Current Research

My current research studies focus on the phylogeography of forest pathogens. I am involved with developing molecular methods to characterize and identify forest pathogens and endophytes. My research also includes studying the effects of climate change on the pathology and distribution of forest pathogens and their hosts.

Research Interests

My research interests reside in forest pathology.

Education

• Washington State University, Pullman, WA, B.S. Natural Resource Management with an emphasis in Wildlife Management and a minor in Range Management 1997
• University of Idaho, Moscow, M.S. Forest Resources with an emphasis in Forest Pathology and Geographical Information Systems 2005

Featured Publications & Products

• Kim, M.-S.; Klopfenstein, N. B.; Hanna, J. W.; Cannon, P.; Medel, R.; Lopez, A. 2010. First report of Armillaria root disease caused by Armillaria tabescens on Araucaria araucana in Veracruz, Mexico.
• Klopfenstein, N. B.; Lundquist, J. E.; Hanna, J. W.; Kim, M.-S.; McDonald, G. I. 2009. First report of Armillaria sinapina, a cause of armillaria root disease, associated with a variety of forest tree hosts on sites with diverse climates in Alaska.
• Klopfenstein, Ned B.; Kim, Mee-Sook; Hanna, John W.; Richardson, Bryce A.; Lundquist, John E. 2009. Approaches to predicting potential impacts of climate change on forest disease: an example with Armillaria root disease.
• Hanna, J. W.; Smith, A. L.; Maffei, H. M.; Kim, M.-S.; Klopfenstein, N. B. 2008. Survey of Armillaria spp. in the Oregon East Cascades: Baseline data for predicting climatic influences on Armillaria root disease.
• Hanna, John W.; Kim, Mee-Sook; Klopfenstein, Ned B.; Smith, Aaron L.; Maffei, Helen M. 2008. Determination of suitable climate space for Armillaria ostoyae in the Oregon East Cascades.

