Michelle Cleary

My research focuses on the health and sustainability of forest ecosystems. As a Forest Pathologist at SLU, I study how native and invasive fungal and oomycete pathogens interact with trees and influence forest resilience. My work spans from understanding the biology of invasive species and tree defense mechanisms to exploring biochemical and genetic interactions between pathogens, host trees, and their environments.

I am Unit Head for the Forest Pathology Research Lab. Together with my colleagues, we develop and apply molecular, chemical, and imaging tools for early detection and diagnostics of damaging forest agents. These approaches not only help safeguard forests against emerging threats but also contribute to sustainable management practices in the face of climate and environmental change.

A major passion of mine is the Save the Ash (Rädda Asken), which has grown into a multifaceted, multidisciplinary effort. Our research spans the resistance biology of ash, tolerance mechanisms to pathogens, biodiversity and ecological impacts of ash dieback, and large-scale field testing. We also promote public participation in identifying tolerant ash trees, collect and screen genotypes, apply advanced phenotyping tools to accelerate breeding, and develop strategies for restoration and long-term management.

I am also working as a Vice Director of the Centre of Excellence Trees For Me - funded by the Swedish Energy Agency and nearly 50 societal partners - which integrates academia, industry, and stakeholders to build scientific competence, inform policy and practice, and train future leaders for Sweden’s forest-based bioeconomy. 

A summary of research outputs is give on these profile links: 

LinkedIn

ORCID

Google Scholar

During my 20+ years career as a Forest Pathologist, I have been conducting research on a broad array of forest pathogens, including root rot pathogens of conifers (Armillaria, Heterobasidion, Inonotus, and Phellinus); invasive forest pathogens including Phytophthora, Hymenoscyphus fraxineus causing ash decline, Cronartium ribicola causing white pine blister rust, and several others causing canker and rust diseases of poplar and larch; and needle and shoot blight diseases of pine. 

My current research projects are focused on:

• Ash decline and resistance breeding; secondary metabolism in ash (Fraxinus spp.); advanced phenotyping tools for rapid resistance screeening; restoration of diseased landscapes. See the external link: Rädda Asken
• Rapid molecular techniques using Loop mediated isothermal amplification and the portable Genie II for pest and disease detection 
• Next generation sequencing (NGS) for RNA and DNA analysis of microbial communities in nurseries, forests and sentinel plants.
• Applications of tools for early detection and monitoring of diseases (VOCs, MinION, FT-IR spectroscopy, drones)
• Tree mycobiome studies (on ash, birch, poplar, pine and Douglas-fir)
• Sentinel plants as a means of screening potential harmful organisms
• Effects of precommercial thinning on root rot incidence and spread
• Drought effects on pine needle diseases
• Phytophthora diseases in nurseries and the urban and peri-urban landscape

I am responsible for the following courses: 

Trees: Structure and Function (BI1452), Autumn (Period 1); 15 Credits; Year 1 of the International Bachelor’s Program in Forest and Landscape

This course gives students basic knowledge of the fundamental principles of tree biology, from the roots to the upper canopy. The course covers theoretical and practical knowledge on conifer and broadleaf tree species identification, growth and development of trees, and tree species silvics relevant for sustainable planning and management of trees in urban and rural forested settings. 

Tree and Forest Health (SV0015), Autumn (Period 4b); 7.5 Credits; Year 2 of the International Bachelor’s Program in Forest and Landscape

The course gives students basic knowledge about biotic and abiotic agents affecting individual tree and forest ecosystem health, including damage caused by insects, pathogens, and other environmental stressors. The course emphasizes the ecological roles of disturbance agents and how they can affect the economic and ecological sustainability of forests. Students learn how to collect samples to identify damage using different diagnostic methods, modern tools and techniques for early detection and monitoring, and mitigation and management options to promote better health and resilience in urban and rural forests. Case study approaches will be used with examples of damaging agents in Sweden and globally. The course includes several field trips to visit insect and disease infestations in urban, peri-urban and rural forests to understand the effects of damage on from different social, ecological and economic perspectives.

I also teach a module in 'Forest Health' in the course “Broadleaves - Forest dynamics, biodiversity and management for multiple use” (15 ECTS) which is part of the Euroforester program. The course itself explores the impact of forest management on biodiversity and evaluate current approaches for conservation and restoration of broadleaf forests. The forest health module that I teach covers current threats and challenges to the function and biodiversity of broadleaf forests, with a focus on exotic tree pathogens, other native insect pests and pathogens and climate stressors.

I have also lectured in the course "Urban Forestry – management of urban forests and trees" (15 ECTS) and other courses at the firt secondy and third-cycle education on various topics related to tree health in the courses “Plant Protection”, “Sustainable Forestry in Southern Sweden”, and "Phenotyping Technologies in Plant-environment Interactions – Integrated Analysis of Omics Data". 

I did my forestry education in Canada at Lakehead University (1998-2001) and later obtained my PhD degree in Forestry (Forest Pathology) in 2007 from the University of British Columbia under the supervision of Prof. Bart van der Kamp and Dr. Duncan Morrison. My PhD thesis dealt with the biology and control of Armillaria root disease in the interior forests of British Columbia; specifically investigating differential resistance among conifers and resistance mechanisms operating in trees.

Between 2006 and 2010 I worked as the Regional Forest Pathologist for the British Columbia Ministry of Forests, Range and Natural Resource Operations, in the Southern Interior Forest Region based in Kamloops, British Columbia, Canada. There I served as the regional expert being responsible for and covering an area approximating 25 million ha (or ~30% of the provincial landbase); and worked with the forest sector and other key stakeholder groups on practical and operational issues as it relates to forest disease and sustainable forest management, including:

• refined policies and practice standards to accomplish disease prevention and control
• development and implementation of applied research and control projects to assess, evaluate and monitor impacts of disturbances, forest pathogen behavior, and the effectiveness of various forest disease management strategies
• extension and training activities activities for the forest sector

Teaching in the subject Forest Pathology: I have been teaching courses in Forest Pathology since 2003 in different capacities as both term courses and distance education at the University of British Columbia and Thompson Rivers University where I held an Adjunct position for 4 years. 

