John Kelly

Professor, Ecology and Evolutionary Biology
Ph.D. University of Chicago, 1996
Primary office:
Haworth Hall


Dr. Kelly studies evolutionary quantitative genetics, molecular population genetics, evolution of pathogens, and kin selection.

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.

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Selected Publications

  • Troth, A., Puzey, J. R., Kim, R. S.,  Willis,J. H., Kelly, J. K. 2018.  Selective tradeoffs maintain alleles underpinning complex trait variation in plants.  Science 361 (6401): 475-478.
  • Wessinger, C. A.  Kelly, J. K., Jiang, P., Rausher, M.D., Hileman, L.C.  2018.  SNP skimming: a fast approach to map loci generating quantitative variation in natural populations.  Molecular Ecology Methods 18(6): 1402-1414.
  • Brown, K., and Kelly, J.K.  2018.  Antagonistic pleiotropy can maintain fitness variation in annual plants.  Journal of Evolutionary Biology 31: 46–56.
  • Colicchio, J. M., Kelly, J. K., and Hileman, L. C.  2018.  Parental experience modifies the Mimulus methylome.  BMC Genomics 19(1): 746.
  • Wessinger, C., and Kelly, J.K.  2018.  Selfing can facilitate transitions between pollination syndromes.  American Naturalist 191(5): 582-594.
  • Koseva, B., Crawford, D. J., Brown, K. E., Mort, M. E., and Kelly, J. K. 2017. The genetic breakdown of sporophytic self-incompatibility in Tolpis coronopifolia (Asteraceae). New Phytologist 216(4): 1256-1267. doi:10.1111/nph.14759 ISSN: 0028-646X
  • Monnahan, P. J., and Kelly, J. K. 2017. The genomic architecture of flowering time varies across space and time in mimulus guttatus. Genetics 206(3): 1621-1635. doi: 10.1534/genetics.117.201483
  • Kerbs, B., Ressler, J., Kelly, J. K., Mort, M. E., Santos-Guerra, A., Gibson, Matthew J. S., Caujape-Castells, J., and Crawford, D. J. 2017. The potential role of hybridization in diversification and speciation in an insular plant lineage: insights from synthetic interspecific hybrids. AoB Plants 9. doi:10.1093/aobpla/plx043
  • Puzey, J. R., Willis, J. H., and Kelly, J. K. 2017. Population structure and local selection yield high genomic variation in Mimulus guttatus. Molecular Ecology, 26(2), 519-535.
  • Akkerman, K. C., Sattarin, A., Kelly, J. K., and Scoville, A. G. 2016. Transgenerational plasticity is sex-dependent and persistent in yellow monkeyflower (Mimulus guttatus). Environmental Epigenetics 2(2): dvw003.
  • Lee, Y. W., Fishman, L., Kelly, J. K., and Willis, J. H. 2016. A Segregating Inversion Generates Fitness Variation in Yellow Monkeyflower (Mimulus guttatus). Genetics 202(4): 1473-84.
  • Crawford, D. J., Hauber,D. P.,  Borges Silva, L., Menezes de Sequeira, M., Moura, M., Santos-Guerra, A.,  Kelly, J. K., and Mort, M. E.  2016. Breeding Relationships in Macaronesian Tolpis (Asteraceae-Cichorieae): F1 Hybrid Pollen Fertility Within and Among Populations from the Azores, Canary Islands, and Madeira. Systematic Botany 41(4): 881-893.
