In review

Pennell, M. W., L. J. Harmon, and J. C. Uyeda. Is there room for punctuated equilibrium in macroevolution? Submitted to Trends in Ecology and Evolution 28 May 2013.

Eastman, J. M., D. Wegmann, C. Leuenberger, and L. J. Harmon. Simpsonian “Evolution by Jumps” in an Adaptive Radiation of Anolis Lizards. Submitted to American Naturalist 17 May 2013. ArXiv.

In press

Harmon, L. J. In press. Macroevolutionary rates. In: J. B. Losos, Ed., The Princeton Guide to Evolution. Princeton University Press.

Anderson, C. J. R. and L. J. Harmon. In press. Ecological and mutation-order speciation in digital organisms. American Naturalist.

Pennell, M. W. and L. J. Harmon. In press. An Integrative View of Phylogenetic Comparative Methods: Connections to Population Genetics, Paleobiology and Community Ecology. The Year in Evolutionary Biology.

Eastman, J. M., L. J. Harmon, and D. C. Tank. In press. Congruification: support for time-scaling large phylogenetic trees. Methods in Ecology and Evolution.


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. OA link.

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. OA link.

Rosindell, J. and L. J. Harmon. 2013. A unified model of species immigration, extinction and abundance on islands. Journal of Biogeography 40: 1107-118. link. pdf.

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. OA link.


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. link. pdf.

Rosindell, J. and L. J. Harmon. 2012. OneZoom: A Fractal Explorer for the Tree of Life. PLoS Biology 10: e1001406. OA link.

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. OA link.

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. link. pdf.

Wagner, C. E., L. J. Harmon, and O. Seehausen. 2012. Ecological opportunity and sexual selection together predict adaptive radiation. Nature 487: 366-369. link. pdf.

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. OA link.

Godsoe, W. and L. J. Harmon. 2012. How do species interactions affect species distribution models? Ecography 35: 811-820. link. pdf.

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. link. pdf.

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. link. pdf.


McInnes, L., W. J. Baker, T. G. Barraclough, K. K. Dasmahapatra, A. Goswami, L. J. Harmon, H. Morlon, A. Purvis, J. Rosindell, G. H. Thomas, S. T. Turvey, and A. B. Phillimore. 2011. Integrating ecology into macroevolutionary research (meeting report). Biology Letters 7: 644-646. OA link. Link to all talks, including mine.

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. link. pdf.

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. link. pdf.

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. OA link.

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. OA link.

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. link. pdf.

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. link. pdf.

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. OA link.

Harmon, L. J. 2011. My island life. In: J. B. Losos, editor. In the Light of Evolution: Essays from Leading Evolutionary Biologists. Roberts & Company Publishers. link to book.

Rosenblum, E. B. and L. J. Harmon. 2011. Same same but different: replicated ecological speciation at White Sands. Evolution 65: 946-960. link. pdf.

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. link. pdf.


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. link. pdf.

Yoder, J. B., S. DesRoches, 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. link. pdf.

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. link. pdf.

Harmon, L. J. and R. E. Glor. 2010. Poor statistical performance of the Mantel test in phylogenetic comparative analyses. Evolution 64: 2173-2178. link. pdf.

Matthews, B., L. J. Harmon, L. M'Gonigle, K. B. Marchinko, and H. Schaschl. 2010. Sympatric and allopatric divergence of MHC genes in threespine stickleback. PLoS ONE 5:e10948. link. pdf.

Hagey, T. J., J. B. Losos, and L. J. Harmon. 2010. Cruise foraging of invasive chameleons (Chamaeleo jacksonii) in Hawaii. Breviora 519:1-7. link. pdf.

Harmon, L. J. 2010. Journal Club: An evolutionary biologist ponders the pace of evolution. Nature 463: 1003. link. pdf.

Harmon, L. J. and S. Braude. 2010. Conservation of Small Populations: Effective Population Size, Inbreeding, and the 50/500 Rule. pp. 125-138 in S. Braude and B. S. Low, Eds., An Introduction to Methods and Models in Ecology and Conservation Biology. Princeton University Press. link.


Alfaro, M. E., F. Santini, C. Brock, H. Alamillo, A. Dornburg, D. L. Rabosky, G. Carnevale, and L. J. Harmon. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. PNAS 106:13410-13414. link. pdf.

Santini, F., L. J. Harmon, G. Carnevale, and M. E. Alfaro. 2009. Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evlutionary Biology 9: 194. link. pdf.

Ingram, T., L. J. Harmon, and J. B. Shurin. 2009. Niche evolution, trophic structure and species turnover in model food webs. American Naturalist 174: 56-67. link. pdf.

Harmon, L. J.*, B. Matthews*, S. DesRoches, J. Chase, J. Shurin, and D. Schluter. 2009. Evolutionary diversification in stickleback affects ecosystem functioning. Nature 458: 1167-1170. link. pdf. supplement. perspective. making the paper.

Nosil, P., L. J. Harmon, and O. Seehausen. 2009. Ecological explanations for (incomplete) speciation. Trends in Ecology and Evolution 24: 145-156. link. pdf.

Nosil, P. and L. J. Harmon. 2009. Niche dimensionality and ecological speciation. In R. Butlin, J. Bridle, and D. Schluter, Eds., Speciation and Patterns of Diversity, Cambridge University Press. link to book.

