Skrede, Inger & Carlsen, Tor [Show all 7 contributors for this article] (2019). A single ectomycorrhizal plant root system includes a diverse and spatially structured fungal community. Mycorrhiza. ISSN 0940-6360. 29(3), p. 167–180. doi: 10.1007/s00572-019-00889-z. Full text in Research Archive Show summary

  Although only a relatively small proportion of plant species form ectomycorrhizae with fungi, it is crucial for growth and survival for a number of widespread woody plant species. Few studies have attempted to investigate the fine scale spatial structure of entire root systems of adult ectomycorrhizal (EcM) plants. Here, we use the herbaceous perennial Bistorta vivipara to map the entire root system of an adult EcM plant and investigate the spatial structure of its root-associated fungi. All EcM root tips were sampled, mapped and identified using a direct PCR approach and Sanger sequencing of the internal transcribed spacer region. A total of 32.1% of all sampled root tips (739 of 2302) were successfully sequenced and clustered into 41 operational taxonomic units (OTUs). We observed a clear spatial structuring of the root-associated fungi within the root system. Clusters of individual OTUs were observed in the younger parts of the root system, consistent with observations of priority effects in previous studies, but were absent from the older parts of the root system. This may suggest a succession and fragmentation of the root-associated fungi even at a very fine scale, where competition likely comes into play at different successional stages within the root system.

• Løken, Solveig Bua; Skrede, Inger & Schumacher, Trond (2019). The Helvella corium species aggregate in Nordic countries - Phylogeny and species delimitation. Fungal Systematics and Evolution. 5, p. 169–186. doi: 10.3114/fuse.2020.05.13. Full text in Research Archive Show summary

  Mycologists have always been curious about the elaborate morphotypes and shapes of species of the genus Helvella. The small, black, cupulate Helvella specimens have mostly been assigned to Helvella corium, a broadly defined morpho-species. Recent phylogenetic analyses, however, have revealed an aggregate of species hidden under this name. We performed a multispecies coalescent analysis to re-assess species limits and evolutionary relationships of the Helvella corium species aggregate in the Nordic countries. To achieve this, we used morphology and phylogenetic evidence from five loci – heat shock protein 90 (hsp), translation elongation factor 1-alpha (tef), RNA polymerase II (rpb2), and the 5.8S and large subunit (LSU) of the nuclear ribosomal DNA. All specimens under the name Helvella corium in the larger university fungaria of Norway, Sweden and Denmark were examined and barcoded, using partial hsp and/or rpb2 as the preferential secondary barcodes in Helvella. Additional fresh specimens were collected in three years (2015–2018) to obtain in vivo morphological data to aid in species discrimination. The H. corium species aggregate consists of seven phylogenetically distinct species, nested in three divergent lineages, i.e. H. corium, H. alpina and H. pseudoalpina sp. nov. in the /alpina-corium lineage, H. alpestris, H. macrosperma and H. nannfeldtii in the /alpestris-nannfeldtii lineage, and H. alpicola as a weakly supported sister to the /alpestris-nannfeldtii lineage. Among the seven species, the ribosomal loci expressed substantial variation in evolutionary rates, suggesting care in the use of these regions alone in delimitation of Helvella species. Altogether, 469 out of 496 available fungarium specimens were successfully barcoded.

• Balasundaram, Sudhagar; Hess, Jaqueline; Durling, Mikael Brandström; Moody, Suzy C.; Thorbek, Birgitte Lisbeth Graae & Progida, Cinzia [Show all 15 contributors for this article] (2018). The fungus that came in from the cold: dry rot’s pre-adapted ability to invade buildings. The ISME Journal. ISSN 1751-7362. 12(3), p. 791–801. doi: 10.1038/s41396-017-0006-8. Full text in Research Archive
• Hess, Jaqueline; Skrede, Inger; Mares, Maryam Chaib De; Hainaut, Matthieu; Henrissat, Bernard & Pringle, Anne (2018). Rapid Divergence of Genome Architectures Following the Origin of an Ectomycorrhizal Symbiosis in the Genus Amanita. Molecular Biology and Evolution (MBE). ISSN 0737-4038. 35(11), p. 2786–2804. doi: 10.1093/molbev/msy179. Full text in Research Archive Show summary

