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Luke J. Harmon

Luke J. Harmon



Life Sciences South 347



Mailing Address

Dept. of Biological Sciences
University of Idaho
875 Perimeter MS 3051
Moscow, Idaho 83844-3051

Research: Ecology & Evolutionary Biology

  • Ph.D. Evolution, Ecology, and Population Biology, Washington University, 2005
  • B.S. Zoology, with honors, summa cum laude, Minor: Mathematics, Iowa State University, 1998

Our research investigates ecological and evolutionary aspects of adaptive radiations. Current projects span a wide range of taxa and time scales, including adaptive radiation in E. coli biofilms, evolution of island lizards in the Caribbean and Indian Ocean, and macroevolutionary dynamics of vertebrates. You will find more information about all of these projects on the research and publications pages.

My research focuses on developing new comparative methods and applying them to large phylogenetic datasets. Ongoing progress in building the tree of life provides a rare opportunity to learn about the dynamics of diversification through time and across clades. Current projects in my lab are focused on testing hypotheses about trait evolution, diversification, and adaptive radiation using statistical comparative methods. I am also interested in the interface between quantitative genetics and comparative methods.

  • Deans, A. R. and 55 others including L. J. Harmon. 2015. Finding our way through phenotypes.PLoS Biology 13: e1002033.
  • Rosindell, J., L. J. Harmon, and R. S. Etienne. 2015. Unifying ecology and macroevolution with individual-based theory. Ecology Letters 18: 472-482.
  • Harmon, L. J. and S. Harrison. 2015. Species diversity is dynamic and unbounded at local and continental scales. The American Naturalist 185: 584-593.
  • Hardwick, K. M., L. J. Harmon, S. D. Hardwick, and E. B. Rosenblum. 2015. When field experiments yield unexpected results: lessons learned from measuring selection in White Sands lizards. PLoS ONE 10: e0118560.
  • Des Roches, S., M. Brinkmeyer, L. J. Harmon, and E. B. Rosenblum. 2015. Ecological release and directional change in White Sands lizard trophic ecomorphology. Evolutionary Ecology 29: 1-16.
  • Nuismer, S. L. and L. J. Harmon. 2015. Predicting rates of interspecific interaction from phylogenetic trees. Ecology Letters 18: 17-28.
  • Jochimsen, D. M., C. R. Peterson, and L. J. Harmon. 2014. Influence of ecology and landscape on snake road mortality in a sagebrush-steppe ecosystem. Animal Conservation 17: 583-592.
  • Muschick, M., P. Nosil, M. Roesti, M. T. Dittman, L. Harmon, and W. Salzburger. 2014. Testing the stages model in the adaptive radiation of cichlid fishes in East African Lake Tanganyika. Proceedings of the Royal Society B 281: 20140605.
  • Uyeda, J. C. and L. J. Harmon. 2014. A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data. Systematic Biology 63: 902-918.
  • Pennell, M. W., J. M. Eastman, G. J. Slater, J. W. Brown, J. C. Uyeda, R. G. Fitzjohn, M. E. Alfaro, and L. J. Harmon. 2014. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics 30: 2216-2218.
  • Davis, C. C., H. Schaefer, W. R. Anderson, Z. Xi, D. A. Baum, M. J. Donoghue, and L J. Harmon. 2014. Long-term morphological stasis maintained by a plant-pollinator mutualism. PNAS 111: 5914-5919.
  • Cranston, K., L. J. Harmon, M. A. O’Leary, and C. Lisle. 2014. Best practices for data sharing in phylogenetic research. PLoS Currents Tree of Life 2014 Jun 19.
  • Hagey, T., J. Puthoff, M. Holbrook, L. J. Harmon, and K. Autumn. 2014. Variation in Setal Micromechanics and Performance of Two Gecko Species. Zoomorphology 133: 111-126.
  • Wagner, C. E., L. J. Harmon, and O. Seehausen. 2014. Cichlid species-area curves are shaped by adaptive radiations that scale with area. Ecology Letters 17: 538-592.
  • Pennell, M. W., L. J. Harmon, and J. C. Uyeda. 2014. Speciation is unlikely to drive divergence rates.Trends in Ecology and Evolution 29: 72-73.
  • Pennell, M. W., L. J. Harmon, and J. C. Uyeda. 2014. Is there room for punctuated equilibrium in macroevolution? Trends in Ecology and Evolution 29: 23-32.
  • DesRoches, S., J. Torresdal, T. Morgan, L. J. Harmon, and E. B. Rosenblum. 2014. Beyond black and white: comparative ecomorphology in three rapidly evolving lizard species at White Sands.Biological Journal of the Linnean Society 111: 169-182.
  • Anderson, C. J. R. and L. J. Harmon. 2014. Ecological and mutation-order speciation in digital organisms. American Naturalist 183: 257-268.
  • Slater, G. J. and L. J. Harmon. 2013. Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution. Methods in Ecology and Evolution 4: 699-702.
  • Pennell, M. W. and L. J. Harmon. 2013. An Integrative View of Phylogenetic Comparative Methods: Connections to Population Genetics, Paleobiology and Community Ecology. The Year in Evolutionary Biology 1289: 90-105.
  • Eastman, J. M., L. J. Harmon, and D. C. Tank. 2013. Congruification: support for time-scaling large phylogenetic trees. Methods in Ecology and Evolution 4: 688-691.
  • Harmon, L. J., J. Baumes, C. Hughes, J. Soberon, C. Specht, B. Thacker, W. Turner, and C. Lisle. 2013. Arbor: Comparative Analysis Workflows for the Tree of Life. PLoS Currents: Tree of Life:  June 21, 2013.