Post-Doc research: I came to SLU in 2011 as a Post-doc in the Department of Forest Mycology and Plant Pathology in Uppsala where I collaborated with Jan Stenlid and Malin Elfstrand on research with ash decline.

Current research: In 2015, I moved to my current Department at the Southern Swedish Forest Research Centre in Alnarp where I am now the Unit leader for the Forest Pathology Lab which hosts a team of Post-docs, PhD students, and technical staff all working with diverse issues in forest pathology: pine needle diseases (Diplodia sapinea, Lecanosticta acicola, Sydowia polyspora, Lophodermium spp.); Heterobasidion root rot in production forests; Armillaria root rot, Ash dieback caused by Hymenoscyphus fraxineus; Phytophthora diseases in forests, urban areas and nurseries; pathogen damage in Christmas tree plantations; fungal endophytes in plants, soil and seeds; tree microbiome; chemical ecology; host-pathogen interactions; molecular diagnostics; and plant biosecurity. 

Currently: I work with two Post-doc researchers: Dr. Tage Rosenqvist and Alice Penanhoat within the EU Life+ Project Life’s A Beech. I am main supervisor currently to three PhD students: Sezer Olivia Kaya who is working with current and future threats to fast-growing broadleaved tree species and funded by the new Centre of Excellence Trees For Me, and Ana Paula Gamba who is working with regeneration and restoration of European ash, and Urszula Boguslawska who is working on biotic and abiotic factors contributing to the rapid decline of resistant ash trees. I am also a co-supervisor to Kinga Storalek who is working within Trees For Me. 

Previously: I have supervised 8 Post-docs, 5 completed PhD theses (including 1 as main supervisor), 15 undergraduate and graduate (Msc.) students, as well as several visiting Bachelors, Masters and PhD students and Post-docs on short-term research stays. 

Peer-reviewed Publications

Díaz-Calafat, J., Peterson, D., De Frenne, P., Felton, A., Öckinger, E., Cousins, S., Roger, F., Cleary, M., and Hedwall, P-O. 202X. Using flower eDNA metabarcoding to identify the effects of forest structure and microclimate on flower-visiting arthropods. Environmental DNA 7, no. 5: e70185. https://doi.org/10.1002/edn3.70185 

Bonello, P., Conrad, A., Sadikovic, D., Liziniewicz, M., and Cleary, M. 2025. Point-of-service diagnostics and resistance phenotyping to combat ash dieback. Plants, People, Planet. 8:1588428. https://doi.org/10.3389/ffgc.2025.1588428 

Garcia-Lozano, C., Pueyo-Ros, J., Canelles, Q., Latombe, G., Adriaens, T., Bacher, S., Cardoso, A.C., Cleary, M., Coromina, L., Courchamp, F., Dawson, W., de Groot, M., Essl, F., Gallardo, B., Golivets, M., Huusela, E., Jauni, M., Jelaska, S.D., Jeschke, J.M., Katsanevakis, S., Kourantidou, M., Kühn, I., Lenzner, B., Leung, B., Marchante, E., O'Flynn, C., Pérez-Granados, C., Pergl, J., Pipek, P., Preda, C., Ribeiro, F., Roy, H., Scalera, R., von Schmalensee, M., Seebens, H., Stefánsson, R.A., Tokarska-Guzik, B., Tricarico, E., Vanderhoeven, S., Vandvik, V., Vilà, M. and Roura-Pascual, N. 2025. Management measures and trends of biological invasions in Europe: A survey-based assessment of local managers. Glob Change Biol. 31: e70028. https://doi.org/10.1111/gcb.70028

Huo, L., Matsiakh, I., Bohlin, J., and Cleary, M. 2025. Estimation of tree vitality reduced by pine needle disease using multispectral drone images. Remote Sensing, 17(2), 271. https://doi.org/10.3390/rs17020271 

Doonan, J.M., Budde, K.B., Kosawang, C., Lobo, A., Verbylaite, R., Brealey, J.C., Martin, M.D., Pliūra, A., Thomas, K., Konrad, H., Seegmüller, S., Liziniewicz, M., Cleary, M., Nemesio-Gorriz, M., Fussi, B., Kirisits, T., Gilbert, M.T.P., Heuertz, M.T.P., Kjær, E.D., Nielsen L.R. 2025. Multiple, single trait GWAS and supervised machine learning reveal the genetic architecture of Fraxinus excelsior tolerance to ash dieback in Europe. Plant, Cell & Environment. https://doi.org/10.1111/pce.15361 

Felton, A., Seidl, R., Lindenmayer, D.B., Messier, C., Löf, M., de Koning, J.H.C., Ranius, T., Cleary, M., Hedwall, P-O., Torres Garcia, M.R., Felton, A.M. 2024. The choice of path to resilience is crucial to the future of production forests. Nat Ecol Evol (2024). https://doi.org/10.1038/s41559-024-02473-x

Franić, I., Cleary, M., Aday Kaya, A.G., Bragança, H., Brodal, G., Cech, T.L., Chandelier, A., Doğmuş-Lehtijärvi, T., Eschen, R., Lehtijärvi, A., Ormsby, M., Prospero, S., Schwanda, K., Sikora, K., Szmidla, H., Talgø, V., Tkaczyk, M., Vettraino, A.M., Perez-Sierra, A. The Biosecurity Risks of International Forest Tree Seed Movements. 2024. Curr. For. Rep. 10, 89–102 (2024). https://doi.org/10.1007/s40725-023-00211-3 

Sherwood, P., Nordström, P., Woodward, S., Bohman, B., and Cleary, M. 2024. Detecting pathogenic Phytophthora species using volatile organic compounds. Molecules 2024, 29, 1749. https://doi.org/10.3390/molecules29081749 

Peterson, D. L., Pecori, F., Luchi, N., Migliorini, D., Santini, A., Kyle, K. E., Rutledge, C., Sallé, A., Kaya, S. O., Ramsfield, T., & Cleary, M. 2023. Development of novel LAMP and qPCR assays for rapid and specific identification of bronze birch borer (Agrilus anxius). Environmental DNA, 5, 1177–1190. https://doi.org/10.1002/edn3.503 

