CV page

Michelle Cleary

Michelle Cleary
I am a Forest Pathologist working with native and alien invasive forest pathogens that threaten the economic and ecological sustainability of forests. I study the intimate relationships between fungal and oomycete organisms and trees, the intricacies underlying invasive biology, and mechanisms by which trees defend themselves against plant pathogens. Understanding biochemical- and genetic-based interactions of pathogens with their host trees and the environment is critical to maintaining healthy, sustainable, and resilient forests in a changing world. Our Forest Pathology group at Alnarp is working several of these aspects. In addition, several new projects in the group include various molecular, chemical and imaging techniques and tools for early detection and diagnostics to identify and monitor damaging agents in trees and forests.


Senior Lecturer in Forest Pathology

Associate Professor (Docent)

Vice Director of the new Centre of Excellence Trees For Me

Deputy Head of the Department for Research


I am responsible for the following courses: 

Trees: Structure and Function (BI1385), 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. 

Urban Tree Health and Forest Health (SV0015), Autumn (Period 2b); 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 also lecture in the course "Urban Forestry – management of urban forests and trees" (15 ECTS). Previously, I have lectured 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". 


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 root dieases, ash decline, and white pine blister rust, canker and rust diseases of poplar and larch; and several native and introduced 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 
  • 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 landscape


I currently collaborate with Dr. Mateusz Liziniewicz (The Forest Research Institute - Skogforsk and Sveaskog on ash dieback), Assoc. Prof. Jonas Rönnberg (SLU; Heterobasidion root rot), Dr. Patrick Sherwood (SLU; biochemistry of host-pathogen interactions of trees; Diplodia shoot and tip blight; VOCs detection; and MinION nanopore sequenicing for detection of fungal pathogens), Dr. Iryna Matsiakh (SLU; pine needle diseases, Phytophthora diseases) and Dr. Jonas Bohlin (SLU; drone montioring in forest health), Dr. Iva Franic and Svenska Skogsplantor (SLU; seed-borne diseases and practical treatments to promote seedling health), Dr. Diana Marciulyniene on the potential for larch (Larix spp.) in future forests, Dr. Dusan Sadikovic (SLU; on pine needle diseases - Lecanosticta acicola and Dothistroma spp.), and Dr. Donnie Peterson (SLU; Emerald ash borer and other pests on the horizon for Sweden).  

Among my international collaborators, currently I have projects running with Prof. Stephen Woodward (University of Aberdeen; foliar diseases of conifers and broadleaves,  chemical volatiles for early detection of pests and pathogens, pathways of introduction for alien invasive species); Prof. Enrico Bonello (Ohio State University; spectroscopy-based tools for advanced phenotyping, tree chemical defenses in Fraxinus, sentinel plantations as early warning for new and emerging pests/pathogens), Dr. Simone Prospero (WSL; invasive Phytophthora diseases, Armillaria root rot), Assoc. Prof. Rein Drenkhan (Estonian University of Life Sciences; emerging pine needle diseases; forest Phytophthora pathogens), Prof. Tuğba Doğmuş Lehtijarvi and Dr. Funda Oskay (Isparta and Çankırı Karatekin Universities, respectively; Diplodia shoot and tip blight diseases and seed-borne diseases; Fraxinus foliar endophytes), Dr. Alberto Santini at the Institute for Sustainable Plant Protection, Italian National Research Council on LAMP diagnostics for forest pests and pathogens, and Dr. Tod Ramsfield with the Canadian Forest Services, Northern Forestry Research Station on pests and diseases of birch, poplar and aspen. 


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 Unversity 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 one of three senior researchers in the Forest Pathology Lab hosting 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); Heterobasidion root rot in production forests; Armillaria root rot, Dutch elm disease; Ash dieback; 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 host four Post-doc researchers: Dr. Dusan Sadikovic - a forest mycologist and expert in pine needle diseaese; Dr. Iva Franic - an expert in sentinel plantations as a tool for early detection of invasive species; fungal community analyses in plants and seeds; Dr. Diana Marciulyniene - an expert in ash decline and studying larch canker diseases; and Dr. Donnie Peterson - MCSA Fellow under the project "EMERALD" and expert on emerald ash borer. I am main supervisor to three PhD students: Ida Nordström who is working with different techniques for early detection of invasive forest pathogens funded by the Swedish Research Council FORMAS, 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 Beatrice Tolio who is working with ash decline and resistance breeding funded by Sveaskog, SLU Forest Damage Centre and other internal research grants. I am also a co-supervisor to Kinga Storalek who is working within Trees For Me (main supervisor: Karin Hjelm). 

Previously: I have supervised 4 Post-docs, 4 completed PhD theses (as co-supervisor), 10 undergraduate and graduate students, as well as several visiting Bachelors, Masters and PhD students and Post-docs on short-term research stays. 

Selected publications


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. Nature Scientific Reports 12, 21661 (2022). 

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. 

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 

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. 2022. 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. 

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. 2022. Climate, host and geography shape insect and fungal communities of trees. Nature Ecology and Evolution [submitted].

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 Pathology. 

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.  

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. Nature Scientific Reports 12, 3060 (2022). 

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).  

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. 

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.

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. 

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.. 2020. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity. 105, 1–16 (2020). 

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.  

Cleary, M., Blomquist, M., Marchand, M., Witzell, J. 2021. Oomycetes in rhizosphere soil of ornamental plants from retail nurseries in Southern Sweden. Forest Pathology. 

Matsiakh, I., Kramarets, V., Cleary, M. 2020. Occurrence and diversity of Phytophthora species in declining broadleaf forests in western Ukraine. Forest Pathology. 

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;   

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 

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. 

Hultberg, T., Sandberg, J., Felton, A., Öhman, K., Witzell, J., Rönnberg, J., Cleary, M. 2020. Ash dieback risks an extinction cascade. Biological Conservation. Volume 244, April 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 

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; 

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; 

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; 

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;

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;

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;

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    

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.  

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.  

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. 

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. 

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 

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) 

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. 

Marčiulynienė, D., Davydenko, K., Stenlid, J., 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 

Marčiulynienė, D., Davydenko, K., Stenlid, J., Shabunin, D., Cleary, M. 2017. Fraxinus excelsior seed is not a probable introduction pathway for Hymenoscyphus fraxineus. Forest Pathology. 2017;e12392. 

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., Cleary, M. 2017. (Invited article) Focused Review: Effects of host variability in the spread of invasive forest diseases. Forests 8, 80; 

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, doi: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. doi: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; doi: 10.1038/srep41801 (2017).

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.

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; doi:10-1038/srep21895 (2016).

Nguyen, D., Cleary, M.R., 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.

40.   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.

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.

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.

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.

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.

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.

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.

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.

Andersson, P.F., Bengtsson, S., Cleary, M.R., Stenlid, J., and A. Broberg. 2012. Viridin-like steroids from Hymenoscyphus fraxineus. Phytochem. 86:195-200.

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.

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.

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.

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.

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.

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. 

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.


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