Matthew Zinkgraf

Associate Professor


I am a Midwesterner, a member of the Brothertown Indian Nation, and have a deep love for the outdoors. My fascination and respect for the natural world was developed at an early age. Having grown up in Fond du Lac, Wisconsin, I spent much of my youth outside running around the forest and working on family farms. In high school, I took on a strong interest in conservation and was active in the school environmental club, which organized trips to local natural areas and did a lot of birding.  

These experiences lead me to enroll at the University of WI – Stevens Point but the actual direction of my degree took some time to figure out because of my broad interest in biology, conservation and the outdoors. As a first-generation college student, I was not sure what it was like to do research, field work or be a scientist. During my undergraduate studies, I had the opportunity to teach rock climbing, lead backpacking trips, conduct biology research on potato susceptibility and have three summers of field work for the US Forest Service in Minnesota and the Rocky Mountains. These were transformational experiences that allowed me to travel to new parts of the country, develop some independence, and explore what it was like to be a scientist. In the end, I pursued a dual major in Biology and Natural Resource Management, and a minor in conservation biology. 

My experiences as an undergraduate ultimately led to my interest in research and gave me the motivation pursue graduate degrees from the University of University of WI – Stevens Point (M.S.) and Northern Arizona University (PhD). During my graduate studies, I conducted research on bioremediation, genetics, ecology and evolution with cottonwood trees. My current research uses computational and genomic approaches to understand how genetic variation and evolutionary processes shape traits in forest trees. 

These opportunities to continue my education and have a career in science would not have happen without the help of countless mentors. For me mentors have taken on many different forms and have ranged from faculty advisors, instructors and IT support staff. Looking back, I have realized that some of the most influential people were those willing to give me a chance because my grades were not always outstanding. These mentors helped give me the confidence to realize that I could be a scientist and helped me independently learn new material to keep up with current technology such as programming and computational biology. This path of independent learning has helped me become more interdisciplinary but has posed some challenges (e.g. self motivation and extra work) and sometimes I feel like an imposter because I have not been formally trained in some of these fields. 

Outside of science, I am an avid woodworker that has built two wooden boats and outdoor enthusiast including fly-fishing, skiing, hiking and camping. Recently, I have started to machine metal and make fly fishing reels. I am not formally trained and hesitate to call myself a machinist (i.e. imposter), but regardless of title, fishing these handmade reels has been an awesome experience. 

Research Interests

My research is focused on the ecological and evolutionary genetics of plants. To accomplish this research, my lab applies an interdisciplinary approach that utilizes methods from computational biology, molecular biology, genetics/genomics and forest ecology. Ongoing research in the lab is concentrated around three main themes: 1) dissecting how genetic variation of populations is structured across the landscape, 2) identifying process that have influenced the adaptation and evolution of populations and 3) understanding the genetic regulation of important ecologically and economically traits such as wood formation, response to abiotic stress and resistance to insects. These studies are primarily focused on undomesticated forest trees because forests are the foundation of many natural systems in the world, which society relies heavily upon for ecosystem services, forest products, and recreation. 

Educational & Professional Experience


  • B.S. in Biology and Natural Resource Management from the University of Wisconsin at Stevens Point, 2001
  • M.S. in Natural Resources from the University of Wisconsin at Stevens Point, 2004 
  • Ph.D. in Biology from Northern Arizona University, 2012

Professional Preparation

  • Postdoctoral Fellow - US-Forest Service, 2013-2014
  • Postdoctoral Fellow - NSF-Plant Genome Research Program, 2015-2017

