On Google scholar

Henao Diaz, L.F., L.J. Harmon, M.T.C. Sugawara, and M.W. Pennell. In review. Macroevolutionary diversification rates show time-dependency. [preprint] [pdf]

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

Falster, D., R.G. FitzJohn, M.W. Pennell, and W.K. Cornwell. In review. Versioned data: why it is needed and how it can be achieved (easily and cheaply). [preprint] [pdf] [repo]

Louca, S., P.M. Shih, M.W. Pennell, W.W. Fischer, L.W. Parfrey, M. Doebeli. 2018 Bacterial diversification through geological time. Nature Ecology and Evolution 2: 1458-1467. [doi] [pdf]

Uyeda, J.C., R. Zenil-Ferguson, and M.W. Pennell. 2018. 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.O. Mooers, D. Mouillot, C.M. Tucker, and W. Pearse. 2018. Prioritizing phylogenetic diversity captures functional diversity unreliably. Nature Communications 9:2888. [doi] [pdf]

Pennell, M.W., Judith E. Mank, and Catherine L. Peichel. 2018. Transitions in sex determination and sex chromosomes across vertebrate species. Molecular Ecology. [doi] [pdf]

Mazel, F., A.O. Mooers, G.V. dalla Riva, and M.W. Pennell. 2017. Conserving phylogenetic diversity can be a poor strategy for conserving functional diversity. Systematic Biology 66:1019-1027. [doi] [pdf]

Zenil-Ferguson, R. and M.W. Pennell. 2017. Trait-dependent diversification and its alternative (Digest). Evolution 71:1732-1734. [doi] [pdf]

D. Schluter and M.W. Pennell. 2017. Speciation gradients and the distribution of biodiversity. Nature 546:48-55. [doi] [pdf]

Pennell, M.W. and M.I. O’Connor. 2017. A modest proposal for unifying macroevolution and ecosystem ecology. The American Naturalist 189:ii-iii [doi] [pdf]

Uyeda, J.C., M.W. Pennell, E.T. Miller, R. Maia, and C.R. McClain. 2017. The evolution of energetic scaling across the vertebrate tree of life. The American Naturalist 190:185-199. [doi] [pdf]

Osmond, M.M., M.A. Barbour, J.R. Bernhardt, M.W. Pennell, J.M. Sunday, and M.I. O’Connor. 2017. Warming induced changes to body size stabilize consumer-resource dynamics. The American Naturalist 189:718-725. [doi] [pdf]

Pennell, M.W.*, R.G. FitzJohn*, and W.K. Cornwell*. 2016. A simple approach for maximizing the overlap of phylogenetic and comparative data. Methods in Ecology and Evolution 7:751-758. [doi] [pdf] [repo]

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. 2015. Nested radiations and the pulse of angiosperm diversification. New Phytologist 207:454-467. [doi] [pdf] [repo]

Pennell, M.W., R.G. FitzJohn, W.K. Cornwell, and L.J. Harmon. 2015. Model adequacy and the macroevolution of angiosperm functional traits. The American Naturalist 186: E33-E50. [doi] [pdf] [repo] [poster]

Pennell, M.W.*, M. Kirkpatrick*, S.P. Otto*, J.C. Vamosi, C.L. Piechel, N. Valenzuela, and J. Kitano. 2015. Y fuse? Sex chromosome fusions in fishes and reptiles. PLoS Genetics 11:e1005237 [doi] [pdf]

Uyeda, J.C., D.S. Caetano, and M.W. Pennell. 2015. Comparative analysis of principal components can be misleading. Systematic Biology 64:677-689. [doi] [pdf] [repo]

Pennell, M.W. 2015. Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology: Concepts and Practice.—Edited by László Zsolt Garamszegi (Book Review). Systematic Biology 64:161-163. [doi] [pdf]

FitzJohn, R.G.*, M.W. Pennell*, A.E. Zanne, P.F. Stevens, D.C. Tank, and W.K. Cornwell. 2014. How much of the world is woody? Journal of Ecology 102:1266-1272. [doi] [pdf] [repo] [project website]

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. 2014. 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. 2014. 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 78:1040-1049. [doi] [pdf]

Lanfear, R. and M.W. Pennell. 2014. Open access is worth considering. Trends in Plant Sciences 19:340-341. [doi] [pdf] [data]

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 15:2216-2218.. [doi] [pdf]

Slater, G.J. and M.W. Pennell. 2014. Robust regression and posterior predictive simulation increase power to detect early bursts of trait evolution. Systematic Biology 63:293-308. [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. 2014. Functional distinctiveness of major plant lineages. Journal of Ecology 102:345-356. [doi] [pdf]

Pennell, M.W., L.J. Harmon, and J.C. Uyeda. 2014. 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. 2014. Is there room for punctuated equilibrium in macroevolution? Trends in Ecology & Evolution 29:23-32. [doi] [pdf]

Maliska, M.E., M.W. Pennell, and B.J. Swalla. 2013. Developmental mode influences diversification in ascidians. Biology Letters 9:20130068. [doi] [pdf]

Pennell, M.W. and L.J. Harmon. 2013. An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology. Annals of the New York Academy of Sciences 1289:90-105. [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. 2013. Phylotastic! Making tree-of-life knowledge accessbile, reusable and convenient. BMC Bioinformatics 14:158. [doi] [pdf]

Pennell, M.W. 2012. Biology in the light of phylogeny. Trends in Ecology & Evolution 27:657-658. [doi] [pdf]

Pennell, M.W., C.R. Stansbury, L.P. Waits, and C.R. Miller. 2012. Capwire: a R package for estimating population census size from non-invasive genetic sampling. Molecular Ecology Resources 13:154-157. [doi] [pdf]

Pennell, M.W., B.A.J. Sarver, and L.J. Harmon. 2012. Trees of unusual size: biased inference of early bursts from large molecular phylogenies. PLOS ONE 7:e43348. [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. 2012. Goldilocks meets Santa Rosalia: an emphemeral speciation model explains patterns of diversification across time scales. Evolutionary Biology 39:255-261. [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 82:11-24. [doi] [pdf]

* indicates equal contribution

Additional writings

Essay inducting Joseph Felsenstein as a honorary lifetime member of the American Society of Naturalists (co-written with Jonathan Losos and Sally Otto) [doi]


PhD Exit Seminar, Moscow, ID. Models, meanings, & macroevolution [slides]

Evolution 2014, Raleigh, NC. The adequacy of phylogenetic trait models (SSB Symposium: The Dark Side of Phylogenetic Comparative Methods) [slides]