  • Colicchio, J. M., Monnahan, P. J., Kelly, J. K., and Hileman, L. C. (2015). Gene expression plasticity resulting from parental leaf damage in Mimulus guttatus. New Phytologist, 205(2), 894–906. doi:10.1111/nph.13081 ISSN: 1469-8137
  • Crawford, D. J., Anderson, G. J., Silva, L. B., de Sequeira, M. M., Moura, M., Santos-Guerra, A., Kelly, J. K., and Mort, M. E. (2015). Breeding systems in Tolpis (Asteraceae) in the Macaronesian islands: the Azores, Madeira and the Canaries. Plant Systematics Evolution 301(8), 1981-1993. doi:10.1007/s00606-015-1210-5 ISSN: 0378-2697
  • Monnahan, P. J., and Kelly, J. K. (2015). Naturally segregating loci exhibit epistasis for fitness. Biology Letters 11(8). doi:10.1098/rsbl.2015.0498 ISSN: 1744-9561
  • Monnahan, P. J., Colicchio, J., and Kelly, J. K. (2015). A genomic selection component analysis characterizes migration-selection balance. Evolution 69(7), 1713-1727. doi:10.1111/evo.12698 ISSN: 0014-3820
  • Colicchio, J. M., Miura, F., Kelly, J. K., Ito, T., and Hileman, L. C. (2015). DNA methylation and gene expression in Mimulus guttatus. BMC Genomics, 16. doi:10.1186/s12864-015-1668-0
  • Fishman, L., and Kelly, J. K. (2015). Centromere-associated meiotic drive and female fitness variation in Mimulus. Evolution 69(5), 1208-1218. doi:10.1111/evo.12661 ISSN: 0014-3820
  • Monnahan, P. J., and Kelly, J. K. (2015). Epistasis Is a Major Determinant of the Additive Genetic Variance in Mimulus guttatus. PLOS Genetics 11(5). doi:10.1371/journal.pgen.1005201
  • Mort, M. E., Crawford, D. J., Kelly, J. K., Santos-Guerra, A., de Sequeira, M. M., Moura, M., and Caujape-Castells, J. (2015). Multiplexed-shortgun-genotyping data resolve phylogeny within a very recently derived insular lineage.  American Journal of Botany 102(4), 634-641. doi:10.3732/ajb.1400551 ISSN: 0002-9122
  • Holeski, L. M., Monnahan, P., Koseva, B., McCool, N., Lindroth, R. L., & Kelly, J. K. (2014). A high-resolution genetic map of yellow monkeyflower identifies chemical defense QTLs and recombination rate variation. G3: Genes| Genomes| Genetics, 4(5), 813–821.
  • Delph, L. F., & Kelly, J. K. (2014). On the importance of balancing selection in plants. New Phytologist, 201(1), 45–56.
  • Soto-Trejo, F., J. K. Kelly, J. K. Archibald, M. E. Mort, A. Santos-Guerra, and D. J. Crawford. 2013. "The genetics of self-compatibility and associated floral characters in Tolpis (Asteraceae) in the Canary Islands" International Journal of Plant Sciences. 174. 171-178.
  • Mojica, J. P., Y. W. Lee, J. H. Willis, and J. K. Kelly. 2012. "Spatially and temporally varying selection on intrapopulation QTL for a life history tradeoff in Mimulus guttatus" Molecular Ecology. 21. 3718-3728.
  • Ward, J. K., D. S. Roy, I. Chatterjee, C. R. Bone, C. J. Springer, and J. K. Kelly. 2012. "Identification of a major QTL that alters flowering time at elevated [CO2] in Arabidopsis thaliana" PLoS ONE. 7. e49028.
  • Storz, J. F., Z. A. Cheviron, F. G. Hoffmann, and J. K. Kelly. 2012. "Altitudinal Variation at Duplicated β-Globin Genes in Deer Mice: Effects of Selection, Recombination, and Gene Conversion" Genetics. 190. 203-216.
  • Koelling, V. A., P. J. Monnahan, and J. K. Kelly. 2012. "A Bayesian Method for the Joint Estimation of Outcrossing Rate and Inbreeding Depression" Heredity. 109. 393-400.
  • McLeod, D. S., J. K. Kelly, and A. Barley. 2012. ""Same-same But Different": Another New Species Of The Limnonectes kuhlii Complex From Thailand (Anura: Dicroglossidae)" Russian Journal of Herpetology. 19(3). 261-274.