  • Stoltzfus, A., H. Lapp, N. Matasci, H. Deus, B. Sidlauskas, C.M. Zmasek, G. Vaidya, E. Pontelli, K. Cranston, R. Vos, C. O. Webb, L. J. Harmon, M. Pirrung, B. O’Meara, M. W. Pennell, S. Mirarab, M. S. Rosenberg, J. P. Balhoff, H. M. Bik, T. Heath, P. Midford, J. W. Brown, E. J. McTavish, J. Sukumaran, M. Westneat, M. E. Alfaro, and A. Steele. 2013. Phylotastic! Making Tree-of-Life Knowledge Accessible, Reusable and Convenient. BMC Bioinformatics 14:158.
  • Des Roches, S., J. B. Shurin, D. Schluter, and L. J. Harmon. 2013. Ecological and evolutionary effects of stickleback on ecosystem function. PLoS ONE 8: e59644. Rosindell, J. and L. J. Harmon. 2013. A unified model of species immigration, extinction and abundance on islands. Journal of Biogeography 40: 1107-118.
  • Tyerman, J. G., J. M. Ponciano, P. Joyce, L. J. Forney and L. J. Harmon. 2013. The evolution of antibiotic susceptibility and resistance during the formation of Escherichia coli biofilms. BMC Evolutionary Biology 13: 22.
  • Slater, G. J., L. J. Harmon, and M. E. Alfaro. 2012. Integrating Fossils with Molecular Phylogenies Improves Inference of Trait Evolution. Evolution 12: 3931-3944.
  • Rosindell, J. and L. J. Harmon. 2012. OneZoom: A Fractal Explorer for the Tree of Life. PLoS Biology 10: e1001406.
  • Pennell, M. W., B. A. J. Sarver, and L. J. Harmon. 2012. Trees of Unusual Size: Sampling Bias Can Influence Inference of Early Bursts from Molecular Phylogenies. PLoS ONE 7: e43348.
  • Ingram. T., L. J. Harmon, and J. B. Shurin. 2012. When should we expect early bursts of trait evolution in comparative data? Predictions from an evolutionary food web model. Journal of Evolutionary Biology 25: 1902-1910.
  • Wagner, C. E., L. J. Harmon, and O. Seehausen. 2012. Ecological opportunity and sexual selection together predict adaptive radiation. Nature 487: 366-369.
  • Rosenblum, E. B.*, B. A. J. Sarver, J. W. Brown, S. Des Roches, K. M. Hardwick, T. D. Hether, J. M. Eastman, M. W. Pennell, and L. J. Harmon*. 2012. Goldilocks meets Santa Rosalia: An ephemeral speciation model explains patterns of diversification across time scales. Evolutionary Biology 39:255-261.
  • Godsoe, W. and L. J. Harmon. 2012. How do species interactions affect species distribution models? Ecography 35: 811-820.
  • Rosindell, J., S. P. Hubbell, F. He, L. J. Harmon, and R. S. Etienne. 2012. The case for ecological neutral theory. Trends in Ecology and Evolution 27: 203-208.
  • Slater, G. J., L. J. Harmon, P. Joyce, L J. Revell, and M. E. Alfaro. 2012. Fitting models of continuous trait evolution to incompletely sampled comparative data using Approximate Bayesian Computation. Evolution 66: 752-762.
  • Des Roches, S., J. M. Robertson, L. J. Harmon, and E. B. Rosenblum. 2011. Ecological release in white sands lizards. Ecology and Evolution 1: 571-578.
  • Eastman, J. M., L. J. Harmon, H.-J. La, P. Joyce, and L. J. Forney. 2011. The onion model, a simple neutral model for the evolution of diversity in bacterial biofilms. J. Evol. Biol. 11: 2496-2504.
  • Eastman, J. M., M. E. Alfaro, P. Joyce, A. L. Hipp, and L. J. Harmon. 2011. A novel comparative method for modeling shifts in the rate of character evolution on trees. Evolution 65: 3578-3589.
  • Stack, J., L. J. Harmon, and B. O’Meara. 2011. RBrownie: An R package for testing hypotheses about rates of evolutionary change. Methods in Ecology and Evolution 2: 660-662.
  • Davies, T. J., G. Smith, D. U. Bellstedt, J. Boatwright, B. Bytebier, R. Cowling, F. Forest, L. J. Harmon, A. M. Muasya, B. D. Schrire, Y. Steenkamp, M. van de Bank, and V. Savolainen. 2011. Extinction risk and diversification are linked in a plant biodiversity hotspot. PLoS Biology 9: e1000620.
  • Smith, K. L.†, L. J. Harmon, L. Shoo†, and J. Melville. 2011. Evidence of constrained phenotypic evolution in a cryptic species complex of agamid lizards. Evolution 65: 976-992.
  • Brock, C. D. †, L. J. Harmon, and M. E. Alfaro. 2011. Testing for Temporal Variation in Diversification Rates When Sampling is Incomplete and Nonrandom. Systematic Biology 60: 410-419.
  • Carlson, B. A., S. M. Hasan, M. Hollmann, D. B. Miller, L. J. Harmon, and M. E. Arnegard. 2011. Brain evolution triggers explosive diversification of species and signals. Science 332: 583-586.
  • Rosenblum, E. B. and L. J. Harmon. 2011. Same same but different: replicated ecological speciation at White Sands. Evolution 65: 946-960.
  • Arnegard, M. E., P. B. McIntyre, L. J. Harmon, M. L. Zelditch, W. G. R. Crampton, J. K. Davis, J.  P. Sullivan, S. Lavoué, and C. D. Hopkins. 2010. Sexual signal evolution outpaces ecological divergence during electric fish species radiation. American Naturalist 176:335-356.
  • Yoder, J. B.†, S. Des Roches†, J. M. Eastman†, L. Gentry†, W. K. W. Godsoe, T. Hagey†, D. Jochimsen†, B. P. Oswald†, J. Robertson, B. A. J. Sarver†, J. J. Schenk†, S. F. Spear†, and L. J. Harmon. 2010. Ecological opportunity and the origin of adaptive radiations. Journal of Evolutionary Biology 23: 1581-1596, doi:10.1111/j.1420-9101.2010.02029.x.
  • Harmon, L. J., J. B. Losos, J. Davies, R. G. Gillespie, J. L. Gittleman, W. B. Jennings, K. Kozak, M. A. McPeek, F. Moreno-Roark†, T. J. Near, A. Purvis, R. E. Ricklefs, D. Schluter, J. A. Schulte II, O. Seehausen, B. Sidlauskas, O. Torres-Carvajal†, J. T. Weir†, & A. Ø. Mooers. 2010. Early bursts of body size and shape evolution are rare in comparative data. Evolution 64: 2385-2396.  doi:10.1111/j.1558-5646.2010.01025.x.