Riit, T.; Cleary, M.; Adamson, K.; Blomquist, M.; Burokienė, D.; Marčiulynienė, D.; Oliva, J.; Poimala, A.; Redondo, M.A.; Strømeng, G.M.; Venche Talgø, V., Tedersoo, L., Thomsen, I.M., Uimari, A., Witzell, J., Drenkhan, R.. Oomycete Soil Diversity Associated with Betula and Alnus in Forests and Urban Settings in the Nordic–Baltic Region. J. Fungi. 2023, 9, 926. https://doi.org/10.3390/jof9090926 

Chang, L.; Li, Y.; Gao, Z.; Bonello, P.; Cleary, M.; Munck, I.A.; Santini, A.; Sun, H. Novel Pathogen–Plant Host Interaction: Colletotrichum jiangxiense and Fraxinus americana L. (White Ash) in a Sentinel Garden in China. 2023. Plants 12, 4001. https://doi.org/10.3390/plants12234001 

Chang, L., Li, L-Y., Gao, Z., Bonello, P., Cleary, M., Munck, I.A., Santini, A., Sun, H. 2023. 2023. First report of Epicoccum latusicollum causing leaf spot disease on red maple (Acer rubrum L.) in China: Insights from a sentinel planting garden. Crop Protection. 175, January 2024, 106439 https://doi.org/10.1016/j.cropro.2023.106439. 

Gossner, M.M.; Perret-Gentil, A.; Britt, E.; Queloz, V.; Glauser, G.; Ladd, T.; Roe, A.D.; Cleary, M.; Liziniewicz, M.; Nielsen, L.R.; Ghosh, S.K.; Bonello, P.; Eisenring, M. 2023. A glimmer of hope – ash genotypes with increased resistance to ash dieback pathogen show cross-resistance to emerald ash borer. New Phytol, 240: 1219-1232. https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.19068 

Hulbert, J.M., Hallett, R.A., Roy H.E., Cleary, M. 2023. Citizen science can enhance strategies to detect and manage invasive forest pests and pathogens. Frontiers in Ecology and Evolution.  11:  https://www.frontiersin.org/articles/10.3389/fevo.2023.1113978 

Peterson, D.L.; Kyle, K.; Sallé, A.; Pecori, F.; Migliorini, D.; Santini, A.; Luchi, N.; Cleary, M. Specificity and sensitivity of a rapid LAMP assay for early detection of Emerald ash borer (Agrilus planipennis) in Europe. Forests 2023, 14, 436. https://doi.org/10.3390/f14020436

Tubby, K.V., Adamcikova, K., Adamson, K., Akiba, M., Barnes, I., Boroń, P., Bragança, H., Bulgakov, T., Burgdorf, N., Capretti, P., Cech, T., Cleary, M., Davydenko, K., Drenkhan, R., Elvira-Recuenco, M., Enderle, R., Gardner, J., Georgieva, M., Ghelardini, L., Husson, C., Iturritxa, E., Vester, M., Markovskaja, S., Mesanza, N., Ogris, N., Oskay, F., Piškur, B., Queloz, V., Raitelaitytė, K., Raposa, R., Soukainen, M., Strasser, L., Vahalík, P., Mullett, M. 2022. The increasing threat to European forests from the invasive foliar pine pathogen, Lecanosticta acicola. SSRN: http://dx.doi.org/10.2139/ssrn.4292683 

Nordström, I., Sherwood, P., Bohman, B., Woodward, S., Peterson, D.L., Niño‑Sánchez, J., Sánchez‑Gómez, T., Javier Díez, J., Cleary, M. 2022. Utilizing volatile organic compounds for early detection of Fusarium circinatum. Scientific Reports 12, 21661 (2022). https://doi.org/10.1038/s41598-022-26078-1

Liziniewicz, M., Tolio, B., & Cleary, M. 2022. Monitoring of long-term tolerance of European ash to Hymenoscyphus fraxineus in clonal seed orchards in Sweden. Forest Pathology, 52, e12773. https://doi.org/10.1111/efp.12773

Kourantidou, M., Verbrugge, L.N.H., Haubrock, P.J., Cuthbert, R.N., Angulo, E., Ahonen, I., Cleary, M., Falk-Andersson, J., Granhag, L., Gíslason, S., Kaiser, B., Kosenius, A-K., Lange, H., Lehtiniemi, M:, Magnussen, K:, Navrud, S., Nummi, P., Oficialdegui, F.J., Ramula, S., Ryttäri, T., von Schmalensee, M., Stefansson, R.A., Diagne, C., Courchamp, F. 2022. The economic costs, management and regulation of biological invasions in the Nordic countries: A review. Ambio. 324, 116374 https://doi.org/10.1016/j.jenvman.2022.116374 

Laas, M., Adamson, K., Barnes, I., Janoušek, J., Mullett, M.S., Adamčíková, K., Akiba, M., Beenken, L., Braganca, H., Bulgakov, T.S., Capretti, P., Cech, T., Cleary, M., Enderle, R., Ghelardini, L., Jankovský, L., Markovskaja, S., Matsiakh, I., Meyer, J.B., Oskay, F., Piškur, B., Raitelaitytė, K., Sadiković, D., Drenkhan, R. Diversity, migration routes, and worldwide population genetic structure of Lecanosticta acicola, the causal agent of brown spot needle blight. Molecular Plant Pathology, 23, 1620– 1639. https://doi.org/10.1111/mpp.13257 

