Publications

Modeling of Biodiversity Dynamics After Forest Clear-cutting by Plot Aggregation

Wigren, Torbjörn; Zachariah, Dave; Jie, Vun Wen; Andermann, Tobias et al.

2026

Report

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Transcriptional divergence among different mating-type strains and their cross of Morchella sextelata during the asexual stage

Ling, Jia; Chen, Meng-Qian; Ryberg, Martin; Yang, Zhu L. et al.

Part of Fungal Biology, 2026

Article in journal

• DOI for Transcriptional divergence among different mating-type strains and their cross of Morchella sextelata during the asexual stage

Quantifying the impact of forestry practices on biodiversity using causal inference methods

Jie, Vun Wen; Nyström, Jakob; Wigren, Torbjörn; Schön, Thomas B. et al.

2026

Conference paper

Living in each other's pockets: insights into the life cycle of Tremella caloplacae s. l.

Freire-Rallo, Sandra; Tuovinen Nogerius, Veera; Wedin, Mats; Millanes, Ana M.

Part of IMA Fungus, 2026

Article in journal

• DOI for Living in each other's pockets: insights into the life cycle of Tremella caloplacae s. l.
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Environmental phylogenetics supports a steady diversification of crown eukaryotes starting from the mid-Proterozoic

Sandin, Miguel M.; Cohen, Phoebe A.; Morlon, Helene; Burki, Fabien

Part of Proceedings of the National Academy of Sciences of the United States of America, 2026

Article in journal

• DOI for Environmental phylogenetics supports a steady diversification of crown eukaryotes starting from the mid-Proterozoic
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Another dark taxon comes to light: Semicentenialomycetes, a new class within the Pucciniomycotina (Basidiomycota), and its first described representative, Semicentenialea rex

Tuovinen Nogerius, Veera; Sanchez-Garcia, Marisol; Kluting, Kerri; Heinonsalo, Jussi et al.

Part of IMA Fungus, 2026

Article in journal

• DOI for Another dark taxon comes to light: Semicentenialomycetes, a new class within the Pucciniomycotina (Basidiomycota), and its first described representative, Semicentenialea rex
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Revealing the plastid symbioses in the marine centrohelid Meringosphaera: a novel model system for plastid evolution

Walraven, Anne

2026

Doctoral thesis, comprehensive summary

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Evaluating the rRNA operon as a universal eukaryotic marker using a nanopore-based metabarcoding workflow

Lassen, Linus

2026

Student thesis

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Experimental demonstration of horizontal gene transfer in fungi

Valová, Zuzana

2026

Student thesis

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Impacts of large herbivores on mycorrhizal fungal communities across the Arctic

Brachmann, Cole G.; Ryberg, Martin; Furneaux, Brendan R.; Rosling, Anna et al.

Part of Ecography, 2026

Article in journal

• DOI for Impacts of large herbivores on mycorrhizal fungal communities across the Arctic
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Functional characterization of a CFEM domain-containing protein in the mycoparasitic fungus Clonostachys rosea reveals antimicrobial activity and a role in conidiation

Iliopoulos, Isaak; Samaras, Anastasios; Sigdel, Susmita; Forslund, Linnea et al.

Part of Molecular Genetics and Genomics, 2026

Article in journal

• DOI for Functional characterization of a CFEM domain-containing protein in the mycoparasitic fungus Clonostachys rosea reveals antimicrobial activity and a role in conidiation
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Properties and Limitations of eDNA Substrates for Terrestrial Animal Monitoring

Zhao, Beilun; Andermann, Tobias

Part of Molecular Ecology Resources, 2026

Article, review/survey

• DOI for Properties and Limitations of eDNA Substrates for Terrestrial Animal Monitoring
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A taxonomic update of the genus Clavija (Theophrastaceae) in Colombia and Ecuador

Ståhl, Bertil

Part of Nordic Journal of Botany, 2026

Article in journal

• DOI for A taxonomic update of the genus Clavija (Theophrastaceae) in Colombia and Ecuador
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NECTAR BARRIER FOR BIRDS IN ANISACANTHUS (ACANTHACEAE) - A KEYHOLE BARRIER

Manktelow, Mariette

Part of The Southwestern naturalist, p. 1-11, 2026

Article in journal

• DOI for NECTAR BARRIER FOR BIRDS IN ANISACANTHUS (ACANTHACEAE) - A KEYHOLE BARRIER

The Apocynaceae: of the Arabian Peninsula and Socotra

Bruyns, Peter V.; Lidén, Magnus; Morrison, David A.