Publications

• Warwell, Marcus V; McDonald, Geral I; Hanna, John W.; Kim, Mee-Sook ; Lalande, Bradley M.; Stewart, Jane E.; Hudak, Andrew T.; Klopfenstein, Ned B. 2019. Armillaria altimontana is associated with healthy western white pine (Pinus monticola): Potential in situ biological control of the Armillaria root disease pathogen, A.
• Warwell, Marcus V; Hanna, John W.; McDonald, Geral I; Kim, Mee-Sook ; Lalande, Bradley M.; Stewart, Jane E.; Bright, Ben C.; Klopfenstein, Ned B. 2019. Armillaria altimontana is not associated with reduced growth or survival of western white pine (Pinus monticola) planted in northern Idaho.
• Hanna, John W.; Kim, Mee-Sook ; Ramsey, Amy C.; Omdal, Dan W.; Mulvey, Robin L.; Goodrich, Betsy A.; Ferguson, Brennan A.; Bronson, Josh J.; Chadwick, Kristen L.; Stewart, Jane E.; Maffei, Helen M.; McDonald, Geral I; Pitman, Eric W. I; Warwell, Marcus V; Klopfenstein, Ned B. 2019. Assessing potential Armillaria spp. distributions in western Oregon, western Washington, and Alaska.
• Lalande, Bradley ; Abdo, Zaid ; Hanna, John W.; Page-Dumroese, Deborah S.; Warwell, Marcus V; Tirocke, Joanne M.; Kim, Mee-Sook ; Klopfenstein, Ned B.; Stewart, Jane E. 2019. Metagenomic approaches to determine soil microbial communities associated with Armillaria root disease.
• Elias-Roman, Ruen Damian; Medel-Ortiz, Rosario ; Alvarado-Rosales, Dionicio ; Hanna, John W.; Ross-Davis, Amy L.; Kim, Mee-Sook ; Klopfenstein, Ned B. 2018. Armillaria mexicana, a newly described species from Mexico.
• Ross-Davis, Amy L.; Graca, Rodrigo N.; Alfenas, Acelino C.; Peever, Tobin L.; Hanna, John W.; Uchida, Janice Y.; Hauff, Rob D.; Kadooka, Chris Y.; Kim, Mee-Sook ; Cannon, Phil G.; Namba, Shigetou ; Minato, Nami ; Simeto, Sofia ; Perez, Carlos A.; Rayamajhi, Min B.; Moran, Mauricio ; Lodge, D. Jean; Arguedas, Marcela ; Medel-Ortiz, Rosario ; Lopez-Ramirez, M. Armando; Tennant, Paula ; Glen, Morag ; McTaggart, Alistair ; Klopfenstein, Ned B. 2018. Genetic and genotypic diversity of Puccinia psidii - the cause of guava/eucalypt/myrtle rust - and preliminary predictions of global areas at risk.
• Kim, M. -S.; Fonseca, N. R.; Hauff, R. D.; Cannon, P. G.; Hanna, John; Klopfenstein, Ned. 2017. First report of the root-rot pathogen, Armillaria gallica, on koa (Acacia koa) and 'Ohi'a lehua (Metrosideros polymorpha) on the island of Kaua'i, Hawai'i.
• Stewart, J. E.; Ross-Davis, A.L.; Graҫa, R. N.; Alfenas, A. C.; Peever, T. L.; Hanna, J. W.; Uchida, J. Y.; Hauff, R. D.; Kadooka, C. Y.; Kim, M.-S.; Cannon, P. G.; Namba, S.; Simeto, S.; Pérez, C. A.; Rayamajhi, M. B.; Lodge, D.J.; Arguedas, M.; Medel-Ortiz, R.; López-Ramirez, M. A.; Tennant, P.; Glen, M.; Machado, P. S.; McTaggart, A. R.; Carnegie, A. J.; Klopfenstein, N. B.; Cleary, M. 2017. Genetic diversity of the myrtle rust pathogen (Austropuccinia psidii) in the Americas and Hawaii: Global implications for invasive threat assessments.
• Klopfenstein, Ned B.; Stewart, Jane E.; Ota, Yuko; Hanna, John W.; Richardson, Bryce A.; Ross-Davis, Amy L.; Elias-Roman, Ruben D.; Korhonen, Kari; Keca, Nenad; Iturritxa, Eugenia; Alvarado-Rosales, Dionicio; Solheim, Halvor; Brazee, Nicholas J.; Lakomy, Piotr; Cleary, Michelle R.; Hasegawa, Eri; Kikuchi, Taisei; Garza-Ocanas, Fortunato; Tsopelas, Panaghiotis; Rigling, Daniel; Prospero, Simone; Tsykun, Tetyana; Berube, Jean A.; Stefani, Franck O. P.; Jafarpour, Saeideh; Antonin, Vladimir; Tomsovsky, Michal; McDonald, Geral I.; Woodward, Stephen; Kim, Mee-Sook. 2017. Insights into the phylogeny of Northern Hemisphere Armillaria: Neighbor-net and Bayesian analyses of translation elongation factor 1- gene sequences.