Franic, I., Allan, E., Prospero, S., Adamson, K., Attorre, F., Auger-Rozenberg, M.A., Augustin, S., Avtzis, D., Baert, W., Barta, M., Bauters, K., Bellahirech, A., Boroń, P., Bragança, H., Brestovanská, T., Brurberg, M.B., Burgess, T., Burokienė, D., Cleary, M., Corley, J., Coyle, D., Csóka, G., Černý, K., Davydenko, K., de Groot, M., Diez, J., Doğmuş Lehtijärvi, H.T., Drenkhan, R., Edwards, J., Elsafy, M., Eötvös, C.B., Falko, R., Fan, J., Feddern, N., Fürjes-Mikó, Á., Gossner, M., Grad, B., Hartmann, M. , Havrdova, L., Kádasi Horáková, M., Hrabětová, M., Just Justesen, M., Kacprzyk, M., Kenis, M., Kirichenko, N., Kovač, M., Kramarets, V., Lacković, N., Lantschner, M.V., Lazarević, J., Leskiv, M., Li, H., Madsen, C.L., Malumphy, C., Matošević, D., Matsiakh, I., May, T., Meffert, J., Migliorini, D., Nikolov, C., O’Hanlon, R., Oskay, F., Paap, T., Parpan, T., Piškur, B., Ravn, H.P., Mbwambo, J., Ronse, A., Roques, A., Ruffner, B., Santini, A., Sivickis, K., Soliani, C., Talgø, V., Томошевич, M., Uimari, A., Ulyshen, M., Vettraino, A.M., Villari, C., Wang, Y., Witzell, J., Zlatković, M., Eschen, R. 2023. Climate, host and geography shape insect and fungal communities of trees. Scientific Reports Sci Rep 13, 11570 (2023). https://doi.org/10.1038/s41598-023-36795-w 

Morrison, D.J.; Rönnberg, J.; Pellow, K.; Cleary, M. 2022. Mortality and growth following precommercial thinning in stands affected by Armillaria, Phellinus and Tomentosus root diseases in southern British Columbia. Forest Ecology and Management. 52, e12778. https://doi.org/10.1111/efp.12778 

Witzell, J., Decker, V.H.G., Agostinelli, M., Romeralo, C., Cleary, M., Albrectsen, B.R. 2022. Aspen Leaves as a “Chemical Landscape” for Fungal Endophyte Diversity—Effects of Nitrogen Addition. Frontiers in Microbiology. 13, 846208. https://10.3389/fmicb.2022.846208  

Oskay, F.; Vettraino, A.M., Doğmuş, H.T., Lehtijärvi, A.; Woodward, S.; Cleary, M.; 2022. Seed quantity affects the fungal community composition detected using metabarcoding. Scientific Reports 12, 3060 (2022). https://doi.org/10.1038/s41598-022-06997-9  

Franić, I., Prospero, S. Adamson, K., Allan, E., Auger-Rozenberg, M-A., Augustin, S., Avtzis, D., Barta, M., Boroń, P., Bragança, H., Brestovanská, T., Burgess, T., Burokienė, D., Černý, K., Cleary, M., Corley, J., Coyle, D.R., Csóka, G., Davydenko, K., Elsafy, M.A.O., Eötvös, C., de Groot, M., Diez, J.J., Doğmuş Lehtijärvi, H.T., Drenkhan, R., Fan, J-T., Grabowski, M., Grad, B., Havrdova, L., Hrabetova, M., Iede, E.T., Kacprzyk, M., Kenis, M., Kirichenko, N., Lacković, N., Lazarević, J., Leskiv, M., Li, H., Madsen, C.L., Matošević, D., Matsiakh, I., Meffert, J., Migliorini, D., Mikó, A., Nikolov, C., O'Hanlon, R., Oskay, F., Paap, T., Parpan, T., Petrakis, P.V., Piškur, B., Ravn, H.P., Ronse, A., Roques, A., Schühli, G.S., Sivickis, K., Talgø, V., Tomoshevich, M., Uimari, A., Ulyshen, M., Vettraino, A.M., Villari, C., Wang, Y., Witzell, J., Zlatković, M., Eschen. R., 2022. Worldwide diversity of endophytic fungi and herbivorous insects associated with dormant tree twigs. Scientific Data. 9, 62 (2022). https://doi.org/10.1038/s41597-022-01162-3 

Felton, A., Felton. A.M., Wam, H.K., Witzell, J., Wallgren, M., Löf, M., Sonesson, J., Lindbladh, M., Björkman, C., Blennow, K., Cleary, M., Jonsell, M., Klapwijk, M.J., Niklasson, M., Petersson, L., Rönnberg, J., Ode Sang, Å., Wrethling, F., Hedwall, P-O. 2021. Forest biodiversity and ecosystem services outcomes from spruce-birch mixtures in Fennoscandia: The potential importance of tree spatial arrangement. Environmental Challenges. https://doi.org/10.1016/j.envc.2021.100407 

Elfstrand, M., Chen, J., Cleary, M., Halecker, S., Ihrmark, K:, Karlsson, M., Davydenko, K., Stenlid, J., Stadler, M., Brandström Durling, M. 2021. Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals difference of transposable elements expansion between a pathogenic and a non-pathogenic fungus. BMC Genomics. 2021 Jul 4;22(1):503. doi: 10.1186/s12864-021-07837-2.

Cleary, M., Morrison, D.J., van der Kamp, B. 2021. Symptom development and mortality rates caused by Armillaria ostoyae in juvenile mixed conifer stands in British Columbia’s southern interior. Forest Pathology. 2021;51:e12675. https://doi.org/10.1111/efp.12675

Põlme, S., Abarenkov, K., Nilsson, R.H., Lindahl, B., Clemmensen, K., Kauserud, H., Kjoller, H., Baldrian, P., Guldberg, T.,  Frøslev, R., Adojaan, K., Vizzini, A., Suija, A., Pfister, D., Baral, H-O, Järv, H., Madrid, H., Nordén, J., Liu, J-K, Pawlowska, J., Põldmaa, K., Pärtel, K., Runnel, K., Hansen, K., Hyde, K.D., Larsson, K-H, Sandoval-Denis, M., Smith, M-E, Toome-Heller, M., Wijayawardene, N.N., Menolli Jr., N.N., Reynolds, N.K., Drenkhan, R., Maharachchikumbura, S.N.S., Gibertoni, T.B., Læssøe, T., Davis, W., Tokarev, Y., Corrales, A., Mayra Soares, A., Agan, A., Argüelles- Moyao, A., Detherige, A., de Meiras-Ottoni, A., Machado, A.R., Verbeken, A., Cui, B., Marín, C., Stanton, D., Gohar, D., Wanasinghe, D.N., Otsing, E., Aslani, F., Griffith, G.W., Grossart, H-P, Masigol, H., Rojas-Jimenez, K., Timling, I., Hiiesalu, I., Mujica, M.I., Oja, J., Geml, J., Alvarez Manjarrez, J., Ilves, K., Loit, K., Adamson, K., Nara, K., Küngas, K., Biteneks, K., Irinyi, L., Nagy, L., Zhou, L-W., Varga, T., Wagner, L., Aime, M.C., Öpik, M., Metsoja, M., Ryberg, M., Vasar, M., Murata, M., Nelsen, M.P., Cleary, M., Samarakoon, M.C., Doilom, M., Bahram, M., Johnston, P., Kohout, P., Chen, Q., Amiri, R., dos Santos Chikowski, R., Mendez-Alvarenga, R-L., Perera, R., Orijel, R.G., Gielen, R., Phookamsak, R., Jayawardena, R.S., Rahimlou, S., Tibpromma, S., Brown, S.P., Sepp, S-K, Mundra, S., Luo, Z-H., Bose, T., Vahter, T., Netherway, T., Yang, T., Lumbsch, H.T., Tian, Q., May, T., Coimbra, V.R.M:, de Lima, V.X., de Oliviera, V.R.T., Lu, Y., Matsuda, Y., Miyamoto, Y., Li, W., Kõljalg, U., Tedersoo, L.. 2021. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity. 105, 1–16 (2020). https://doi.org/10.1007/s13225-020-00466-2 