  Fungi are evolutionary shape shifters and adapt quickly to new environments. Ectomycorrhizal (EM) symbioses are mutualistic associations between fungi and plants and have evolved repeatedly and independently across the fungal tree of life, suggesting lineages frequently reconfigure genome content to take advantage of open ecological niches. To date analyses of genomic mechanisms facilitating EM symbioses have involved comparisons of distantly related species, but here, we use the genomes of three EM and two asymbiotic (AS) fungi from the genus Amanita as well as an AS outgroup to study genome evolution following a single origin of symbiosis. Our aim was to identify the defining features of EM genomes, but our analyses suggest no clear differentiation of genome size, gene repertoire size, or transposable element content between EM and AS species. Phylogenetic inference of gene gains and losses suggests the transition to symbiosis was dominated by the loss of plant cell wall decomposition genes, a confirmation of previous findings. However, the same dynamic defines the AS species A. inopinata, suggesting loss is not strictly associated with origin of symbiosis. Gene expansions in the common ancestor of EM Amanita were modest, but lineage specific and large gene family expansions are found in two of the three EM extant species. Even closely related EM genomes appear to share few common features. The genetic toolkit required for symbiosis appears already encoded in the genomes of saprotrophic species, and this dynamic may explain the pervasive, recurrent evolution of ectomycorrhizal associations.

• Balasundaram, Sudhagar Veerabadran; Hess, Jaqueline; Durling, Mikael Brandström; Moody, Suzy Clare; Thorbek, Lisbeth & Progida, Cinzia [Show all 15 contributors for this article] (2018). The fungus that came in from the cold: dry rot’s pre-adapted ability to invade buildings. The ISME Journal. ISSN 1751-7362. 12(3), p. 791–801. doi: 10.1038/s41396-017-0006-8. Full text in Research Archive
• Skrede, Inger; Carlsen, Tor & Schumacher, Trond (2017). A synopsis of the saddle fungi (Helvella: Ascomycota) in Europe – species delimitation, taxonomy and typification. Persoonia. ISSN 0031-5850. 39, p. 201–253. doi: 10.3767/persoonia.2017.39.09. Full text in Research Archive Show summary

  Helvella is a widespread, speciose genus of large apothecial ascomycetes (Pezizomycete: Pezizales) that are found in terrestrial biomes of the Northern and Southern Hemispheres. This study represents a beginning on assessing species limits and applying correct names for Helvella species based on type material and specimens in the university herbaria (fungaria) of Copenhagen (C), Harvard (FH) and Oslo (O). We use morphology and phylogenetic evidence from four loci – heat shock protein 90 (hsp), translation elongation factor alpha (tef), RNA polymerase II (rpb2) and the nuclear large subunit ribosomal DNA (LSU) – to assess species boundaries in an expanded sample of Helvella specimens from Europe. We combine the morphological and phylogenetic information from 55 Helvella species from Europe with a small sample of Helvella species from other regions of the world. Little intraspecific variation was detected within the species using these molecular markers; hsp and rpb2 markers provided useful barcodes for species delimitation in this genus, while LSU provided more variable resolution among the pertinent species. We discuss typification issues and identify molecular characteristics for 55 European Helvella species, designate neo- and epitypes for 30 species, and describe seven Helvella species new to science, i.e., H. alpicola, H. alpina, H. carnosa, H. danica, H. nannfeldtii, H. pubescens and H. scyphoides.

• Balasundaram, Sudhagar Veerabadran; Engh, Ingeborg Bjorvand; Skrede, Inger & Kauserud, Håvard (2015). How many DNA markers are needed to reveal cryptic fungal species? Fungal Biology. ISSN 1878-6146. 119(10), p. 940–945. doi: 10.1016/j.funbio.2015.07.006. Full text in Research Archive
• Balasundaram, Sudhagar; Engh, Ingeborg Bjorvand; Skrede, Inger & Kauserud, Håvard (2015). How many DNA markers are needed to reveal cryptic fungal species? Fungal Biology. ISSN 1878-6146. 119(10), p. 940–945. doi: 10.1016/j.funbio.2015.07.006. Full text in Research Archive
• Gustafsson, A Lovisa S; Skrede, Inger; Rowe, Heather C.; Gussarova, Galina; Borgen, Liv & Rieseberg, Loren [Show all 8 contributors for this article] (2014). Genetics of cryptic speciation within an arctic Mustard, Draba nivalis. PLOS ONE. 9(4). doi: 10.1371/journal.pone.0093834. Full text in Research Archive Show summary