Bailey, J. K., A. Hendry, M. Kennison, D. Post, E. Palkovacs, F. Pelletier, L. J. Harmon, and J. A. Schweitzer. 2009. From genes to ecosystems: an emerging synthesis of eco-evolutionary dynamics. New Phytologist 184: 746–749. link. pdf.


Pinto, G., D. L. Mahler, L. J. Harmon, and J. B. Losos. 2008. Testing the island effect in adaptive radiation: rates and patterns of morphological diversification in Caribbean and mainland Anolis lizards. Proceedings of the Royal Society B 275: 2749-2757. link. pdf.

Revell, L. J., L. J. Harmon, and D. C. Collar. 2008. Phylogenetic signal, evolutionary process, and rate. Systematic Biology 57:591-601. link. pdf.

Harmon, L. J., J. Melville, A. Larson, and J. B. Losos. 2008. The Role of Geography and Ecological Opportunity in the Diversification of Day Geckos (Phelsuma). Systematic Biology 57:562-573. link. pdf.

Revell, L. J. and L. J. Harmon. 2008. Testing quantitative genetic hypotheses about the evolutionary rate matrix for continuous characters. Evolutionary Ecology Research 10:311-321. link. pdf.

Harmon, L. J., J. Weir, C. Brock, R. E. Glor, and W. Challenger. 2008. GEIGER: Investigating evolutionary radiations. Bioinformatics 24:129-131. link, pdf.


Harmon, L. J., L. L. Harmon, and C. G. Jones. 2007. Competition and community structure in diurnal arboreal geckos (genus Phelsuma) in the Indian Ocean. Oikos 116: 1863-1878. link, pdf

Vellend, M., L. J. Harmon, J. L. Lockwood, M. M. Mayfield, A. R. Hughes, J. P. Wares, and D. F. Sax. 2007. Effects of exotic species on evolutionary diversification. Trends in Ecology and Evolution 22: 481-488. link, pdf

Nicholson, K. E., L. J. Harmon, and J. B. Losos. 2007. Evolution of Anolis lizard dewlap diversity. PLoS ONE 2(3): e274 .link

Revell, L. J., L. J. Harmon, R. B. Langerhans, and J. J. Kolbe. 2007. A phylogenetic approach to determining the importance of constraint on phenotypic evolution in the neotropical lizard Anolis cristatellus. Evolutionary Ecology Research 9: 261-282. link, pdf

Mooers, A.O., Harmon, L.J., Wong, D.H.J., and S.B. Heard. 2007. Some models of phylogenetic tree shape. Pages 149-170 in Reconstructing Evolution: New Mathematical and Computational Advances (O. Gascuel and M. Steel, eds.), Oxford University Press, Oxford. book


Harmon, L. J. and R. Gibson. 2006. Multivariate phenotypic evolution among island and mainland populations of the ornate day gecko, Phelsuma ornata. Evolution 60: 2622-2632. link, pdf

Melville, J., L. J. Harmon, and J. B. Losos. 2006. Intercontinental community convergence of ecology and morphology in desert lizards. Proceedings of the Royal Society Series B: Biological Sciences 273: 557-563. link, pdf


Harmon, L. J. and J. B. Losos. 2005. The effect of intraspecific sample size on type I and type II error rates in comparative studies. Evolution 59:2705-2710. link, pdf

Revell, L. J., L. J. Harmon, and R. E. Glor. 2005. Under-parameterized model of sequence evolution leads to bias in the estimation of diversification rates from molecular phylogenies. Systematic Biology 54: 973-983. link,pdf

Weisrock, D. W., L. J. Harmon, and A. Larson. 2005. Resolving deep phylogenetic relationships in salamanders: analyses of mitochondrial and nuclear genomic data. Systematic Biology 54:758-777. link, pdf

Kozak, K. H., A. Larson, R. M. Bonett, and L. J. Harmon. 2005. Phylogenetic analysis of ecomorphological divergence, species coexistence, and diversification rates in dusky salamanders (Plethodontidae, Desmognathinae). Evolution 59: 2000-2016. link, pdf

Harmon, L. J., K. Bauman, M. McCloud, J. Parks, S. Howell, and J. B. Losos. 2005. What the free-ranging animals do at the zoo: a study of the behavior and habitat use of opossums (Didelphis virginiana) on the grounds of the St. Louis Zoo. Zoo Biology 24: 197-213. link, pdf

Harmon, L. J., J. J. Kolbe, J. M. Cheverud, and J. B. Losos.2005. Convergence and the multidimensional niche. Evolution 59: 409-421. link, pdf


Harmon, L. J., J. A. Schulte, J. B. Losos, and A. Larson. 2003. Tempo and mode of evolutionary radiation in iguanian lizards. Science 301:, pdf, supporting materials

Harmon, L. J. 2002. Some observations of the natural history of the prehensile-tailed skink, Corucia zebrata, in the Solomon Islands. Herpetological Review 33: 177-179.

Harmon, L. J. 2000. A Translocation Strategy for Confiscated Pancake Tortoises. Chelonian Conservation and Biology 3(4):738-743.

Kolbe, J. J., L. J. Harmon, and D. A. Warner. 1999. New state record lengths and associated natural history notes for some Illinois snakes. Transactions of the Illinois State Academy of Science 92:133-135. pdf

A note on links and pdfs

For some of the papers above, you will see both a link to the paper on the journals homepage and a pdf file hosted here. If you have institutional access to the journal in question, please try the "link" first; only download the pdf if that doesn't work. Journals are starting to use web hits as an index of scientific impact, so using these links helps us all.