Shaffer, J.D. 2023. "Competition and Herbivory Influence the Survival, Growth, and Physiology of Native Tree Seedlings in the Kentucky Inner Bluegrass Savanna-Woodland." Theses and Dissertations--Biology. Paper 93. https://uknowledge.uky.edu/biology_etds/93/
Westneat, D.F., Potts, L.J., Sasser, K.L., and Shaffer, J.D. 2019. Causes and consequences of phenotypic plasticity in complex environments. Trends in Ecology & Evolution 34(6): 555-568. https://doi.org/10.1016/j.tree.2019.02.010
Shaffer, J.D., Gleeson, S.K., and Cox, J.J. 2016. Incorporating Disturbance Ecology into Native Hardwood Tree Seedling Restorations of the Kentucky Inner Bluegrass Savanna-Woodland. Kentucky Department of Fish and Wildlife Resources Annual Research Highlights, 2015. Volume IX. Publication of the Wildlife and Fisheries Division. November 2016, 85 pp. https://fw.ky.gov/More/documents/2015researchhighlights.pdf
Shaffer, J.D. 2016. Emerald Ash Borer Threatens Native Ash Trees. EcoLink: Newsletter of the Ecological Research and Education Center (Field Station of the Bluegrass). Ecolink 1(2): 2. http://darwin.uky.edu/~erec/documents/EcoLink_V01-I02.pdf
Shaffer, J.D. 2016. Tree Restoration in Kentucky Bluegrass Woodlands. EcoLink: Newsletter of the Ecological Research and Education Center (Field Station of the Bluegrass). Ecolink 1(1): 2. http://darwin.uky.edu/~erec/documents/EcoLink_V01-I01_Feb2016.pdf
Shaffer, J.D., Gleeson, S.K., Cox, J.J, and Lhotka, J.M. 2014. Ecological Factors Influencing Native Hardwood Seedling Establishment in the Kentucky Inner Bluegrass Blue Ash-Oak Savanna-Woodland. Kentucky Department of Fish and Wildlife Resources Annual Research Highlights, 2013. Volume VII. Publication of the Wildlife and Fisheries Division. October 2014: 90pp (p 45). http://fw.ky.gov/More/Documents/2013ResearchHighlights.pdf
Shaffer, J.D. 2013. "Factors Influencing the Establishment and Survival of Native Hardwood Tree Seedlings of the Kentucky Inner Bluegrass Blue Ash-Oak Savanna-Woodland". Theses and Dissertations--Biology. Paper 15. http://uknowledge.uky.edu/biology_etds/15/