Agostinelli, M., Nguyen, D., Witzell, J., Cleary, M. 2021. Mycobiome of Fraxinus excelsior with different phenotypic susceptibility to ash dieback. Frontiers in Forests and Global Change 4:580514. https://doi.org/10.3389/ffgc.2021.580514 

Cleary, M., Blomquist, M., Marchand, M., Witzell, J. 2021. Oomycetes in rhizosphere soil of ornamental plants from retail nurseries in Southern Sweden. Forest Pathology. https://doi.org/10.1111/efp.12673 

Matsiakh, I., Kramarets, V., Cleary, M. 2021. Occurrence and diversity of Phytophthora species in declining broadleaf forests in western Ukraine. Forest Pathology. 51(1) e12662. https://doi.org/10.1111/efp.12662 

Chaudhary, R., Rönneburg, T., Stein Åslund, M., Lundén, K., Brandström Durling, M., Ihrmark, K., Menkis, A., Stener, L-G., Elfstrand, M., Cleary, M., Stenlid, J. 2020. Marker-trait associations for tolerance to ash dieback in common ash. Forests 2020, 11(10), 1083; https://doi.org/10.3390/f11101083  

Eshghi Sahraeil, S., Cleary, M., Stenlid, J., Brandström-Durling, M., Elfstrand, M. 2020. Transcriptional responses in developing lesions of European ash reveal genes responding to fungal infection by Hymenoscyphus fraxineus. BMC Plant Biology. 20:455 https://doi.org/10.1186/s12870-020-02656-1 

Drenkhan, R.; Ganley, B.; Martín-García, J.; Vahalík, P.; Adamson, K.; Adamčíková, K.; Ahumada, R.; Blank, L.; Bragança, H.; Capretti, P.; Cleary, M.; Cornejo, C.; Davydenko, K.; Diez, J.J.; Lehtijärvi, H.T.D.; Dvořák, M.; Enderle, R.; Fourie, G.; Georgieva, M.; Ghelardini, L.; Hantula, J.; Ioos, R.; Iturritxa, E.; Kanetis, L.; Karpun, N.N.; Koltay, A.; Landeras, E.; Markovskaja, S.; Mesanza, N.; Milenković, I.; Musolin, D.L.; Nikolaou, K.; Nowakowska, J.A.; Ogris, N.; Oskay, F.; Oszako, T.; Papazova-Anakieva, I.; Paraschiv, M.; Pasquali, M.; Pecori, F.; Rafoss, T.; Raitelaitytė, K.; Raposo, R.; Robin, C.; Rodas, C.A.; Santini, A.; Sanz-Ros, A.V.; Selikhovkin, A.V.; Solla, A.; Soukainen, M.; Soulioti, N.; Steenkamp, E.T.; Tsopelas, P.; Vemić, A.; Vettraino, A.M.; Wingfield, M.J.; Woodward, S.; Zamora-Ballesteros, C.; Mullett, M.S. Global Geographic Distribution and Host Range of Fusarium circinatum, the Causal Agent of Pine Pitch Canker. Forests 2020, 11, 724. https://doi.org/10.3390/f11070724 

Hultberg, T., Sandberg, J., Felton, A., Öhman, K., Witzell, J., Rönnberg, J., Cleary, M. Ash dieback risks an extinction cascade. Biological Conservation. Volume 244, April 2020, 108516 https://doi.org/10.1016/j.biocon.2020.108516 

Blomquist, M., Larsson Herrera, S. Hofmann, J., Beram, R.C., Cleary, M., Rönnberg, J. 2020. Size matters but is big always better? Effectiveness of urea and Phlebiopsis gigantea as treatment against Heterobasidion on Picea abies stumps of variable size. Forest Ecology and Management. 462, 117998 https://doi.org/10.1016/j.foreco.2020.117998 

Xu, X., Wang, W., Cleary, M., Wang, P., Lu, N., Sun, Y., Rönnberg, J. 2020. Slope position affects arbuscular mycorrhizal fungi (AMF) rather than thinning intensity in Chinese fir plantations. Forests 2020, 11(3), 273; https://doi.org/10.3390/f11030273 

Elvira-Recuenco, M.; Cacciola, S.O.; Sanz-Ros, A.V.; Garbelotto, M.; Aguayo, J.; Solla, A.; Mullett, M.; Drenkhan, T.; Oskay, F.; Aday Kaya, A.G.; Iturritxa, E.; Cleary, M.; Witzell, J.; Georgieva, M.; Papazova-Anakieva, I.; Chira, D.; Paraschiv, M.; Musolin, D.L.; Selikhovkin, A.V.; Varentsova, E.Y.; Adamčíková, K.; Markovskaja, S.; Mesanza, N.; Davydenko, K.; Capretti, P.; Scanu, B.; Gonthier, P.; Tsopelas, P.; Martín-García, J.; Morales-Rodríguez, C.; Lehtijärvi, A.; Doğmuş Lehtijärvi, H.T.; Oszako, T.; Nowakowska, J.A.; Bragança, H.; Fernández-Fernández, M.; Hantula, J.; Díez, J.J. 2020. Potential interactions between invasive Fusarium circinatum and other pine pathogens in Europe. Forests 2020, 11(1), 7; https://doi.org/10.3390/f11010007 