• Stewart, J. E.; Sahashi, N.; Hattori, T.; Akiba, M.; Ota, Y.; Shuey, L.; Schlub, R. L.; Atibalentia, N.; Brooks, F.; Tang, A. M. C.; Lam, R. Y. C.; Leung, M. W. K.; Chu, L. M.; Kwan, H. S.; Farid, A. Mohd; Lee, S. S.; Chung, C. -L.; Lee, H. -H.; Huang, Y.- C.; Liou, R. -F.; Tsai, J. -N.; Cannon, P. G.; Hanna, J. W.; Klopfenstein, N. B.; Kim, M. -S. 2017. Phylogenetic and population analyses of the invasive brown root-rot pathogen (Phellinus noxius) highlight the existence of at least two distinct populations.
• Hanna, J. W.; Kim, M. -S.; Klopfenstein, N. B.; Ramsey, A. C.; Omdal, D. W.; Mulvey, R. L.; Goodrich, B. A.; Ferguson, B. A.; Winton, L. M.; Goheen, E. M.; Bronson, J. J.; Kearns, H. S. J.; Chadwick, K. L.; Murray, M.; Shaw, D. C.; McDonald, G. I.; Pitman, E. W. I.; Warwell, M. V. 2017. Toward a west-wide model of Armillaria root disease: New surveys needed in western Oregon, western Washington, and Alaska.
• Klopfenstein, Ned B.; Pitman, Eric W. I.; Hanna, John W.; Cannon, Phil G.; Stewart, Jane E.; Sahashi, Norio; Ota, Yuko; Hattori, Tsutomu; Akiba, Mitsuteru; Shuey, Louise; Schlub, Robert L.; Brooks, Fred; Atibalentja, Ndeme; Tang, Alvin M. C.; Lam, Regent Y. C.; Leung, Mike W. K.; Chu, L. M.; Kwan, H. S.; Farid bin Ahmad, Mohd; Lee, Su See; Lee, Hsin-Han; Tsai, Jyh-Nong; Huang, Yu-Ching; Chung, Chia-Lin; Liou, Ruey-Fen; Kim, Mee-Sook. 2016. A preliminary bioclimatic approach to predicting potential distribution of Phellinus noxious and geographical areas at risk from invasion.
• Jafarpour, Saeideh; Fotouhifar, Khalil-Berdi; Javan-Nikhhah, Mohammad; Asef, Mohhamad Reza; Davis, Anthony S.; Ross-Davis, Amy L.; Hanna, John W.; Margaritescu, Simona; Moncalvo, Jean-Marc; Klopfenstein, Ned B. 2016. An integrated taxonomic approach to survey Armillaria in Iran.
• Hanna, John; Warwell, M. V.; Maffei, H.; Fairweather, M. L.; Blodgett, J. T.; Zambino, P. J.; Worrall, J.; Burns, K. S.; Jacobs, J. J.; Ashiglar, S. M.; Lundquist, J. E.; Kim, M. -S.; Ross-Davis, Amy; Hoffman, C.; Mathiasen, R.; Hofstetter, R.; Shaw, John; Pitman, E. W. I.; Nelson, E. V.; McDonald, Geral I.; Cleary, M. R.; Brar, S.; Richardson, B.; Klopfenstein, Ned. 2016. Bioclimatic modeling predicts potential distribution of Armillaria solidipes and Pseudotsuga menziesii (Douglas-fir) under contemporary and changing climates in the interior western U.S.A.
• Kim, Mee-Sook; Ross-Davis, Amy L.; Stewart, Jane E.; Hanna, John W.; Warwell, Marcus V.; Zambino, Paul J.; Cleaver, Christy; McDonald, Geral I.; Page-Dumroese, Deborah; Moltzan, Bruce; Klopfenstein, Ned B. 2016. Can metagenetic studies of soil microbial communities provide insights toward developing novel management approaches for Armillaria root disease.
• Ross-Davis, Amy; Stewart, Jane E.; Settles, Matt; Hanna, John W.; Shaw, John D.; Hudak, Andrew T.; Page-Dumroese, Deborah S.; Klopfenstein, Ned B. 2016. Fine-scale variability of forest soil fungal communities in two contrasting habitat series in northern Idaho, USA identified with microbial metagenomics.
• Blodgett, James T.; Hanna, John W.; Pitman, Eric W. I.; Ashiglar, Sara M.; Lundquist, John E.; Kim, Mee-Sook; Ross-Davis, Amy L.; Klopfenstein, Ned B. 2015. Bioclimatic models estimate areas with suitable climate for Armillaria spp. in Wyoming.
• Ross-Davis, Amy; Settles, Matt; Hanna, John W.; Shaw, John D.; Hudak, Andrew T.; Page-Dumroese, Deborah S.; Klopfenstein, Ned B. 2015. Using a metagenomic approach to improve our understanding of Armillaria root disease.
• Cannon, Phil; Klopfenstein, Ned B.; Schlub, Robert L.; Kim, Mee-Sook; Ota, Yuko; Sahashi, Norio; Quitugua, Roland J.; Hanna, John W.; Ross-Davis, Amy L.; Sweeney, J. D. 2014. Characterizing butt-rot fungi on USA-affiliated islands in the western Pacific.
• Cannon, Phil; Klopfenstein, Ned B.; Kim, Mee-Sook; Ota, Yuko; Sahashi, Norio; Schlub, Robert L.; Brown, Roger; Ashiglar, Sara M.; Ross-Davis, Amy L.; Hanna, John W. 2014. Characterizing forest root and butt rot fungi in Yap, Palau, Pohnpei, Kosrae, Guam and Saipan Chapter III.
