THE Applied Phylogenetics Lab at USC


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Bold text indicates a lab member // *Indicates equal contribution


Pennell, M. Alternate histories in macroevolution. Proceedings of the National Academy of Sciences. [doi] [pdf]

Dimayacyac, J.R., S. Wu, and M. Pennell. Evaluating the performance of widely used phylogenetic models for gene expression evolution. BioRχiv. [doi] [pdf]

Pennell, M., O.L. Rodriguez, C.T. Watson, and V. Greiff. The evolutionary and functional significance of germline immunoglobulin gene variation. Trends in Immunology. [doi] [pdf]


Pyron, R.A., and M. Pennell. Macroevolutionary perspectives on Anthropocene Extinction. Biological Conservation. [doi] [pdf]

Louca, S., L.F. Henao Diaz, and M.Pennell. The scaling of diversification rates with age is likely explained by sampling bias. Evolution. [doi] [pdf]

Garcia-Porta, J., D. Sol, M. Pennell, F. Sayol, A. Kaliontzopolou, and C.A. Botero. Niche expansion and the adaptive divergence in the global radiation of crows and ravens. Nature Communications. [doi] [pdf]

MacPherson, A., S. Louca, A. MacLaughlin, J.B. Joy, and M.W. Pennell. A General Birth-Death-Sampling Model for Epidemiology and Macroevolution. Systematic Biology. [doi] [pdf]

Mull, C.G., M.W. Pennell, K.E. Yopak, and N.K Dulvy. Maternal investment evolves with larger body size and higher diversification rate in sharks and rays. BioRχiv [doi] [pdf]


Porto, D.S., E.A.B. Almeida, and M.W. Pennell. Investigating Morphological Complexes Using Informational Dissonance and Bayes Factors: A Case Study in Corbiculate Bees. Systematic Biology. [doi] [pdf]

Freeman, B.F. and M.W. Pennell. The latitudinal taxonomy gradient. Trends in Ecology and Evolution. [doi] [pdf]

Harmon, L.J., M.W. Pennell, L.F. Henao-Diaz, J. Rolland, B. Sipley, and J.C. Uyeda. Causes and consequences of the ubiquitous time-scaling of all evolutionary rates. Annual Reviews of Ecology, Evolution, and Systematics. [doi] [pdf]

Neto-Bradley, B.M., C.D. Muir, J. Whitton, and M.W. Pennell. Phylogenetic history of vascular plant metabolism revealed using a macroevolutionary common garden. Proceedings of the Royal Society B: Biological Sciences. [doi] [pdf]

Uyeda, J.C., N. Bone, S. McHugh, J. Rolland, and M.W. Pennell. How should functional relationships be evaluated using phylogenetic comparative methods? A case study using metabolic rate and body temperature. Evolution. [doi] [pdf]

Louca, S. and M.W. Pennell. Why extinction estimates from extant phylogenies are so often zero. Current Biology. [doi] [pdf]

Louca, S., A. McLaughlin, A. MacPherson, J.B. Joy, and M.W. Pennell. Fundamental identifiability limits in molecular epidemiology. Molecular Biology and Evolution. [doi] [pdf]

Neto-Bradley, B.M., J. Whitton, L.P.J. Lipsen, and M.W. Pennell. Macroevolutionary history predicts flowering time but not phenological sensitivity to temperature in grasses. American Journal of Botany. [doi] [pdf]


Louca, S. and M.W. Pennell. Extant timetrees are consistent with a myriad of diversification scenarios. Nature. [doi] [pdf]

Smith, S.D., M.W. Pennell, C.W. Dunn, and S.V. Edwards. Phylogenetics is the new genetics (for most of biodiversity). Trends in Ecology and Evolution. [doi] [pdf]


Henao Diaz, L.F., L.J. Harmon, M.T.C. Sugawara, E.T. Miller, and M.W. Pennell. Reply to Wiens and Scholl: The time dependency of diversification rates is a widely observed phenomenon. Proceedings of the National Academy of Sciences. [doi] [pdf]

Guzman, L.M., M.W. Pennell, E. Nikelski, and D.S. Srivastava. Successful integration of data science in undergraduate biostatistics courses using cognitive load theory. CBE Life Sciences Education. [doi] [pdf]

Guzman, L.M., and M.W. Pennell. Mathematical statistics for biologists and other interesting people. Trends in Ecology and Evolution. [doi] [pdf]

Kaur, K.M., and M.W. Pennell. Digest: Process-based phylogenetic models provide unique insights into the evolution of mutualistic networks. Evolution. [doi] [pdf]

Louca, S., and M.W. Pennell. A general and efficient algorithm for the likelihood of diversification and discrete-state evolutionary models. Systematic Biology. [doi] [pdf]