Zamora-Ballesteros, C.; Diez, J.J.; Martín-García, J.; Witzell, J.; Solla, A.; Ahumada, R.; Capretti, P.; Cleary, M.; Drenkhan, R.; Dvořák, M.; Elvira-Recuenco, M.; Fernández-Fernández, M.; Ghelardini, L.; Gonthier, P.; Hernández-Escribano, L.; Ioos, R.; Markovskaja, S.; Martínez-Álvarez, P.; Muñoz-Adalia, E.J.; Nowakowska, J.A.; Oszako, T.; Raposo, R.; Santini, A.; Hantula, J. 2019. Pine Pitch Canker (PPC): Pathways of Pathogen Spread and Preventive Measures. Forests 2019, 10(12), 1158; https://doi.org/10.3390/f10121158  

Vainio, E.J., Bragança, H., Cleary, M., Fourie, G., Georgieva, M., Ghelardini, L., Hannunen, S., Ioos, R., Martín-García, J., Martínez Álvarez, P. Mullett, M:, Oszako, T., Papazova –Anakieva, I., Piškur, B., Romeralo, C., Sanz-Ros, A-V., Steenkamp, E.T., Tubby, K., Wingfield, M.J., Diez, J.J. 2019. Sampling and detection strategies for the Pine Pitch Canker (PPC) disease pathogen Fusarium circinatum in Europe. Forests 2019, 10(9), 723; https://doi.org/10.3390/f10090723

Fernández, M.M.; Naves, P.; Musolin, D.L.; Selikhovkin, A.V.; Cleary, M.; Chira, D.; Paraschiv, M.; Papazova-Anakieva, I.; Drenkhan, T.; Georgieva, M.; Altunisik, A.; Morales, C.; Tabaković-Tošić, M.; Avtzis, D.N.; Georgiev, G.; Doychev, D.; Nacheski, S.; Trestic, T.; Elvira-Recuenco, M.; Diez J.J., Witzell, J. 2019. Pitch canker disease and insects: Regional risks, environmental regulation and practical management options. Forests 2019, 10(8), 649; https://doi.org/10.3390/f10080649

Cleary, M., Oskay, F., Doğmuş-Lehtijärvi, T., Lehtijarvi, A., Woodward, S., Vettraino, A.M. 2019. Cryptic risks to forest biosecurity associated with the global movement of commercial seed. Forests. 10, 459; http://dx.doi.org/10.3390/f10050459 

Felton, A., Petersson, L., Nilsson, O., Witzell, J., Cleary, M., Felton, A.M., Björkman, C., Ode Sang, Å., Jonsell, M., Holmström, E., Nilsson, U., Rönnberg, J., Kalén, C., Lindbladh, M. 2019. The tree species matters: Biodiversity and ecosystem service implications of replacing Scots pine production stands with Norway spruce. Ambio https://doi.org/10.1007/s13280-019-01259-x    

Cleary, M., Laas, M., Oskay, F., Drenkhan, R. 2019. First report of Lecanosticta acicola on exotic Pinus mugo in southern Sweden. Forest Pathology. 2019;49:e12507 https://doi.org/10.1111/efp.12507  

Morales-Rodríguez, C., Anslan, Sten., Auger-Rozenberg, M., Augustin, S., Baranchikov, Y., Bellahirech, A., Burokiene, D., Cepukoit, D., Çota, E., Davydenko, K., Doğmuş-Lehtijärvi, T., Drenkhan, R., Drenkhan, T., Eschen, R., Glavendekić, M., de Groot, M., Kacprzyk, M., Kenis, M., Kirichenko, N., Matsiakh, I., Musolin, D. L., Nowakowsa, J. A., O’Hanlon, R., Prospero, S., Roques A., Santini, A., Talgø, V., Tedersoo, L., Uimari, A., Vannini, A., Witzell, J., Woodward, S., Zambounis, A., and Cleary, M. 2019. Forewarned is forearmed: preventive detection of potentially invasive pests and pathogens in sentinel plantings. Neobiota. 47: 95-123.  https://doi.org/10.3897/neobiota.47.34276 

Tedersoo, L., Drenkhan, R., Anslan, S. Morales-Rodriguez, C., and Cleary, M. 2019. High-throughput identification and diagnostics of pathogens and pests: overview and practical recommendations. Molecular Ecology Resources. 19, 47-76. https://doi:10.1111/1755-0998.12959  

Roy H, Groom Q, Adriaens T, Agnello G, Antic M, Archambeau A, Bacher S, Bonn A, Brown P, Brundu G, López B, Cleary M, Cogălniceanu D, de Groot M, De Sousa T, Deidun A, Essl F, Fišer Pečnikar Ž, Gazda A, Gervasini E, Glavendekic M, Gigot G, Jelaska S, Jeschke J, Kaminski D, Karachle P, Komives T, Lapin K, Lucy F, Marchante E, Marisavljevic D, Marja R, Martín Torrijos L, Martinou A, Matosevic D, Mifsud C, Motiejūnaitė J, Ojaveer H, Pasalic N, Pekárik L, Per E, Pergl J, Pesic V, Pocock M, Reino L, Ries C, Rozylowicz L, Schade S, Sigurdsson S, Steinitz O, Stern N, Teofilovski A, Thorsson J, Tomov R, Tricarico E, Trichkova T, Tsiamis K, van Valkenburg J, Vella N, Verbrugge L, Vétek G, Villaverde C, Witzell J, Zenetos A, Cardoso A (2018) Increasing understanding of alien species through citizen science (Alien-CSI). Research Ideas and Outcomes 4: e31412. https://doi.org/10.3897/rio.4.e31412

Agostinelli, M., Cleary, M., Martín, J.A., Albrectsen, B., Witzell, J. 2018. Pedunculate oaks (Quercus robur L.) differing in vitality as reservoirs for fungal biodiversity. Frontiers in Microbiology 9: 1758 https://doi.org/10.3389/fmicb.2018.01758  

Villari, C., Dowkiw, A., Enderle, R., Ghasemkhani, M., Kirisits, T., Kjaer, E., Marčiulynienė, D., McKinney, L., Metzler, B., Rostgaard Nielsen, L., Pliūra, A., Stener, L-G., Suchockas, V., Rodriguez-Saona, L., Bonello, P., and Cleary, M. 2018. Advanced spectroscopy-based phenotyping offers solutions to the ash dieback epidemic. Nature Scientific Reports. 8, Article number: 17448 (2018) https://www.nature.com/articles/s41598-018-35770-0 

Cleary, M., Oskay, F., Rönnberg, J., Woodward, S. 2018. First report of Pleuroceras pseudoplatani on Acer rubrum, A. griseum, A. saccharinum, A. negundo, A. circinatum, and A. macrophyllum in Scotland. Forestry Chronicle. 94: 147-150. 