• Hanna, John W.; Blodgett, James T.; Pitman, Eric W. I.; Ashiglar, Sarah M.; Lundquist, John E.; Kim, Mee-Sook; Ross-Davis, Amy L.; Klopfenstein, Ned B. 2014. Climate-based species distribution models for Armillaria solidipes in Wyoming: A preliminary assessment.
• Klopfenstein, N. B.; Hanna, J. W.; Cannon, P. G.; Medel-Ortiz, R.; Alvarado-Rosales, D.; Lorea-Hernandez, F.; Elias-Roman, R. D.; Kim, M. -S. 2014. First report of the Armillaria root-disease pathogen, Armillaria gallica, associated with several woody hosts in three states of Mexico.
• Ross-Davis, Amy L.; Stewart, Jane E.; Hanna, John W.; Shaw, John D.; Hudak, Andrew T.; Jain, Theresa B.; Denner, Robert J.; Graham, Russell T.; Page-Dumroese, Deborah S.; Tirocke, Joanne M.; Kim, Mee-Sook; Klopfenstein, Ned B. 2014. Forest soil microbial communities: Using metagenomic approaches to survey permanent plots.
• Hoffman, Christ W.; Mathiasen, Robert L.; Hofstetter, Richard W.; Fairweather, Mary Lou; Shaw, John D.; Hanna, John W.; Klopfenstein, Ned B. 2014. Survey for Armillaria by plant associations in northern Arizona.
• Ashiglar, Sara M.; Hanna, John W.; Ross-Davis, Amy L.; Klopfenstein, Ned B. 2014. The USDA Forest Service-RMRS forest fungi collection: Resource for fungal identification, developing biological controls, predicting invasive pathogens, and predicting potential impacts of climate change.
• Ross-Davis, Amy L.; Graca, Rodrigo N.; Alfenas, Acelino C.; Peever, Tobin L.; Hanna, Jack W.; Uchida, Janice Y.; Hauff, Rob D.; Kadooka, Chris Y.; Kim, Mee-Sook; Cannon, Phil G.; Namba, Shigetou; Minato, Nami; Simeto, Sofia; Perez, Carlos A.; Rayamajhi, Min B.; Moran, Mauricio; Lodge, D. Jean; Arguedas, Marcela; Medel-Ortiz, Rosario; Lopez-Ramirez, M. Armando; Tennant, Paula; Glen, Morag; Klopfenstein, Ned B. 2014. Tracking the distribution of Puccinia psidii genotypes that cause rust disease on diverse myrtaceous trees and shrubs.
• Klopfenstein, Ned B.; Hanna, John W.; Ross-Davis, Amy L.; Stewart, Jane E.; Ota, Yuko; Medel-Ortiz, Rosario; Lopez-Ramirez, Miguel Armando; Elias-Roman, Ruben Damian; Alvarado-Rosales, Dionicio; Kim, Mee-Sook. 2013. Armillaria phylogeny based on tef-1α sequences suggests ongoing divergent speciation within the boreal floristic kingdom.
• Case, Anna E.; Ashiglar, Sara M.; Cannon, Phil G.; Militante, Ernesto P.; Tadiosa, Edwin R.; Quintos-Manalo, Mutya; Pampolina, Nelson M.; Hanna, John W.; Brooks, Fred E.; Ross-Davis, Amy L.; Kim, Mee-Sook; Klopfenstein, Ned B. 2013. DNA-based approaches to identify forest fungi in Pacific Islands: A pilot study.
• Elias-Roman, Ruben D.; Klopfenstein, Ned B.; Kim, Mee-Sook; Alvarado-Rosales, Dionicio; Hanna, John W.; Ross-Davis, Amy L.; Guzman-Plazola, Remigio Anastacio; Calderon-Zavala, Guillermo; Mora-Aguilera, Antonio. 2013. DNA-based identification of Armillaria isolates from peach Prunus persica (l.) batsch orchards in m xico state, Mexico.
• Ross-Davis, Amy L.; Kim, Mee-Sook; Stewart, Jane E.; Hanna, John W.; Shaw, John D.; Klopfenstein, Ned B. 2013. From diagnostics to metagenomics: Applications of DNA-based tools in forest pathology.
• Ross-Davis, A. L.; Stewart, J. E.; Hanna, J. W.; Kim, M.-S.; Knaus, B. J.; Cronn, R.; Rai, H.; Richardson, B. A.; McDonald, G. I.; Klopfenstein, N. B. 2013. Transcriptome of an Armillaria root disease pathogen reveals candidate genes involved in host substrate utilization at the host -pathogen interface.
• Hanna, J. W.; Graca, R. N.; Kim, M. -S.; Ross-Davis, A. L.; Hauff, R. D.; Uchida, J. W.; Kadooka, C. Y.; Rayamajhi, M. B.; Arguedas Gamboa, M.; Lodge, D. J.; Medel-Ortiz, R. Medel; Lopez Ramirez, A.; Cannon, P. G.; Alfenas, A. C.; Klopfenstein, N. B. 2012. A bioclimatic approach to predict global regions with suitable climate space for Puccina psidii.