Henao Diaz, L.F., L.J. Harmon, M.T.C. Sugawara, E.T. Miller, and M.W. Pennell. Macroevolutionary diversification rates show time-dependency. Proceedings of the National Academy of Sciences. [doi] [pdf]

C.M. Tucker, T. Aze, M.W. Cadotte, J.L. Cantalapiedra, C. Chisholm, S. Díaz, R. Grenyer, D. Huang, F. Mazel, W.D. Pearse, M.W. Pennell, M. Winter, and A.Ø. Mooers. Assessing the utility of conserving evolutionary history. Biological Reviews. [doi] [pdf]

Cantalapiedra, J.L., T. Aze, M.W. Cadotte, G.V. Dalla Riva, D.Huang, F. Mazel, M.W. Pennell, M. Ríos, and A.Ø. Mooers. Conserving evolutionary history does not result in greater diversity over geological time scales. Proceedings of the Royal Society B: Biological Sciences. [doi] [pdf]

Falster, D., R.G. FitzJohn, M.W. Pennell, and W.K. Cornwell. Datastorr: a workflow and package for delivering successive versions of ‘evolving data’ directly into R. Gigascience. [doi] [pdf]

Harmon, L.J., C.S. Andreazzi, F. Débarre, J. Drury, E.E. Goldberg, A.B. Martins, C.J. Melián, A. Narwani, S.L. Nuismer, M.W. Pennell, S.M. Rudman, O. Seehausen, D. Silverstro, M. Weber, and B. Matthews. Detecting the Macroevolutionary Signal of Species Interactions. Journal of Evolutionary Biology. [doi] [pdf]

O’Connor, M.I., M.W. Pennell, F. Altermatt, B. Matthews, C.J. Melián, and A. Gonzalez. Principles of ecology revisited: integrating information and ecological theories for a more unified science. Frontiers in Ecology and Evolution. [doi] [pdf]

Sarver, B.A.J., M.W. Pennell, J.W. Brown, S. Keeble, K.M. Hardwick, J. Sullivan, and L.J. Harmon. The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates. PeerJ. [doi] [pdf]

Pennell, M.W. What explains latitudinal diversity gradients? Trends in Ecology & Evolution. [doi] [pdf]

Mazel, F., M.W. Pennell, M. Cadotte, S. Diaz, G.V. dalla Riva, R. Grenyer, F. Leprieur, A.Ø. Mooers, D. Mouillot, C.M. Tucker, and W. D. Pearse. Reply to “Global conservation of phylogenetic diversity captures more than just functional diversity”. Nature Communications. [doi] [pdf]


Louca, S., P.M. Shih, M.W. Pennell, W.W. Fischer, L.W. Parfrey, M. Doebeli. Bacterial diversification through geological time. Nature Ecology and Evolution. [doi] [pdf]

Uyeda, J.C., R. Zenil-Ferguson, and M.W. Pennell. Rethinking phylogenetic comparative methods. Systematic Biology. [doi] [pdf]

Mazel, F., M.W. Pennell, M. Cadotte, S. Diaz, G.V. dalla Riva, R. Grenyer, F. Leprieur, A.Ø. Mooers, D. Mouillot, C.M. Tucker, and W. Pearse. Prioritizing phylogenetic diversity captures functional diversity unreliably. Nature Communications. [doi] [pdf]

Pennell, M.W., Judith E. Mank, and Catherine L. Peichel. Transitions in sex determination and sex chromosomes across vertebrate species. Molecular Ecology. [doi] [pdf]


Mazel, F., A.Ø. Mooers, G.V. dalla Riva, and M.W. Pennell. Conserving phylogenetic diversity can be a poor strategy for conserving functional diversity. Systematic Biology. [doi] [pdf]

Zenil-Ferguson, R. and M.W. Pennell. Trait-dependent diversification and its alternative. Evolution. [doi] [pdf]

Schluter, D. and M.W. Pennell. Speciation gradients and the distribution of biodiversity. Nature. [doi] [pdf]

Pennell, M.W. and M.I. O’Connor. A modest proposal for unifying macroevolution and ecosystem ecology. The American Naturalist. [doi] [pdf]

Uyeda, J.C., M.W. Pennell, E.T. Miller, R. Maia, and C.R. McClain. The evolution of energetic scaling across the vertebrate tree of life. The American Naturalist. [doi] [pdf]

Osmond, M.M., M.A. Barbour, J.R. Bernhardt, M.W. Pennell, J.M. Sunday, and M.I. O’Connor. Warming induced changes to body size stabilize consumer-resource dynamics. The American Naturalist. [doi] [pdf]


Pennell, M.W.*, R.G. FitzJohn*, and W.K. Cornwell*. A simple approach for maximizing the overlap of phylogenetic and comparative data. Methods in Ecology and Evolution. [doi] [pdf]