  Crossing experiments indicate that hybrid sterility barriers frequently have developed within diploid, circumpolar plant species of the genus Draba. To gain insight into the rapid evolution of postzygotic reproductive isolation in this system, we augmented the linkage map of one of these species, D. nivalis, and searched for quantitative trait loci (QTLs) associated with reproductive isolation. The map adds 63 new dominant markers to a previously published dataset of 31 co-dominant microsatellites. These markers include 52 amplified fragment length polymorphisms (AFLPs) and 11 sequence-specific amplified polymorphisms (SSAPs) based on retrotransposon sequence. 22 markers displaying transmission ratio distortion were further included in the map. We resolved eight linkage groups with a total map length of 894 cM. Significant genotype-trait associations, or quantitative trait loci (QTL), were detected for reproductive phenotypes including pollen fertility (4 QTLs), seed set (3 QTLs), flowering time (3 QTLs) and number of flowers (4 QTLs). Observed patterns of inheritance were consistent with the influence of both nuclear-nuclear interactions and chromosomal changes on these traits. All seed set QTLs and one pollen fertility QTL displayed underdominant effects suggestive of the involvement of chromosomal rearrangements in hybrid sterility. Interestingly, D. nivalis is predominantly self-fertilizing, which may facilitate the establishment of underdominant loci and contribute to reproductive isolation.

• Maurice, Sundy; Skrede, Inger; LeFloch, Gaetan; Barbier, Georges & Kauserud, Håvard (2014). Population structure of Serpula lacrymans in Europe with an outlook to the French population. Mycologia. ISSN 0027-5514. 106(5), p. 889–895. doi: 10.3852/12-344. Full text in Research Archive
• Hess, Jaqueline; Skrede, Inger; Wolfe, Benjamin E.; LaButti, Kurt; Ohm, Robin A. & Grigoriev, Igor V. [Show all 7 contributors for this article] (2014). Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi. Genome Biology and Evolution (GBE). 6(7), p. 1564–1578. doi: 10.1093/gbe/evu121. Full text in Research Archive
• Skrede, Inger; Maurice, Sandy & Kauserud, Håvard (2013). Molecular Characterization of Sexual Diversity in a Population of Serpula lacrymans, a Tetrapolar Basidiomycete. G3: Genes, Genomes, Genetics. 3(2), p. 145–152. doi: 10.1534/g3.112.003731. Full text in Research Archive
• Kauserud, Håvard; Knudsen, Henning; Högberg, Nils & Skrede, Inger (2012). Evolutionary origin, worldwide dispersal, and population genetics of the dry rot fungus Serpula lacrymans. Fungal Biology Reviews. ISSN 1749-4613. 26(2-3), p. 84–93. doi: 10.1016/j.fbr.2012.08.001. Full text in Research Archive
• Skrede, Inger; Carlsen, Tor; Stensrud, Øyvind & Kauserud, Håvard (2012). Genome wide AFLP markers support cryptic species in Coniophora (Boletales). Fungal Genetics and Biology. ISSN 1087-1845. 116(7), p. 778–784. doi: 10.1016/j.funbio.2012.04.009. Full text in Research Archive
• Eastwood, Daniel C.; Floudas, Dimitrios; Binder, Manfred; Majcherczyk, Andrzej; Schneider, Patrick & Aerts, Andrea [Show all 48 contributors for this article] (2011). The Plant Cell Wall-Decomposing Machinery Underlies the Functional Diversity of Forest Fungi. Science. ISSN 0036-8075. 333(6043), p. 762–765. doi: 10.1126/science.1205411. Full text in Research Archive Show summary

  Brown rot decay removes cellulose and hemicelluloses from wood, residual lignin contributing up to 30% of forest soil carbon, and is derived from an ancestral white rot saprotrophy where both lignin and cellulose are decomposed. Comparative and functional genomics of the “dry rot” fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy was accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and belowground biota.

• Skrede, Inger; Engh, Ingeborg Bjorvand; Binder, Manfred; Carlsen, Tor; Kauserud, Håvard & Bendiksby, Mika (2011). Evolutionary history of Serpulaceae (Basidiomycota): molecular phylogeny, historical biogeography and evidence for a single transition of nutritional mode. BMC Evolutionary Biology. 11(230). doi: 10.1186/1471-2148-11-230. Full text in Research Archive
• Engh, Ingeborg Bjorvand; Skrede, Inger; Sætre, Glenn-Peter & Kauserud, Håvard (2010). High variability in a mating type linked region in the dry rot fungus Serpula lacrymans caused by frequency-dependent selection? BMC Genetics. 11. doi: 10.1186/1471-2156-11-64. Full text in Research Archive Show summary