• Ross-Davis, Amy L.; Hanna, John W.; Kim, Mee-Sook; Klopfenstein, Ned B. 2012. Advances toward DNA-based identification and phylogeny of North American Armillaria species using elongation factor-1 alpha gene.
• Kim, Mee-Sook; Hanna, John; Ross-Davis, Amy; Klopfenstein, Ned. 2012. Application of molecular genetic tools for forest pathology.
• Hanna, John; Ashiglar, Sara; Case, Anna; Fairweather, Mary Lou; Hoffman, Chris; Kim, Mee-Sook; Maffei, Helen; Mathiasen, Robert; McDonald, Geral; Nelson, Erik; Ross-Davis, Amy; Shaw, John; Klopfenstein, Ned. 2012. Armillaria root disease in the western USA.
• Klopfenstein, Ned B.; Kim, Mee-Sook; Hanna, John W.; Ross-Davis, Amy L.; Ashiglar, Sara M.; McDonald, Geral I. 2012. Armillaria species: Primary drivers of forest ecosystem processes and potential impacts of climate change.
• Roman, Ruben Damian Elias; Klopfenstein, Ned B.; Rosales, Dionicio Alvarado; Kim, Mee-Sook; Case, Anna E.; Ashiglar, Sara M.; Hanna, John W.; Ross-Davis, Amy L.; Guzman Plazola, Remigio A. 2012. DNA-based identification of Armillaria isolates from peach orchards in Mexico state.
• Ross-Davis, Amy L.; Stewart, Jane E.; Hanna, John W.; Kim, Mee-Sook; Cronn, Rich C.; Rai, Hardeep S.; Richardson, Bryce A.; McDonald, Geral I.; Klopfenstein, Ned B. 2012. De novo assembly and transcriptome characterization of an Armillaria solidipes mycelial fan.
• Klopfenstein, N. B.; Hanna, J. W; Fairweather, M. L.; Shaw, J. D.; Mathiasen, R.; Hoffman, C.; Nelson, E.; Kim, M. -S.; Ross-Davis, A. L. 2012. Developing a prediction model for Armillaria solidipes in Arizona.
• Hanna, J. W.; Klopfenstein, N. B.; Kim, M. -S.; Ashiglar, S. M.; Ross-Davis, A. L.; McDonald, G. I. 2012. Discovery of cryptic Armillaria solidipes genotypes within the Colorado Plateau.
• Klopfenstein, N. B.; Hanna, J. W.; Graca, R. N.; Ross-Davis, A. L.; Cannon, P. G.; Alfenas, A. C.; Kim, M. -S. 2011. Approaches to predicting current and future distributions of Puccinia psidii in South America under climate change scenarios.
• Klopfenstein, Ned B.; Kim, Mee-Sook; Hanna, John W.; Richardson, Bryce A.; Lundquist, John E. 2011. Approaches to predicting potential impacts of climate change on forest disease: An example with Armillaria root disease.
• Ross-Davis, Amy L.; Hanna, John W.; Klopfenstein, Ned B. 2011. DNA-based identification and phylogeny of North American Armillaria species.
• McDonald, Geral I.; Hanna, John W.; Smith, Aaron L.; Maffei, Helen M.; Kim, Mee-Sook; Ross-Davis, Amy L.; Klopfenstein, Ned B. 2011. Preliminary report on the ecology of Armillaria in the East Cascades of Oregon.
• Kim, M.-S.; Hanna, J. W.; Klopfenstein, N. B. 2010. First report of an Armillaria root disease pathogen, Armillaria gallica, associated with several new hosts in Hawaii.
• Cannon, Phil; Klopfenstein, Ned B.; Kim, Mee-Sook; Hanna, John W.; Rosales, Dionicio Alvarado. 2008. An Armillaria survey in Mexico: A basis for determining evolutionary relationships, assessing potentially invasive pathogens, evaluating future impacts of climate change, and developing international collaborations in forest pathology.
• Hanna, J. W.; Klopfenstein, N. B.; Kim, M. -S. 2007. First report of the root-rot pathogen, Armillaria nabsnona, from Hawaii.
• Hanna, J. W.; Klopfenstein, N. B.; Kim, M. -S.; McDonald, G. I.; Moore, J. A. 2007. Phylogeographic patterns of Armillaria ostoyae in the western United States.
• Kim, M. -S.; Klopfenstein, N. B.; Hanna, J. W.; McDonald, G. I. 2006. Characterization of North American Armillaria species: Genetic relationships determined by ribosomal DNA sequences and AFLP markers.

Research Highlights

Highlight	Title	Year
RMRS-2017-202	Using DNA to correctly identify destructive vs. beneficial Armillaria fungus Species of the fungal genus Armillaria are associated with forest ecosystems worldwide. Some species are destructive root disease pathogens, whi ...	2017