  • Magwene, P. M., J. H. Willis, and J. K. Kelly. 2011. "The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing" PLoS Computational Biology. 7(11). e1002255.
  • Zhou, Y., J. K. Kelly, and M. D. Greenfield. 2011. "Testing the Fisherian Mechanism: Examining the Genetic Correlation between Male Song and Female Response in Waxmoths" Evolutionary Ecology. 25. 307-309.
  • Bodbyl-Roels, S. A. and J. K. Kelly. 2011. "Rapid evolution caused by pollinator loss in Mimulus guttatus" Evolution. 65. 2541-2552.
  • Kelly, J. K. and J. P. Mojica. 2011. "Interactions among flower size QTLs of Mimulus guttatus are abundant but highly variable in nature" Genetics. 189. 1461-1471.
  • Scoville, A. G., Y. W. Lee, J. H. Willis, and J. K. Kelly. 2011. "Explaining the heritability of an ecologically significant trait in terms of individual QTLs" Biology Letters. 7. 896-898.
  • Scoville, A. G., L. L. Barnett, S. A. Bodbyl-Roels, J. K. Kelly, and L. C. Hileman. 2011. "Differential regulation of a MYB transcription factor is correlated with transgenerational epigenetic inheritance of trichome density in Mimulus guttatus" New Phytologist. 191. 251-263.
  • Mojica, J. P. and J. K. Kelly. 2010. "Viability selection prior to trait expression is an essential component of natural selection" Proceedings of the Royal Society, London Series B. 277. 2945-2950.
  • Holeski, L. M., R. Chase-Alone, and J. K. Kelly. 2010. "The genetics of phenotypic plasticity and ontogenetic variation in a plant defense: Trichome production in Mimulus guttatus" American Naturalist. 175. 391-400.
  • Eckert, C. G. et al. 2010. "Plant mating systems in a changing world" TREE. 25(1). 35-43.
  • Crawford, D. J., J. K. Archibald, J. K. Kelly, M. E. Mort, and A. Santos-Guerra. 2010. "Mixed mating system in obligately outcrossing Tolpis (Asteraceae) in the Canary Islands" Plant Species Biology. 25. 114-119.
  • Porcher, E., J. K. Kelly, P. Cheptou, C. G. Eckert, M. O. Johnston, and S. Kalisz. 2009. "The genetic consequences of fluctuating inbreeding depression and the evolution of plant mating systems" Journal of Evolutionary Biology. 22. 708-717.
  • Scoville, A. G., Y. W. Lee, J. H. Willis, and J. K. Kelly. 2009. "The contribution of chromosomal polymorphisms to the G-matrix of Mimulus guttatus" New Phytologist. 183. 803-815.
  • Wacker, M. J., L. M. Kosloski, W. J. R. Gilbert, C. D. Touchberry, D. S. Moore, J. K. Kelly, M. A. Brotto, and J. A. Orr. 2009. "Inhibition of thromboxane A2-induced arrhythmias and intracellular calcium changes in cardiac myocytes by blockade of the IP3 pathway" Journal of Pharmacology and Experimental Therapeutics. 331. 917-924.
  • Marriage, T. N. and J. K. Kelly. 2009. "Inbreeding depression in an asexual population of Mimulus guttatus" The Journal of Experimental Biology. 22. 2320-2331.
  • Johnston, M. O. et al. 2009. "Genetic correlations among fertility components are likely to maintain mixed mating in plants" American Naturalist. 173. 1-11.
  • Storz, J. F., A. M. Runck, S. J. Sabatino, J. K. Kelly, N. Ferrand, A. Fago, R. E. Weber, and H. Moriyama. 2009. "Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin" Proceedings of the National Academy of Sciences of the United States of America. 106. 14450-14455.
  • Marriage, T. N., S. Hudman, M. E. Mort, M. E. Orive, R. G. Shaw, and J. K. Kelly. 2009. "Direct estimation of the mutation rate at dinucleotide microsatellite loci in Arabidopsis thaliana (Brassicaceae)" Heredity. 103. 310-317.