  Background The mating type loci that govern the mating process in fungi are thought to be influenced by negative frequency-dependent selection due to rare allele advantage. In this study we used a mating type linked DNA marker as a proxy to indirectly study the allelic richness and geographic distribution of mating types of one mating type locus (MAT A) in worldwide populations of the dry rot fungus Serpula lacrymans. This fungus, which causes serious destruction to wooden constructions in temperate regions worldwide, has recently expanded its geographic range with a concomitant genetic bottleneck. Results High allelic richness and molecular variation was detected in the mating type linked marker as compared to other presumably neutral markers. Comparable amounts of genetic variation appeared in the mating type linked marker in populations from nature and buildings, which contrast the pattern observed with neutral genetic markers where natural populations were far more variable. Some geographic structuring of the allelic variation in the mating type linked marker appeared, but far less than that observed with neutral markers. In founder populations of S. lacrymans, alleles co-occurring in heterokaryotic individuals were more divergent than expected by chance, which agrees with the expectation for populations where few mating alleles exists. The analyzed DNA marker displays trans-species polymorphism wherein some alleles from the closely related species S. himantoides are more similar to those of S. lacrymans than other alleles from S. himantoides. Conclusions Our results support the idea that strong negative frequency-dependent selection maintains high levels of genetic variation in MAT-linked genomic regions, even in recently bottlenecked populations of S. lacrymans.

• Skrede, Inger; Carlsen, Tor; Rieseberg, LH & Brochmann, Christian (2009). Microsatellites for three distantly related genera in the Brassicaceae. Conservation Genetics. ISSN 1566-0621. 10(3), p. 643–648. doi: 10.1007/s10592-008-9598-x. Full text in Research Archive

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• Naranjo-Ortiz, Miguel Angel; Skrede, Inger; Peris, David; Krabberød, Anders Kristian; Lü, Dabao Sun & Bendiksby, Mika (2025). Expansive pangenome sin the Agaricomycetes. Full text in Research Archive Show summary

  Trichaptum abietinum (Dicks.) Ryvarden (Hymenochaetales) is a pioneer wood rot mushroom common across the Northern Hemisphere, usually growing on conifer wood. The species has emerged in recent years as a model for mushroom genomics, and extensive genomic resources are available. Here, we have analyzed patterns of gene presence-absence variation across a dataset covering T. abietinum known intraspecific geographical and genetic diversity. Our results suggest that Trichaptum abietinum has a large proportion of its genome under Presence-Absence variation, over 40% of all genes for any particular strain. This pattern seem to be common across Agaricomycetes, but not across other groups of Fungi. Core and accessory genes have distinct properties. Core genes also tend to cluster towards chromosome centers, while accessory genes are more abundant at the extremes. Core genes tend to be longer, have more introns and appear closer to other genes. Distribution of Accessory genes across the species depends on genetic distance, but this variable alone can only explain a fraction of the observed pattern. Unlike most other groups of fungi that tend to be haploid, Agaricomycetes spend most of their life cycle as a dikaryotic mycelium. Cell division in this mycelium is typically tightly regulated, which would be unnecessary were this a simple diploid. We hypothesize that extensive PAV has the potential of causing interference during mitotic recombination events, thus promoting genomic unstability. This is then prevented by keeping the two nuclei separated until meiosis. This life cycle would allow these fungi to access a much larger gene pool than it would be possible for any single haploid genet.