Tank, D.C., J.M. Eastman, M.W. Pennell, P.S. Soltis, D.E. Soltis, C.E. Hinchliff, J.W. Brown, E.B. Sessa, and L.J. Harmon. Nested radiations and the pulse of angiosperm diversification. New Phytologist. [doi] [pdf]

Pennell, M.W., R.G. FitzJohn, W.K. Cornwell, and L.J. Harmon. Model adequacy and the macroevolution of angiosperm functional traits. The American Naturalist. [doi] [pdf] 

Pennell, M.W.*, M. Kirkpatrick*, S.P. Otto*, J.C. Vamosi, C.L. Piechel, N. Valenzuela, and J. Kitano. Y fuse? Sex chromosome fusions in fishes and reptiles. PLoS Genetics. [doi] [pdf]

Uyeda, J.C., D.S. Caetano, and M.W. Pennell. Comparative analysis of principal components can be misleading. Systematic Biology. [doi] [pdf]

Pennell, M.W. Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology: Concepts and Practice.—Edited by László Zsolt Garamszegi (Book Review). Systematic Biology. [doi] [pdf]


FitzJohn, R.G.*, M.W. Pennell*, A.E. Zanne, P.F. Stevens, D.C. Tank, and W.K. Cornwell. How much of the world is woody? Journal of Ecology 102:1266-1272. [doi] [pdf]

The Tree of Sex Consortium; T. Ashman, D. Bachtrog, H. Blackmon, E.E. Goldberg, M.W. Hahn, M. Kirkpatrick, J. Kitano, J.E. Mank, I. Mayrose, R. Ming, S.P. Otto, C.L. Peichel, M.W. Pennell, N. Perrin, L. Ross, N. Valenzuela, and J.C. Vamosi. Tree of Sex: a database of sexual systems. Scientific Data 1:140015. [doi] [pdf]

Stansbury, C.R., D.E. Ausband, P. Zager, C.M. Mack, C.R. Miller, M.W. Pennell, and L.P. Waits. A long term population monitoring approach to a wide-ranging carnivore: noninvasive genetic sampling of gray wolf rendezvous sites in Idaho, U.S.A. Journal of Wildlife Management. [doi] [pdf]

Lanfear, R. and M.W. Pennell. Open access is worth considering. Trends in Plant Sciences. [doi] [pdf]

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. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics. [doi] [pdf] 

Slater, G.J. and M.W. Pennell. Robust regression and posterior predictive simulation increase power to detect early bursts of trait evolution. Systematic Biology. [doi] [pdf]

Cornwell, W.K., M. Westoby, D.S. Falster, R.G. FitzJohn, B.C. O’Meara, M.W. Pennell, D.J. McGlinn, J.M. Eastman, A.T. Moles, P.B. Reich, D.C. Tank, I.J. Wright, L.Aarssen, J.M. Beaulieu, R.M. Kooyman, M.R. Leishman, E.T. Miller, U. Niinemets, J. Oleksyn, A. Ordonez, D.L. Royer, S.A. Smith, P.F. Stevens, L. Warman, P. Wilf, and A.E. Zanne. Functional distinctiveness of major plant lineages. Journal of Ecology. [doi] [pdf]

Pennell, M.W., L.J. Harmon, and J.C. Uyeda. Speciation is unlikely to drive divergence rates. Trends in Ecology & Evolution 29:72-73. [doi] [pdf]

Pennell, M.W., L.J. Harmon, and J.C. Uyeda. Is there room for punctuated equilibrium in macroevolution? Trends in Ecology & Evolution. [doi] [pdf]


Maliska, M.E., M.W. Pennell, and B.J. Swalla. Developmental mode influences diversification in ascidians. Biology Letters. [doi] [pdf]

Pennell, M.W. and L.J. Harmon. An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology. Annals of the New York Academy of Sciences. [doi] [pdf]

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.A. Heath, P.E. Midford, J.W. Brown, E.J. McTavish, J. Sukumaran, M. Westneat, M.E. Alfaro, A. Steele, and G. Jordan. Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinformatics. [doi] [pdf]


Pennell, M.W. Biology in the light of phylogeny. Trends in Ecology & Evolution. [doi] [pdf]

Pennell, M.W., C.R. Stansbury, L.P. Waits, and C.R. Miller. Capwire: a R package for estimating population census size from non-invasive genetic sampling. Molecular Ecology Resources. [doi] [pdf]

Pennell, M.W., B.A.J. Sarver, and L.J. Harmon. Trees of unusual size: biased inference of early bursts from large molecular phylogenies. PLoS ONE. [doi] [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. Goldilocks meets Santa Rosalia: an ephemeral speciation model explains patterns of diversification across time scales. Evolutionary Biology. [doi] [pdf]


Green, D.J., K.B. Loukes, M.W. Pennell, J. Jarvis, and W.E. Easton. 2011. Reservoir water levels do not influence daily mass gain of warblers at a riparian stopover site. Journal of Field Ornithology. [doi] [pdf]