  • Adaptive radiation:
    We are investigating repeated and predictable patterns of speciation and trait change across clades of diversifying species. If adaptive radiations are driven by divergent natural selection following entry into new adaptive zones, then diversification during such radiations may be both repeatable and predictable. We test these hypotheses using natural experiments of lizards, mammals, fish, plants, and other organisms.
  • Comparative methods:
    We are developing new comparative approaches to answer ecological and evolutionary questions about the tempo and mode of diversification. The statistical techniques that I have developed in my work are now implemented in a software package, Geiger, written in the R language.
  • “Reading” the Tree of Life: 
    We are searching for the signature of diversification and species interactions across broad sections of the tree of life. First, we are working to combine both paleontological data (fossils) and phylogenetic data together to fit models of diversification through time. Second, we have implemented more advanced statistical approaches that can more flexibly fit a wider range of models to data, including models that capture the dynamics of species’ interactions. These new approaches may help us understand the processes that cause new species to form on the Earth.

  • 2011: Early-Career Faculty Award, University of Idaho
  • 2009: Young Investigators Prize, American Society of Naturalists
  • 2006: Just Desserts Award (for services to graduate students), University of British Columbia


Department of Biological Sciences

Physical Address:
Life Sciences South 252

Mailing Address:
875 Perimeter Drive MS 3051
Moscow, ID 83844-3051

Phone: 208-885-6280

Fax: 208-885-7905


Web: Department of Biological Sciences