• Skrede, Inger; Kauserud, Håvard; Martin-Sanchez, Pedro María; Estensmo, Eva Lena Fjeld; Botnen, Synnøve Smebye & Morgado, Luis [Show all 8 contributors for this article] (2024). Fungal diversity in daycare centers and private homes – yeast play in daycares while the molds stay at home. Full text in Research Archive
• Ronikier, Michal; Suchan, Tomasz; White, Dawson; Ree, Richard; Meireles, Jose & Brochmann, Christian [Show all 7 contributors for this article] (2024). Divergent lineages reveal a complex biogeographical history in the European range of the arctic-alpine keystone species Dryas octopetala. Full text in Research Archive
• Ortiz, Miguel Angel Naranjo; Skrede, Inger; Bendiksby, Mika; Lü, Dabao Sun; Navarro, David Peris & Krabberød, Anders Kristian (2024). Pangenome analyses of the mushroom Trichaptum abietinum (Hymenochaetales) reveals extensive presence-absence variation. Full text in Research Archive
• Skrede, Inger; Peris, David; Lü, Dabao Sun & Håvard, Kauserud (2024). TBD. Full text in Research Archive
• Maurice, Sundy; Miettinen, Otto; Boddy, Lynne; Navarro, David; Chaduli, Delphine & Recorder, Monica [Show all 10 contributors for this article] (2024). Is no company better than the wrong company? Fungal assembly history in dead wood decomposition. Full text in Research Archive
• Angel, Naranjo-Ortiz Miguel; Skrede, Inger; Peris, David; Krabberød, Anders K; Lü, Dabao Sun & Bendiskby, Mika (2024). Pangenome analyses of the mushroom Trichaptum abietinum (Hymenochaetales) revel extensive pressence-absence variation. Full text in Research Archive
• Lü, Dabao Sun; Methlie, Ine-Susanne Hopland; Vera-Castellanos, M; Henrik, Sønstebø Jørn; A, Andersen & Helleland, K [Show all 10 contributors for this article] (2024). Investigating the history and consequences of secondary contact between divergent populations of Trichaptum abietinum in Europe. Full text in Research Archive
• Ronold, Eivind Kverme; Maurice, Sundy; Torp, Vilde Åvesland; Kostich-Nilsen, Celina Alexandria; Methlie, Ine-Susanne Hopland & Schmidt, Frida [Show all 17 contributors for this article] (2024). USING eDNA TO ASSESS THE EFFECTS OF CLEAR-CUTTING FORESTRY ON FUNGAL DIVERSITY IN BOREAL SPRUCE FORESTS. Full text in Research Archive
• Lü, Dabao Sun; Peris, David; Sønstebø, Jørn Henrik; James, Timothy Y.; Rieseberg, Loren H. & Maurice, Sundy [Show all 9 contributors for this article] (2024). Article Reticulate evolution and rapid development of reproductive barriers upon secondary contact in a forest fungus. Full text in Research Archive
• Orellana-Muñoz, Sara; Borg, Nora; Nygård, Elise; Kauserud, Håvard; Skrede, Inger & Peris, David (2023). Yeast bioprospecting and genomics for a food circular bioeconomy. Full text in Research Archive
• Orellana-Muñoz, Sara; Stelkens, Rike; Kauserud, Håvard; Skrede, Inger & Peris, David (2023). Generating a large collection of Saccharomyces polyploids to study their adaptation to food-related industrial conditions. Full text in Research Archive
• Andersen, Anneli; Lü, Dabao Sun; Helleland, Kathleen Theresia; Methlie, Ine-Susanne Hopland; Castellanos, Michelle Vera & Kauserud, Håvard [Show all 7 contributors for this article] (2023). Investigating the extent, history and outcomes of secondary contact between divergent populations of Trichaptum abietinum in Norway. Full text in Research Archive
• Lü, Dabao Sun; Peris, David; Sønstebø, Jørn Henrik; Maurice, Sundy; Kauserud, Håvard & Ravinet, Mark [Show all 7 contributors for this article] (2023). Population genomics reveal multiple lineages with leaky intersterility barriers in the widespread forest fungus Trichaptum abietinum. Full text in Research Archive
• Lü, Dabao Sun; Peris, David; Sønstebø, Jørn Henrik; Maurice, Sundy; Kauserud, Håvard & Ravinet, Mark [Show all 7 contributors for this article] (2023). Understanding the nature of the reproductive barriers within the wood decay species Trichaptum abietinum. Full text in Research Archive
• Skrede, Inger (2022). Fungal divergence and speciation – examples from wood decay fungi. Full text in Research Archive
• Orellana-Muñoz, Sara; Stelkens, Rike; Kauserud, Håvard; Skrede, Inger & Peris, David (2022). A high-throughput pipeline for studying the effects of polyploidization during adaptive evolution in yeasts. Full text in Research Archive
• Lü, Dabao Sun; Peris, David; Sønstebø, Jørn Henrik; Maurice, Sundy; Kauserud, Håvard & Ravinet, Mark [Show all 7 contributors for this article] (2022). Understanding the nature of the reproductive barriers within the wood decay species Trichaptum abietinum. Full text in Research Archive
• Peris, David; Lü, Dabao Sun; Kinneberg, Vilde Bruhn; Methlie, Ine-Susanne Hopland; Dahl, Malin Stapnes & James, Timothy Y. [Show all 8 contributors for this article] (2022). Long-term balancing selection in a white-root fungi. Full text in Research Archive
• Kinneberg, Vilde Bruhn; Lü, Dabao Sun; Peris, David; Ravinet, Mark & Skrede, Inger (2022). Ancient introgression between highly divergent fungal sister species. Full text in Research Archive
• Navarro, David Peris; Lü, Dabao Sun; Kinneberg, Vilde Bruhn; Methlie, Ine-Susanne Hopland; James, Timothy & Kauserud, Håvard [Show all 7 contributors for this article] (2022). Ancient mating alleles maintained by balancing selection in basidiomycete fungi. Full text in Research Archive
• Lü, Dabao Sun; Navarro, David Peris; Sønstebø, Jørn Henrik; Maurice, Sundy; Kauserud, Håvard & Ravinet, Mark [Show all 7 contributors for this article] (2022). Global phylogeography of a wood decay fungus indicates reinforcement on secondary contact. Full text in Research Archive
• Skrede, Inger (2022). Fungal divergence and speciation – examples from wood decay fungi. Full text in Research Archive
• Lü, Dabao Sun; Methlie, Ine-Susanne Hopland; Navarro, David Peris; Kauserud, Håvard & Skrede, Inger (2022). Postglacial history of a widespread forest fungus in Europe: Migration out of multiple refugia followed by secondary admixture. Full text in Research Archive
