You can also find my complete list of publications on Google Scholar.
MacPherson, A., S. Louca, A. MacLaughlin, J.B. Joy, and M.W. Pennell. A General Birth-Death-Sampling Model for Epidemiology and Macroevolution. [BioRxiv]
Freeman, B.F. and M.W. Pennell. The latitudinal taxonomy gradient. Trends in Ecology and Evolution.
Harmon, L.J., M.W. Pennell, L.F. Henao-Diaz, J. Rolland, B. Sipley, and J.C. Uyeda. The causes and consequences of the ubiquitous time-scaling of all evolutionary rates. Annual Reviews of Ecology, Evolution, and Systematics.
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.
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. [BioRxiv]
Louca, S., A. McLaughlin, A. MacPherson, J.B. Joy, and M.W. Pennell. Fundamental identifiability limits in molecular epidemiology. Molecular Biology and Evolution. [BioRxiv]
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]
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]
- Commentary by Mark Pagel in Nature
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 116:24401. [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 18:ar49. [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 116:7403-7408. [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 94:1740-1760. [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 286. [doi] [pdf]
- datastorr: a R package to build and distribute versioned datasets with GitHub.
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 32:769-782. [doi] [pdf]
O’Connor, M.I., M.W. Pennell, F. Altermatt, B. Matthews, C.J. Melián, and A. Gonzalez. Principles of ecology revisted: integrating information and ecological theories for a more unified science. Frontiers in Ecology and Evolution 7:219. [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:e6334 [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 10:858. [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 9:2888. [doi] [pdf]
- recommended by Faculty of 1000
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 189:718-725. [doi] [pdf]
- phyndr: a R implementation of the algorithms described in our paper
- taxonlookup: a R data package containing a versioned and dynamic taxonomic resource for plants
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 207:454-467. [doi] [pdf] [repo]
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 64:161-163. [doi] [pdf]
- traitfill (R implementation of approach):
- Post on the ROpenSci blog on reproducibility
- Post on the Journal of Ecology blog
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 78:1040-1049. [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 15:2216-2218.. [doi] [pdf] [repo]
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 102:345-356. [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 1289:90-105. [doi] [pdf]
- recommended by Faculty of 1000
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 accessbile, reusable and convenient. BMC Bioinformatics 14:158. [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 13:154-157. [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 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]