  • Kelly, J. K.. 2009. "Connecting QTLs to the G-Matrix of evolutionary quantitative genetics" Evolution. 63(4). 813-825.
  • Kelly, J. K., L. M. Holeski, and H. S. Arathi. 2008. "The genetic correlation between flower size and water use efficiency in Monkeyflowers" Evolutionary Ecology Research. 10. 147-152.
  • Kelly, J. K.. 2008. "Testing the rare-alleles model of quantitative variation by artificial selection" Genetica. 132. 187-198.
  • Springer, C. J., R. A. Orozco, J. K. Kelly, and J. K. Ward. 2008. "Elevated CO2 Influences the Expression of Floral-Initiation Genes in Arabidopsis thaliana" New Phytologist. 178(1). 63-67.
  • Crawford, D. J., J. K. Archibald, D. Stoermer, M. E. Mort, J. K. Kelly, and A. Santos-Guerra. 2008. "A test of Baker's Law: Breeding systems and the radiation of Tolpis (Asteraceae) in the Canary Islands" International Journal of Plant Sciences. 169(6). 782-791.
  • Wacker, M. J., M. P. Godard, E. H. McCabe, J. E. Donnelly, and J. K. Kelly. 2008. "A sex-limited association between the angiotensin converting enzyme I/D polymorphism and obesity" Medical Science Monitor. 14(7). 353-357.
  • Kelly, J. K.. 2007. "Mutation-selection balance in mixed mating populations" Journal of Theoretical Biology. 246. 345-365.
  • Kelly, J. K. and M. K. Tourtellot. 2006. "The genetic analysis of family structured inbreeding depression studies" Heredity. 97. 346-354.
  • Holeski, L. M. and J. K. Kelly. 2006. "Mating system and the evolution of quantitative traits: An experimental study of Mimulus guttatus" Evolution. 60(4). 711-723.
  • Kelly, J. K.. 2006. "Geographical variation in selection, from phenotypes to molecules" American Naturalist. 167(4). 481-495.
  • Danielson-François, A., J. K. Kelly, and M. D. Greenfield. 2006. "Genotype ´ environment interaction for male attractiveness in an acoustic moth: evidence for plasticity and canalization" Journal of Evolutionary Biology. 19. 532-542.
  • Kelly, J. K.. 2006. "Evolutionary and dynamic models of infection with internal host structure" Disease evolution: Models, concepts, and data analyses. edited by Feng, Z., U. Dieckmann, and S. Levin. 67-86.
  • Orive, M. E., M. N. Stearns, J. K. Kelly, M. Barfield, M. S. Smith, and R. D. Holt. 2005. "Viral infection in internally structured hosts. I. Conditions for persistent infection" Journal of Theoretical Biology. 232(4). 453-466.
  • Archibald, J. K., M. E. Mort, D. J. Crawford, and J. K. Kelly. 2005. "Life History Affects The Evolution Of Reproductive Isolation Among Species Of Coreopsis (Asteraceae)" Evolution. 59(11). 2362-2369.
  • Archibald, J. K., M. E. Mort, D. J. Crawford, and J. K. Kelly. 2005. "Life history affects the evolution of reproductive isolation among species of Coreopsis (Asteraceae)" Evolution. 59. 2362-2369.
  • Kelly, J. K.. 2005. "Family-level inbreeding depression and the evolution of plant mating systems" New Phytologist. 165. 55-62.
  • Kelly, J. K.. 2005. "Epistasis in monkeyflowers" Genetics. 171. 1917-1931.
  • Williamson, S., S. M. Perry, C. D. Bustamante, M. E. Orive, M. N. Stearns, and J. K. Kelly. 2005. "A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients" Molecular Biology and Evolution. 22(3). 456-468.
  • Ward, J. K. and J. K. Kelly. 2004. "Scaling up evolutionary responses to elevated CO2: lessons from Arabidopsis" Ecology Letters. 7. 427-440.