• Skrede, Inger (2022). Fungal divergence and speciation – examples from wood decay fungi. Full text in Research Archive
• Birkemoe, Tone; Skrede, Inger & Methlie, Ine-Susanne Hopland (2022). Mindre mat for kresne biller. https://forskning.no/. Full text in Research Archive
• Peris, David; Lü, Dabao Sun; Kinneberg, Vilde Bruhn; Methlie, Ine-Susanne Hopland; Dahl, Malin Stapnes & James, Timothy Y. [Show all 8 contributors for this article] (2021). Northern hemisphere fungal specimens unravel dynamic and polymorphic nature of mating loci. Full text in Research Archive
• Lu, Dabao Sun; Skrede, Inger; Kauserud, Håvard; Navarro, David Peris; Sønstebø, Jørn Henrik & Maurice, Sandy [Show all 7 contributors for this article] (2020). Population genomics of Trichaptum abietinum - a window into fungal speciation. Full text in Research Archive
• Lu, Dabao Sun; Skrede, Inger; Kauserud, Håvard; Navarro, David Peris; Maurice, Sandy & Ravinet, Mark [Show all 7 contributors for this article] (2020). Population genomics of Trichaptum abietinum - a window into fungal speciation. Full text in Research Archive
• Hess, Jaqueline; Balasundaram, Sudhagar; Bakkemo, Reneè Isabel; Drula, Elodie; Henrissat, Bernard & Högberg, Nils [Show all 8 contributors for this article] (2020). Niche differentiation underlies evolution of the wood decay machinery in the invasive fungus Serpula lacrymans. Full text in Research Archive
• Skrede, Inger (2019). How to decompose a house? Comparative and population genomic analyses of the dry rot fungus. Full text in Research Archive
• Skrede, Inger; Hess, Jaqueline; Eastwood, Daniel C. & Kauserud, Håvard (2018). Evolutionary necessities for invading buildings, comparative and population genomic analyses of the dry rot fungus. Full text in Research Archive
• Skrede, Inger (2018). Artsbestemmelse i soppslekten Helvella– Hvorfor og hvordan? Full text in Research Archive
• Skrede, Inger; Hess, Jaqueline; Sønstebø, Jørn Henrik; Maurice, Sundy Ursula Mary Jane; Eastwood, Daniel C. & Kauserud, Håvard (2018). How to decompose a house? Comparative and population genomic analyses of the dry rot fungus. Full text in Research Archive
• Tørresen, Ole K.; Skrede, Inger; Sandve, Simen Rød; Jentoft, Sissel; Jakobsen, Kjetill Sigurd & Borge, Ole Johan (2018). Gendykk i norsk natur gir ny kunnskap. Genialt. ISSN 0804-225X. p. 16–18. Full text in Research Archive
• Skrede, Inger; Hess, Jaqueline; Balasundaram, Sudhagar; Högberg, Nils; Maurice, Sundy Ursula Mary Jane & Kohler, Annegret [Show all 9 contributors for this article] (2017). Evolutionary necessities for invading buildings, comparative and population genomic analyses in the dry rot fungus. Full text in Research Archive
• Skrede, Inger (2016). Evolutionary necessities for invading buildings, comparative and population genomic analyses in the dry rot fungus. Full text in Research Archive
• Skrede, Inger; Hess, Jaqueline; Balasundaram, Sudhagar; Kauserud, Håvard; Eastwood, Daniel C. & Högberg, Nils [Show all 10 contributors for this article] (2016). Invasiveness of the harmful house-invader Serpula lacrymans – population genomics of the Japanese and European populations. Full text in Research Archive
• Bakkemo, Reneé Isabel; Hess, Jaqueline & Skrede, Inger (2016). Comparative genomics of dry rot fungus Serpula lacrymans reveal nutrient transport mechanisms. Full text in Research Archive
• Hess, Jaqueline; Balasundaram, Sudhagar; Eastwood, Daniel C.; Durling, Mikael Brandström; Fossdal, Carl Gunnar & Högberg, Nils [Show all 8 contributors for this article] (2016). Exploring specialization in wood decay mechanisms in the harmful house-invader Serpula lacrymans using an evolutionary transcriptomics approach. Full text in Research Archive
• Skrede, Inger; Hess, Jaqueline; Balasundaram, Sudhagar; Kauserud, Håvard; Eastwood, Daniel C. & Boddy, Lynne M [Show all 9 contributors for this article] (2016). The fungus that came in from the cold: Dry rots pre-adapted ability to invade buildings. Full text in Research Archive
• Skrede, Inger & Durling, Mikael Brandström (2015). Population genomic analyses revealpossible drivers of populationdivergence. Molecular Ecology. ISSN 0962-1083. 24, p. 2598–2600. doi: 10.1111/mec.13209. Full text in Research Archive
• Skrede, Inger; Carlsen, Tor & Schumacher, Trond (2015). Artsavgrensning i slekten Helvella ved hjelp av morfologi og molekylære markører ble langt mer utfordrende enn vi hadde regnet med. Full text in Research Archive
• Hess, Jaqueline & Skrede, Inger (2015). Genomics of the destructive dry rot fungus. META. ISSN 1890-1956. p. 16–19. Full text in Research Archive
• Skrede, Inger; Hess, Jaqueline; Balasundaram, Sudhagar; Eastwood, D; Kohler, Annegret & Murat, Claude [Show all 11 contributors for this article] (2015). Invasiveness of the harmful house decomposer Serpula lacrymans - population genomic approaches. Full text in Research Archive
• Skrede, Inger; Carlsen, Tor & Schumacher, Trond (2014). Molecular systematics of the genus Helvella redefines species boundaries and uncover high species diversity. Full text in Research Archive
• Skrede, Inger; Durling, Mikael Brandström; Stenlid, Jan; Kauserud, Håvard & Högberg, Nils (2010). Comparative genomics of various lineages of the dry rot fungus Serpula lacrymans. Full text in Research Archive
• Skrede, Inger; Durling, Mikael Brandström; Stenlid, Jan; Kauserud, Håvard & Högberg, Nils (2010). Comparative genomics of various lineages of the dry rot fungus Serpula lacrymans. Full text in Research Archive
• Ronold, Eivind Kverme; Kauserud, Håvard; Maurice, Sundy & Skrede, Inger (2025). Concerning fungi: Community ecology and diversity in natural and managed boreal forests. Universitetet i Oslo. Full text in Research Archive Show summary

