Dr. John K Kelly

Dr. John Kelly
  • Professor
  • Research Interests: Evolutionary Genetics, Quantitative Genetics, Evolutionary Theory, Science

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Office: Haworth Hall 5005


Dr. John Kelly studies evolutionary genetics.


It is widely believed that evolutionary processes are too slow to allow direct measurement of genetic changes. For this reason, most applications of evolutionary theory are historical in nature. A theory is tested by comparing its predictions to extant patterns of variation in nature, either within or across taxa. However, when evolutionary changes occur at a rapid pace, it is possible to directly test the dynamical predictions of evolutionary models. There are now many documented examples of rapidly evolving biological systems. One of our primary objectives is to construct and test models that predict observable changes in the genetic composition of populations. These "dynamical studies" augment historical analyses and directly address a wide range of fundamental questions in evolutionary biology. At present, our laboratory is mainly concerned with quantitative trait evolution in the wildflower Mimulus guttatus (yellow monkeyflower). Given that most interesting traits are complex (influenced by both genes and the environment), quantitative genetics provides a natural framework for predicting trait evolution. We use a mixture of classical techniques (e.g. controlled crosses, inbreeding, and artificial selection), along with modern molecular approaches (e.g. QTL mapping). Principle questions are: (1) How do mutation, migration, genetic drift and natural selection interact to maintain genetic variation in nature? (2) What is the genetic architecture of variation in ecologically important traits such as flower size and pollen viability? (3) How does non-random mating, particularly the tendency of many plant species to self-fertilize, affect evolutionary change? and (4) Do genetic 'complexities' such as pleiotropy and epistasis qualitatively alter the evolutionary process? A secondary interest in our laboratory is gene sequence evolution, with a particular focus on viral pathogens. Many viral pathogens, including the Human Immunodeficiency Virus (HIV), undergo extensive genetic evolution within a single host. Elucidating the causes and consequences of these genetic changes for disease transmission and pathogenesis is a major challenge for both evolutionary biology and epidemiology.

Research interests:

  • quantitative trait evolution in plant populations
  • molecular evolution
  • evolution in viruses and other pathogens
  • kin selection


Teaching interests:

  • statistics

Selected Publications

  • Brown, K. E., & Kelly, J. K.  2020. Severe inbreeding depression is predicted by the “rare allele load” in Mimulus guttatus. Evolution 74(3), 587-596. doi:10.1111/evo.13876
  • Colicchio, J., Monnahan, P., Wessinger, C. A., Keely, B., Kern, J. R., and Kelly, J. K.  2020.  Individualized mating system estimation using genomic data.  Molecular Ecology Resources 20:333-347.  doi:10.1111/1755-0998.13094
  • Kelly, J. K. and K. A. Hughes. 2019. Pervasive Linked Selection and Intermediate-Frequency Alleles Are Implicated in an Evolve-and-Resequencing Experiment of Drosophila simulans. Genetics 211(3): 943-961.
  • Troth, A., J.R Puzey, R.S. Kim, J.H. Willis, J.K. Kelly. 2018.  Selective tradeoffs maintain alleles underpinning complex trait variation in plants.  Science, Vol. 361, Issue 6401, pp. 475-478.
  • Monnahan, P., J. Colicchio, and J.K. Kelly.  2015.  A genomic selection component analysis characterizes migration-selection balance.  Evolution, 69(7): 1713–1727.
  • Monnahan, Patrick J., and John K. Kelly. “Epistasis Is a Major Determinant of the Additive Genetic Variance in Mimulus Guttatus.” Journal Articles. PLOS GENETICS 11, no. 5 (2015). https://doi.org/10.1371/journal.pgen.1005201.