  • Arathi, H. S. and J. K. Kelly. 2004. "Corolla morphology facilitates both autogamy and bumble bee pollination in Mimulus guttatus" International Journal of Plant Science. 165(6). 1039-1045.
  • Kelly, J. K., S. Williamson, M. E. Orive, M. S. Smith, and R. D. Holt. 2003. "Linking dynamical and population genetic models of persistent viral infection" American Naturalist. 162. 14-28.
  • Kelly, J. K. and H. S. Arathi. 2003. "Inbreeding and the genetic variance of floral traits in Mimulus guttatus" Heredity. 90(1). 77-83.
  • Kelly, J. K.. 2003. "Deleterious mutations and the genetic variance of male fitness components in Mimulus guttatus" Genetics. 164. 1071-1085.
  • Arathi, H. S., A. Rasch, C. Cox, and J. K. Kelly. 2002. "Autogamy and floral longevity in Mimulus guttatus" International Journal of Plant Science. 163(4). 567-573.
  • Kelly, J. K., A. Rasch, and S. Kalisz. 2002. "A method to estimate pollen viability from pollen size variation" American Journal of Botany. 89. 1021-1023.
  • Kelly, J. K. and J. H. Willis. 2002. "A manipulative experiment to estimate bi-parental inbreeding in Monkeyflowers" International Journal of Plant Science. 163(4). 575-579.
  • Kelly, J. K. and J. H. Willis. 2001. "Deleterious mutations and genetic variation for flower size in Mimulus guttatus" Evolution. 55. 937-942.
  • Kelly, J. K. and S. Williamson. 2000. "Predicting response to selection on a quantitative trait: A comparison between models for mixed-mating populations" Journal of Theoretical Biology. 207. 37-56.
  • Kelly, J. K. and M. J. Wade. 2000. "Molecular evolution near a two locus balanced polymorphism" Journal of Theoretical Biology. 204. 83-101.
  • Kelly, J. K.. 2000. "Epistasis, linkage, and balancing selection" Epistasis and the Evolutionary Process. edited by Wolf, J. B., E. D. Brodie, and M. J. Wade. 146-157.
  • Kelly, J. K.. 1999. "Response to selection in partially self fertilizing populations. II. Selection on multiple traits" Evolution. 53. 350-357.
  • Kelly, J. K.. 1999. "Response to selection in partially self fertilizing populations. I. Selection on a single trait" Evolution. 53. 336-349.
  • Kelly, J. K.. 1999. "An experimental method for evaluating the contribution of deleterious mutations to quantitative trait variation" Genetic Research. 73. 263-273.
  • Kelly, J. K.. 1997. "Distinguishing hard selection from soft selection in a subdivided population of the annual plant Impatiens capensis" Evolution. 51. 1100-1111.
  • Kelly, J. K.. 1997. "A test of neutrality based on inter-locus associations" Genetics. 146. 1197-1206.
  • Kelly, J. K. and M. A. F. Noor. 1996. "Speciation by Reinforcement: A Model Derived from Studies of Drosophila" Genetics. 143. 1485-1497.
  • Kelly, J. K.. 1996. "Kin Selection in the Annual Plant Impatiens capensis" American Naturalist. 147. 899-918.
  • Kelly, J. K.. 1994. "The Evolution of Communal Foraging in Hierarchically Structured Populations" Behavioral Ecology and Sociology. 35. 205-212.
  • Kelly, J. K.. 1994. "The Effect of Scale Dependent Processes on Kin Selection: Mating and Density Regulation" Theoretical Population Biology. 46. 32-57.
  • Kelly, J. K.. 1994. "An Application of Population Genetic Theory to Synonymous Gene Sequence Evolution in the Human Immunodeficiency Virus (HIV)" Genetical Research. 64. 1-9.
  • Kelly, J. K.. 1992. "Restricted Migration and the Evolution of Altruism" Evolution. 46. 1492-1495.
  • Kelly, J. K.. 1992. "Kin Selection in Density Regulated Populations" Journal of Theoretical Biology. 157. 447-461.

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