Uppsala University, 2026

Book

Evolutionary Dynamics of Dosage Compensation and Sex-biased Gene Expression in Morabine Grasshopper Vandiemenella viatica

Jayaprasad, Suvratha; Schielzeth, Holger; Palacios-Gimenez, Octavio M.

Part of Genome Biology and Evolution, 2026

Article in journal

• DOI for Evolutionary Dynamics of Dosage Compensation and Sex-biased Gene Expression in Morabine Grasshopper Vandiemenella viatica
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The evolutionary genomics of meiotic drive

Presgraves, Daven C.; Dawe, R. Kelly; Dyer, Kelly A.; Fishman, Lila et al.

Part of Molecular biology and evolution, 2026

Article, review/survey

• DOI for The evolutionary genomics of meiotic drive
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Phylogenomic tree of Cercozoa based on single-cell transcriptomes from 100 uncultured cells

Lax, Gordon; Cooney, Elizabeth C.; Zlatogursky, Vasily; Mtawali, Mahara et al.

Part of BMC Biology, 2026

Article in journal

• DOI for Phylogenomic tree of Cercozoa based on single-cell transcriptomes from 100 uncultured cells
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Genomic Connectivity and Adaptation Signals of the Freshwater Sponge Ephydatia muelleri Across Its Distribution

de la Cruz-Castillejo, Laura; Cassidy, Robert; Mitsi, Konstantina; Galia-Camps, Carles et al.

Part of Journal of Biogeography, 2026

Article in journal

• DOI for Genomic Connectivity and Adaptation Signals of the Freshwater Sponge Ephydatia muelleri Across Its Distribution
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Identification of a deep-branching lineage of algae using environmental plastid genomes

Jamy, Mahwash; Huber, Thomas; Antoine, Thibault; Ruscheweyh, Hans-Joachim et al.

Part of Nature Communications, 2026

Article in journal

• DOI for Identification of a deep-branching lineage of algae using environmental plastid genomes
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B chromosome retrotransposed sequences persist through speciation, contributing to genomic and regulatory innovations in the fish genus Psalidodon (Characiformes, Acestrorhamphidae)

Lasmar, Lucas F.; Vidal, Mateus R.; Nadai, Pamela C. F.; Dos Santos, Rodrigo Zeni et al.

Part of PLOS ONE, 2026

Article in journal

• DOI for B chromosome retrotransposed sequences persist through speciation, contributing to genomic and regulatory innovations in the fish genus Psalidodon (Characiformes, Acestrorhamphidae)
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The Apocynaceae of the Arabian Peninsula and Socotra

Bruyns, Peter

Acta Universitatis Upsaliensis, 2026

Book

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First report of Hexamita nelsoni in blue mussel (Mytilus edulis): morphology, phylogeny, and host-parasite interaction

Alfjorden, Anders; Jerlström-Hultqvist, Jon; Svärd, Staffan; Burki, Fabien

Part of Journal of Invertebrate Pathology, 2026

Article in journal

• DOI for First report of Hexamita nelsoni in blue mussel (Mytilus edulis): morphology, phylogeny, and host-parasite interaction

Chromosome-level assembly of the club-legged grasshopper (Gomphocerus sibiricus) genome

Palacios-Gimenez, Octavio M.; Varma, Mahendra; Cheng, Xinyi; Mosbech, Mai-Britt et al.

Part of G3, 2025

Article in journal

• DOI for Chromosome-level assembly of the club-legged grasshopper (Gomphocerus sibiricus) genome
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Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales

Hallgren, Joel; Dharamshi, Jennah; Rodriguez-Gijon, Alejandro; Nuy, Julia et al.

Part of Nature Communications, 2025

Article in journal

• DOI for Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales
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Fungal diversity notes 2017-2122: taxonomic and phylogenetic contributions to freshwater fungi and other fungal taxa

Dong, Wei; Hyde, Kevin D.; Jeewon, Rajesh; Karunarathna, Samantha C. et al.