Grenville-Briggs, L-J., Kushwaha, S.K., Cleary, M.R., Witzell, J., Chawade, A., Savenkov, E., Whisson, S.C., Vetukuri, R.R. 2017. Draft Genome of the Oomycete pathogen Phytophthora cactorum Strain LV007 isolated from European Beech (Fagus sylvatica) Genom Data 12: 155–156. DOI: 10.1016/j.gdata.2017.05.010. 

Marčiulynienė, D., Davydenko, K., Stenlid, J., and Cleary, M. 2017. Can pruning help maintain vitality of ash trees affected by ash dieback in urban landscapes? Urban Forestry and Urban Greening. 27: 69-75 https://doi.org/10.1016/j.ufug.2017.06.017 . 

Marčiulynienė, D., Davydenko, K., Stenlid, J., Shabunin, D., and Cleary, M. 2017. Fraxinus excelsior seed is not a probable introduction pathway for Hymenoscyphus fraxineus. Forest Pathology. 2017;e12392. https://doi.org/10.1111/efp.12392 . 

Stenlid, J., Elfstrand, M., Cleary, M., Ihrmark, K., Karlsson, M., Davydenko, K., Brandström-Durling, M. 2017. Genomes of Hymenoscyphus fraxineus and Hymenoscyphus albidus encode surprisingly large cell wall degrading potential, balancing saprotrophic and necrotrophic signatures. Baltic Forestry. 23: 41-51. 

Prospero, S., and Cleary, M. 2017. (Invited article) Focused Review: Effects of host variability in the spread of invasive forest diseases. Forests 8, 80; https://doi.org/10.3390/f8030080  

Klopfenstein, N.B., Stewart, J.E., Ota, Y., Hanna, J.W., Richardson, B., Ross-Davis, A., Elías-Román, R., Korhonen, K., Keča, N., Iturritxa, E., Alvarado-Rosales, D., Solheim, H., Brazee, N., Łakomy, P., Cleary, M.R., Haegawa, E., Kikuchi, T., Garza-Ocañas, F., Tsopelas, P., Rigling, D., Prospero, S., Tsykun, T., Bérubé, J., Stefani, F., Jafapour, S., Antonín, V., Tomšovský, M., McDonald, G., Woodward, S., Kim, M.-S. 2016. Insights into the phylogeny of northern hemisphere Armillaria: split-network and Bayesian analyses of translation elongation factor 1-α sequences. Mycologia. 109:1, 75-91, DOI: 10.1080/00275514.2017.1286572. 

Skovsgaard, J-P., Wilhelm, G-J., Thomsen, I.M., Metzler, B., Kirisits, T., Havrdová, L., Enderle, R., Dobrowolska, D., Cleary, M., Clark, J. 2017. Silvicultural strategies for Fraxinus excelsior in response to dieback caused by Hymenoscyphus fraxineus. Forestry 2017; 90, 455–472, https://doi.org/10.1093/forestry/cpx012 

Power, M.W.P., Hopkins, A.J.M., Chen, J., Bengtsson, S.B.K., Vasaitis, R., and Cleary, M.R. 2017. European Fraxinus species introduced into New Zealand retain many of their native endophytic fungi. Baltic Forestry. 23: 74-81. 

Cleary, M., Blomquist, M., Vetukuri R.R., Böhlenius, H., Witzell, J. 2017. Susceptibility of common tree species in Sweden to Phytophthora cambivora, P. plurivora and P. cactorum. Forest Pathology 47, 3, e12329. https://doi.org/10.1111/efp.12329 

Nguyen, D., Boberg, J., Cleary, M., Bruelheide, H., Hönig, L., Koricheva, J., Stenlid, J. 2017. Foliar fungi of silver birch in pure and mixed tree species stands: comparing high-throughput sequencing and morphological assessment. Nature: Scientific Reports 7, 41801; https://doi.org/10.1038/srep41801 

Cleary, M., Blomquist, M., Ghasemkhani, M., and Witzell, J. 2016. First report of Phytophthora gonapodyides causing stem canker on European beech (Fagus sylvatica) in southern Sweden. Plant Disease. 100:2174. https://doi.org/10.1094/PDIS-04-16-0468-PDN

Cleary M., Nguyen D., Marčiulynienė D., Berlin A., Vasaitis R., Stenlid J. 2016. Friend or foe? Biological and ecological traits of the European ash dieback pathogen Hymenoscyphus fraxineus in its native environment. Nature: Scientific Reports. 6, 21895; https://doi.org/10.1038/srep21895 

Nguyen D, Cleary MR, Enderle R, Stenlid J. 2016. Analyses of the ash dieback pathogen Hymenoscyphus fraxineus, suggest role of tree species diversity on colonization and population structure differentiation. Forest Pathol 46: 82-84. https://doi.org/10.1111/efp.12236

Madigan A, Bełka M, Taylor A, Cleary M, Nguyen D, Elfstrand M, Woodward S. 2015. Does Hymenoscyphus fraxineus infect other hardy members of the Oleaceae? Forest Pathol 45:426-429.  https://doi.org/10.1111/efp.12207