Recent Publications

  1. Lee, S.R.; D.A. Pollard; D.F. Galati; M.L. Kelly**; B. Miller; C. Mong**; M.N. Morris**; K. Roberts- Nygren**; G.M. Kapler; M. Zinkgraf; H.Q. Dang; E. Branham; E. Tessier**; C. Yoshiyama**; J. Sasser**; M. Matsumoto**; G. Turman**. 2021. Disruption of constitutive RNA interference pathway leads to DNA damage in Tetrahymena thermophila. Molecular Biology of the Cell 32(15):1331-1407. ** designates WWU undergraduate researcher
  2. Lamit, L.J.; K.A. Meinhardt; L. Flores-Rentería; Z.I. Kovacs; M. Zinkgraf; T.G. Whitham; C.A. Gehring. 2021. Ectomycorrhizal fungal communities differ among parental and hybrid Populus cross types within a natural riparian habitat. Fungal Ecology 50:101059.
  3. Zinkgraf, M.*; S.-T Zhao*; C. Canning; S. Gerttula; M.-Z. Lu; V. Filkov; and A. Groover. 2020. Evolutionary network genomics of wood formation in a phylogenetic survey of angiosperm forest trees. New Phytologist 228: 1811-1823. *designates equal contribution
  4. Bastiaanse, H.; M.S. Zinkgraf; C. Canning; H. Tsai; M. Lieberman; L. Comai; I.M. Henry; and A.T. Groover 2019. Effect of gene dosage variation on phenology and biomass in Populus trees. Proceedings of the National Academy of Sciences 116 (27): 13690-13699.
  5. Body, M.; M.S. Zinkgraf; T.G. Whitham; C.-H. Lin; R.A. Richardson; H.M. Appel; and J.C. Schultz. 2019. Heritable phytohormone profiles of poplar genotypes vary in resistance to a galling aphid. Molecular Plant-Microbe Interactions 32(6): 654-672.
  6. Zinkgraf, M.S.; A.T. Groover and V. Filkov. 2018. Reconstructing gene networks of forest trees from gene expression data: Toward higher-resolution approaches. ICT Innovations 2018. Engineering and Life Sciences. Cham: Springer International Publishing, Switzerland. pp. 3-12. 
  7. Zinkgraf, M.S.; S. Gerttula; S. Zhao; V. Filkov and A.T. Groover. 2018. Transcriptional and temporal response of Populus stems to gravi-stimulation. Journal Integrated Plant Biology 60(7): 578-590. 
  8. Woolbright, S.A.; B.J. Rehill, R.L. Lindroth, S.P. DiFazio, G.D. Martinsen, M.S. Zinkgraf, G.J. Allan, P. Keim and T.G. Whitham. 2018. Large effect quantitative trait loci for salicinoid phenolic glycosides in Populus: Implications for gene discovery. Ecology and Evolution 8(7): 3726-3737. 
  9. Zinkgraf, M.S.; S. Gerttula and A.T. Groover. 2017. Transcript profiling of a novel plant meristem, the monocot cambium. Journal Integrated Plant Biology 59:436-449.
  10. Zinkgraf, M.S.; L. Liu; A. Groover and V. Filkov. 2017. Identifying gene co-expression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions. New Phytologist 214:1464-1478.
  11. Zinkgraf, M.S.; K. Haiby; M. Lieberman; L. Comai, I. Henry and A. Groover. 2016. Creation and analysis of irradiation hybrids in Populus. Current Protocols in Plant Biology 1:431-450.
  12. Zinkgraf, M.S.; N. Meneses; T.G. Whitham and G. Allan. 2016. Genetic variation in NIN1 and C/VIF1 genes is significantly associated with Populus angustifolia resistance to a galling herbivore, Pemphigus betae. Journal of Insect Physiology 84:50-59.
  13. Gerttula, S.; M.S. Zinkgraf; G.K. Muday; D.R. Lewis; F.M. Ibatullin; H. Brumer; F. Hart; S.D. Mansfield; V. Filkov and A.T. Groover 2015. Transcriptional and hormonal regulation of gravitropism of woody stems in Populus. Plant Cell 27:2800-2813.
  14. Henry, I.M.; M.S. Zinkgraf; A.T. Groover and L. Comai. 2015. A system for dosage-based functional genomics in Poplar. Plant Cell 27:2370-2383.
  15. Lamit, L.J.; P.E. Busby; M.K. Lau; Z.G. Compson; T. Wojtowicz; A.R. Keith; M.S. Zinkgraf; J.A. Schweitzer; S.M. Shuster; C.A. Gehring and T.G. Whitham. 2015. Tree genotype mediates covariance among communities from microbes to lichens and arthropods. Journal of Ecology. 103:840-850.
  16. Liu, L.; T. Ramsay; M. Zinkgraf; D. Sundell; N.R. Street; V. Filkov and A. Groover. 2015. A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus. Plant Journal 82:887-898.
  17. Liu, L.; M. Zinkgraf; H.E. Petzold; E.P. Beers; V. Filkov and A. Groover. 2015. The Populus ARBORKNOX1 homeobox transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function. New Phytologist 205:68-694
  18. Liu, L.; V. Missirian; M. Zinkgraf; A. Groover and V. Filkov. 2014. Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees. BMC Genomics 15:S3
  19. Holeski, L.M.; M.S. Zinkgraf; J.J. Couture; T.G. Whitham; R.L. Lindroth and S. Bonser. 2013.Transgenerational effects of herbivory in a group of long-lived tree species: maternal damage reduces offspring allocation to resistance traits, but not growth. Journal of Ecology 101: 1062-1073.
  20. Adams, R.I.; S. Goldberry; T.G. Whitham; M.S. Zinkgraf and R. Dirzo. 2011. Genetic diversity of a dominant tree positively correlates with understory plant diversity. American Journal of Botany 98:1623-1632.
  21. Compson, Z.G.; K.C. Larson; M.S. Zinkgraf and T.G. Whitham. 2011. A genetic basis for the manipulation of sink-source relationships by the galling aphid, Pemphigus betae. Oecologia 167:711-721.
  22. Lamit, L.J.; T. Wojtowicz; Z. Kovacs; S.C. Wooley; M. Zinkgraf; T.G. Whitham; R.L. Lindroth and C.A. Gehring. 2011. Hybridization among foundation tree species influences the structure of associated understory plant communities. Botany 89:165-174.
  23. Lamit, L.J.; M.A. Bowker; L.M. Holeski; R. Naeborg; S.C. Wooly; M. Zinkgraf; R.L. Lindroth; T.G. Whitham and C.A. Gehring. 2011. Genetically-based trait variation within a foundation tree species influences a dominant bark lichen. Fungal Ecology 4:103-106.