Part of Fungal diversity, p. 185-459, 2025

Article in journal

• DOI for Fungal diversity notes 2017-2122: taxonomic and phylogenetic contributions to freshwater fungi and other fungal taxa

Orkidéexplosion vid E4:an

Thulin, Mats

Part of Daphne, p. 5, 2025

Article in journal

Ölandsstarr i Uppland, hur kan det ha gått till?

Thulin, Mats

Part of Svensk Botanisk Tidskrift, p. 274-281, 2025

Article in journal

Pangeneric analyses reveal the divergent genome evolution and ecologies between morels and truffles in the Morchellaceae

Bonito, Gregory; Miyauchi, Shingo; Hayes, Richard D.; Tan, Hao et al.

Part of Current Biology, p. 4135-4150000000, 2025

Article in journal

• DOI for Pangeneric analyses reveal the divergent genome evolution and ecologies between morels and truffles in the Morchellaceae

Early germline sequestration in a basidiomycete fungus

Hiltunen Thorén, Markus; Olsson, Boel; Vonk, Peter Jan; Siljestam, Mattias et al.

Part of Science, p. 720-723, 2025

Article in journal

• DOI for Early germline sequestration in a basidiomycete fungus

The role of toxin/antidote genes in the maintenance and evolution of accessory chromosomes in Fusarium

Sandell, Linnea; Forsythe, Adrian; Mirandola, Anna; Jorayev, Samuel et al.

Part of Genetics, 2025

Article in journal

• DOI for The role of toxin/antidote genes in the maintenance and evolution of accessory chromosomes in Fusarium
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The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication

Monsen, Oystein; Gronvold, Lars; Datsomor, Alex; Harvey, Thomas et al.

Part of Genome Research, p. 475-488, 2025

Article in journal

• DOI for The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication

Scientific plant names derived from the surname of Pehr Forsskål: their histrory, orthography, legitimacy, and current use

Friis, Ib; Thulin, Mats

Det Kongelige Danske Videnskabernes Selskab, 2025

Book

A taxonomic revision of the “Quadrispina clade” of Barleria sect. Prionitis

Defty, Ellie; Hatt, Sebastian; Thulin, Mats; Lidetu, Hanny et al.

Part of Webbia, p. 93-120, 2025

Article in journal

• DOI for A taxonomic revision of the “Quadrispina clade” of Barleria sect. Prionitis
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Euphorbia balsamifera subsp. adenensis (Euphorbiaceae) new to Socotra and notes on its taxonomy

Thulin, Mats; Weber, Michael H.; Mubarak, Sami Ali Mohammed

Part of Nordic Journal of Botany, 2025

Article in journal

• DOI for Euphorbia balsamifera subsp. adenensis (Euphorbiaceae) new to Socotra and notes on its taxonomy
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The Linnaean revolution - A history of the Natural System

Lidén, Magnus

Part of Taxon, p. 1011-1034, 2025

Article in journal

• DOI for The Linnaean revolution - A history of the Natural System
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Accumulation of a Biparentally Inherited Neptune Transposable Element in Natural Killifish Hybrids (Fundulus diaphanus x F. heteroclitus)

Roussel, Alexandre-James; Suh, Alexander; Ruiz-Ruano, Francisco J.; Dion-Cote, Anne-Marie

Part of Molecular biology and evolution, 2025

Article in journal

• DOI for Accumulation of a Biparentally Inherited Neptune Transposable Element in Natural Killifish Hybrids (Fundulus diaphanus x F. heteroclitus)
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A mosaic of modular variation at a single gene underpins convergent plumage coloration

Lutgen, Dave; Peona, Valentina; Chase, Madeline A.; Kakhki, Niloofar Alaei et al.

Part of Science, 2025

Article in journal

• DOI for A mosaic of modular variation at a single gene underpins convergent plumage coloration

Estimating national Red List statuses for fungi in Sweden: An improved deep learning approach to account for unbalanced data

Gomes De Almeida, Filipe; Baggström, Adrian; Andermann, Tobias

Part of Ecological Informatics, 2025

Article in journal

• DOI for Estimating national Red List statuses for fungi in Sweden: An improved deep learning approach to account for unbalanced data
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Evolution of Large Polymorphic Inversions in a Panmictic Songbird

Pei, Yifan; Forstmeier, Wolfgang; Suh, Alexander; Bambach, Lynn et al.