Cleary, M.R., Andersson, P.F., Broberg, A., Elfstrand, M., Daniel, G. and J. Stenlid. 2014. Genotypes of Fraxinus excelsior with different susceptibility to the ash dieback pathogen Hymenoscyphus fraxineus and their response to the phytotoxin viridiol - a metabolomic and microscopic study. Phytochem. 102:115-125. https://doi.org/10.1016/j.phytochem.2014.03.005

Wang, L-Y., Zhang, J., Drobyshev, I., Cleary, M.R., and J. Rönnberg. 2014. Incidence and impact of root infection by Heterobasidion spp., and the justification for preventative silvicultural measures on Scots pine trees: A case study in southern Sweden. Forest Ecol Manag. 315:153-159. https://doi.org/10.1016/j.foreco.2013.12.023

Cleary, M.R., Daniel, G., and J. Stenlid. 2013. Light and scanning electron microscopy studies of the early infection stages of Hymenoscyphus fraxineus on Fraxinus excelsior. Plant Pathol. 62:1294-1301. https://doi.org/10.1111/ppa.12048

Vyse, A., Cleary, M. and I. Cameron. 2013. Species selection in the Interior-Cedar-Hemlock zone in the southern Interior of British Columbia. Forestry Chron. 89:382-391. https://doi.org/10.5558/tfc2013-068 

Cleary, M.R., Arhipova, N., Gaitnieks, T., Stenlid, J., and R. Vasaitis. 2013. Natural infection of Fraxinus excelsior seeds by Chalara fraxinea. Forest Pathol. 43:83-85.          https://doi.org/10.1111/efp.12012

Cleary, M.R., Arhipova, N., Morrison, D.J., Thomsen, I.M., Sturrock, R, Vasaitis, R., Gaitnieks, T., and J. Stenlid. 2013. Stump removal to control root disease in Canada and Scandinavia: A synthesis of results from long-term trials. Forest Ecol Manag. 290:5-14. https://doi.org/10.1016/j.foreco.2012.05.040

Rönnberg, J., Berglund, M., Johansson, U., and M. Cleary. 2013. Incidence of Heterobasidion spp. following different thinning practices in Norway spruce. Forest Ecol Manag. 289:409-415. https://doi.org/10.1016/j.foreco.2012.10.013

Andersson, P.F., Bengtsson, S., Cleary, M.R., Stenlid, J., and A. Broberg. 2012. Viridin-like steroids from Hymenoscyphus fraxineus. Phytochem. 86:195-200. https://doi.org/10.1016/j.phytochem.2012.09.012

Cleary, M.R., van der Kamp, B.J. and D.J. Morrison. 2012. Pathogenicity and virulence of Armillaria sinapina and host response to infection in Douglas-fir, western hemlock, and western redcedar in the southern interior of British Columbia. Forest Pathol. 42:481-491. https://doi.org/10.1111/j.1439-0329.2012.00782.x

Cleary, M., van der Kamp, B.J., and D.J. Morrison. 2012. Effects of wounding and fungal infection with Armillaria ostoyae in three conifer species. I. Host response to abiotic wounding in non-infected roots.  Forest Pathol. 42:100-108.  https://doi.org/10.1111/j.1439-0329.2011.00726.x

Cleary, M., van der Kamp, B.J., and D.J. Morrison. 2012. Effects of wounding and fungal infection with Armillaria ostoyae in three conifer species. II. Host response to the pathogen.  Forest Pathol. 42:109-123.  https://doi.org/10.1111/j.1439-0329.2011.00727.x

Rönnberg, J. and M. Cleary. 2012. Presence of Heterobasidion infections in Norway spruce stumps six years after treatment with Phlebiopsis gigantea. Forest Pathol. 42:144-149. https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1439-0329.2011.00731.x

Redhead, S.A., Bérubé, J, Cleary, M.R., Holdenrieder, O., Hunt, R.S., Korhonen, K., Marxmüller, H., and D.J. Morrison. 2011. (2033) Proposal to conserve Armillariella ostoyae (Armillaria ostoyae) against Agaricus obscurus, Agaricus occultans, and Armillaria solidipes (Basidiomycota). Taxon. 60:1770-1771. 

Cleary, M. and T. Holmes. 2011. Traumatic resin duct formation in the phloem of western red cedar (Thuja plicata) following abiotic wounding and infection by Armillaria ostoyae. IAWA. 32:351-359. 

Cleary, M., Sturrock, R. and J. Hodge. 2011. British Columbia’s southern interior forests: Phellinus root disease stand establishment decision aid. BC JEM. 12:17-20. https://jem-online.org/index.php/jem/article/view/94/79

Zeglen, S., Hunt, R. and M. Cleary. 2009. British Columbia’s forests: White Pine Blister Rust Forest Health Stand Establishment Decision Aid. BC JEM. 10:97–100. https://jem-online.org/index.php/jem/article/view/414/329

Cleary, M., van der Kamp, B.J. and D.J. Morrison. 2008. British Columbia’s southern interior forests: Armillaria root disease stand establishment decision aid. BC JEM. 9:60–65. https://jem-online.org/index.php/jem/article/view/397/312

Non-peer-reviewed scientific publications 
Witzell, J. and Cleary, M. 2017. Hantering av Phytophthora i sydsvenska lövskogar. SLU, Institutionen för sydsvensk skogsvetenskap. Alnarp 2017. 56 pp. https://www.skogssallskapet.se/download/18.2ebe46a615a36cbb4313972/1486989798017/1314-124+165-9+Hantering+av+Phytophthora.pdf 

Hunt, R., Roke, G., Cleary, M., Carlson, M., and V. Berger. 2011. Dothistroma needle blight       in western white pine. Canadian Plant Disease Survey. 91:158-167.

Book Chapter
Cleary, M., Nguyen, D., Stener, L-G., Stenlid, J., and Skovsgaard, J-P. 2017. Ash and ash dieback in Sweden: A review of disease history, current status, pathogen and host dynamics, host tolerance and management options in forests and landscapes. In: “Dieback of European Ash (Fraxinus spp.) - Consequences and Guidelines for Sustainable Management. Eds: Vasaitis R, & Enderle R pp. 195-208. 

Book 
Roques, A., Cleary, M. Matsiakh, I., Eschen, R. 2017. Field guide for the identification of damage on woody sentinel plants. CAB International. 292 pp.