Dabao Sun Lü

• 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.

• 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.

• 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.

• 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.

• 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.

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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.

• 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
• 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
• 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
• Lü, Dabao Sun (2024). Investigating the history and consequences of secondary contact between divergent populations of Trichaptum abietinum in Europe. 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 (2023). Artsdannelse og evolusjon i fiolkjuke 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
• Aakre, Gina & Lü, Dabao Sun (2023). Er soppuniverset i The Last of Us realistisk? [Internet]. Titan. 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
• 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
• 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
• Lü, Dabao Sun (2021). Inferring the origin of reproductive barriers in the purplepore bracket fungus Trichaptum abietinum. Full text in Research Archive
• Lü, Dabao Sun (2021). Inferring the origin of reproductive barriers in the purplepore bracket fungus Trichaptum abietinum. Full text in Research Archive
• Lü, Dabao Sun (2021). Inferring the origin of reproductive barriers in the purplepore bracket fungus Trichaptum abietinum. Full text in Research Archive
• Lü, Dabao Sun (2021). Inferring the origin of reproductive barriers in the purplepore bracket fungus Trichaptum abietinum. 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
• 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.

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