Part of Molecular biology and evolution, 2025

Article in journal

• DOI for Evolution of Large Polymorphic Inversions in a Panmictic Songbird
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Examining the presence of photosymbionts in amphitremids and centrohelids

Billiau, Steffi

2025

Student thesis

Corydalis shiyomiensis (Papaveraceae), a new species from Arunachal Pradesh, India

Khanal, Madhusudhan; Sivaranjani, S.; Singpho, Jaseng; Sarkar, Shuvadip et al.

Part of Phytotaxa, p. 87-92, 2025

Article in journal

• DOI for Corydalis shiyomiensis (Papaveraceae), a new species from Arunachal Pradesh, India

Protist genomics: key to understanding eukaryotic evolution

Schoenle, Alexandra; Francis, Ore; Archibald, John M.; Burki, Fabien et al.

Part of Trends in Genetics, p. 868-882, 2025

Article in journal

• DOI for Protist genomics: key to understanding eukaryotic evolution
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Giant transposons promote strain heterogeneity in a major fungal pathogen

Gluck-Thaler, Emile; Forsythe, Adrian; Puerner, Charles; Gutierrez-Perez, Cecilia et al.

Part of mBio, 2025

Article in journal

• DOI for Giant transposons promote strain heterogeneity in a major fungal pathogen
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Paulinella acadia sp. nov., a New Photosynthetic Species Isolated From a Brackish Beach in British Columbia (Canada)

Pardasani, Yash; Palka, Maia V.; Leander, Brian S.; Burki, Fabien

Part of Journal of Eukaryotic Microbiology, 2025

Article in journal

• DOI for Paulinella acadia sp. nov., a New Photosynthetic Species Isolated From a Brackish Beach in British Columbia (Canada)
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Morphology, Systematics and Life Cycle of Ozanamia fimbriatus (Haptista: Centroplasthelida), With Notes on Evolution of Organic Skeleton in Centrohelids

Drachko, Daria; Zlatogursky, Vasily V.

Part of Journal of Eukaryotic Microbiology, 2025

Article in journal

• DOI for Morphology, Systematics and Life Cycle of Ozanamia fimbriatus (Haptista: Centroplasthelida), With Notes on Evolution of Organic Skeleton in Centrohelids
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Metagenomic insights into the diet and past Kolyma Lowland habitat from the intestinal content of a Late Pleistocene steppe bison

Jin, Chenyu; Forsythe, Adrian; Balint, Miklos; Kienast, Frank et al.

Part of Quaternary Science Reviews, 2025

Article in journal

• DOI for Metagenomic insights into the diet and past Kolyma Lowland habitat from the intestinal content of a Late Pleistocene steppe bison
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Boswellia oropedionis (Burseraceae) sp. nov., a frankincense tree from Socotra, and notes on B. ameero and B. bullata

Thulin, Mats; Weber, Michael H.; Mubarak, Sami Ali Mohammed

Part of Nordic Journal of Botany, 2025

Article in journal

• DOI for Boswellia oropedionis (Burseraceae) sp. nov., a frankincense tree from Socotra, and notes on B. ameero and B. bullata
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Koenigia arunachalensis sp. nov. (Polygonaceae), a new species from Eastern Himalaya, India

Hajong, Bipankar; Lidén, Magnus; Bharali, Pankaj

Part of Nordic Journal of Botany, 2025

Article in journal

• DOI for Koenigia arunachalensis sp. nov. (Polygonaceae), a new species from Eastern Himalaya, India

Few genetic loci control the green-brown colour polymorphism in the meadow grasshopper Pseudochorthippus parallelus

Varma, Mahendra; Winter, Gabe; Ebeling, Anne; Lehmann, Angela et al.

Part of Journal of Evolutionary Biology, p. 639-651, 2025

Article in journal

• DOI for Few genetic loci control the green-brown colour polymorphism in the meadow grasshopper Pseudochorthippus parallelus
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