  Fungal communities in Norwegian forests are highly diverse and species-rich. Fulfilling roles as mutualists, pathogens, parasites and decomposers, it is hard to imagine how a forest ecosystem would function without fungi. In this thesis I describe fungal communities in Norwegian boreal forests and how they are structured by the environment and the composition of vegetation and how forestry may impact fungal communities following clear-cutting. In the first paper I use DNA-metabarcoding to describe how soil fungal communities in a forest reserve with negligible human impact are structured and influenced by the vegetation composition, soil edaphic parameters and topographic factors in the landscape. Soil was sampled along several transects representing transition from moist, shaded spruce forests to dry and topographically exposed pine forests, a common landscape characteristic in boreal ecosystem. I show that vegetation composition is the major driver of fungal community structure, more so than either topography or soil parameters. This likely reflects the tight symbiosis between many fungal species and plants, and the fact that vegetation and soil fungi are structured by similar processes over longer time scales. The next three papers are from the EcoForest project, investigating fungal communities in south-eastern Norwegian spruce forests in the context of clear-cutting and long-term regeneration of community composition. By setting up 12 paired forest sites, with a plot in a five-to-nine-decade old previously clear-cut forest and a nearby plot in a forest that has never been clear-cut, we aim to investigate to what extent fungal communities in soil and deadwood y recover following clear-cutting, using the near-natural sites as reference. Applying DNA-metabarcoding, I found no differences in species richness or species diversity between soil fungal communities in the previous clear-cut and the near-natural forests. Instead, species identity and the relative abundances of species in the community are different. Previously clear-cut plots seemingly have a larger abundance of soil fungi adapted for faster nutrient turnover and more accessible forms of nutrients, while the near-natural forest soil fungal communities supported more slow-growing fungi adapted to accessing organically bound nutrients and slower nutrient turnover. I also describe a long-term shift in the deadwood-inhabiting fungal communities. Many wood-decomposing fungi in the Polyporales, Hymenochaetales and Helotiales were more abundant in near-natural forest sites. This was not simply due to the forest type but was strongly driven by the diversity and variability of the deadwood on the forest floor. In essence, a previous clear-cut forest with high diversity of deadwood would host higher fungal richness and diversity than a near-natural forest with low deadwood variability. The majority of red-listed fungal species, however, were restricted to the near-natural forests. I found, in addition, a vast diversity of yeasts outnumbering the more conspicuous deadwood decomposing fungi. This community also exhibited compositional shifts in response to deadwood variability among sites. Finally, I combine the data from soil and deadwood to investigate how certain species in the ectomycorrhizal community may grow and proliferate within deadwood on the forest floor. The few ectomycorrhizal species inhabiting deadwood were consistent across sites and comprised species known to access and mobilize nitrogen bound in complex organic forms. For some species this may represent an important adaptation in boreal forest soils, where soluble nitrogen is generally low and competition with soil saprotrophs is high, additionally, there is competition with other ectomycorrhizal species more specialized for the fast absorption of mineral nutrients. Deadwood on the forest floor may thus act as “nutrient banks” for certain ectomycorrhizal species adapted to this habitat, characterized by low carbon availability, but high concentrations of organic nitrogen and other vital nutrients.

• Braut-Solheim, Astrid; Baalsrud, Helle Tessand; Skrede, Inger & Methlie, Ine-Susanne Hopland (2024). A population genomic study of the effect of clear-cut forestry on the beetle Gyrophaena boleti. Norges miljø- og biovitenskapelige universitet (NMBU). Full text in Research Archive Show summary

  The boreal forest is the home to several thousands of species, and about 2/3 of the forests are under management, mostly for timber production. In Norway only two percent of the forests are natural, and only 21% of this area is protected. The main logging strategy in Norway is clear-cutting followed by planting, altering the composition of both living trees and dead wood. Clear-cut forests are in particular danger of losing biodiversity. Gyrophaena boleti is a small rove beetle inhabiting bracket fungi in these forests, living in both mature previously clear-cut and near-natural forests. How the different management strategies are affecting the genetic diversity of this beetle is currently unknown. Utilizing pooled whole genome sequencing to do a population genomic study of G. boleti from nine paired forest sites, we show that G. boleti in the clear-cut forests tend to have slightly lower genetic diversity than G. boleti from near-natural forests. Although generally the genetic diversity is high. We also found little genome-wide population structure between sites with paired forest stands. However, we found peaks of differentiation between populations in different forest sites and stands which could be genomic regions involved in local adaptation. This is the first genomic study of the species G. boleti, contributing to the knowledge of how small, specialized insect species are affected by habitat change. This understanding could help support the development of conservation strategies and management practices of the boreal forests.

• Lü, Dabao Sun; Peris, David; Skrede, Inger; Kauserud, Håvard; Ravinet, Mark & Sønstebø, Jørn Henrik [Show all 8 contributors for this article] (2023). Fungi contain multitudes: Tempo and modes of evolution in the purplepore bracket fungus Trichaptum. Universitetet i Oslo. Full text in Research Archive Show summary

  Evolution has brought to life an immense diversity of forms, lifestyles and species in the fungi. Yet our knowledge about how this diversity has been generated remains sparse. I have taken a closer look at evolution in a group of wood decay fungi in genus Trichaptum, with the aim of gaining more insight about the speciation process in fungi. Trichaptum species are common, easy to culture, and can be crossed in the lab. Moreover, they have varying degrees of reproductive barriers, and these attributes make them suitable for speciation studies as the development of reproductive barriers is central to the speciation process. I have established a comprehensive culture collection that have been put through crossing experiments and whole genome DNA sequencing to investigate the evolutionary history of different Trichaptum lineages and the genetic causes of their reproductive barriers. Analyses of the sequenced genomes revealed multiple hybridization events, which speaks to the importance of reticulate evolution in these fungi. The studies cover evolution in genus Trichaptum at multiple scales, from the relatively recent changes occurring within Europe in T. abietinum, to changes that have happened between continents and distinctly differentiated species across larger time spans. Altogether this work demonstrates how multiple evolutionary forces across different temporal and genetic scales have interacted to shape the current diversity and genomic landscape in Trichaptum.

• Andreasen, Mathias; Skrede, Inger & Nordén, Björn (2020). Lophiostomataceae and Lophiotremataceae. A phylogenetic and taxonomic study of two ascomycete families. Master of Science thesis : Bioscience - BIOS5960 60 ECTS. Universiitet i Oslo. Full text in Research Archive

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