Publications

You can also find our complete list of publications on Google Scholar

All our software and code can be found on our lab GitHub page

PreprintS

Jiang, D., M. Pennell, L. Sallan. A general evolutionary model for the emergence of novel characters from serial homologs. [BioRχiv]

Pospelova, M., K.A. Voss, A. Zamyatin, C.T. Watson, K.-P. Koepfli, M. Pennell, and Y. Safonova. Comparative analysis of mammalian adaptive immune loci revealed spectacular divergence and common genetic patterns. [BioRχiv]

Jiang, D. and M. Pennell. Alternative mutational architectures producing identical M-matrices can lead to different patterns of evolutionary divergence. [BioRχiv]

MacPherson, A. and M. Pennell. The untapped potential of tree size in reconstructing evolutionary and epidemiological dynamics. [BioRχiv]

2025

David, K.T, J.G. Schraiber, J.G. Crandall, A.L. LaBella, D.A. Opulente, M.-C. Harrison, X. Zhou, X.-X. Shen, M. Groenewald, C.T. Hittinger, M. Pennell, and A. Rokas. Convergent expansions of keystone gene families drives metabolic innovation in a major eukaryotic clade. PNAS.

J. Parker, and M. Pennell. The cellular substrate of evolutionary novelty. Current Biology.

Zhu, Y., C.T. Watson, Y. Safonova, M. Pennell, A. Bankevich. Assessing assembly errors in immunoglobulin loci: a comprehensive evaluation of long-read genome assemblies across vertebrates. Genome Biology.

Cope, A.L., J.G. Schraiber, and M. Pennell. 2025. Macroevolutionary divergence of gene expression driven by selection on protein abundance. Science. [doi] [pdf]

Jiang, D., N. Kejiou, Y. Qiu, A.F. Palazzo, and M. Pennell. Genetic and selective constraints on the optimization of gene product diversity. Molecular Systems Biology. [doi] [pdf]

Pennell, M. and A. MacPherson. 2025. Reading Yule in light of the history and present of macroevolution. Philosophical Transactions of the Royal Society B: Biological Sciences 380:20230299. [doi]

D.A. Yoo, A. Rhie, P. Hebbar, F. Antonacci, G.A. Logsdon, S.J. Solar, D. Antipov, B.D. Pickett, Y. Safonova, F. Montinaro, Y. Luo, J. Malukiewicz, J.M. Storer, J. Lin, A.N. Sequeira, R.J. Mangan, G. Hickey, G.M. Anez, P. Balachandran, A. Bankevich, C.R. Beck, A. Biddanda, M. Borchers, G.G. Bouffard, E. Brannan, S.Y. Brooks, L. Carbone, L. Carrel, A.P. Chan, J. Crawford, M. Diekhans, E. Engelbrecht, C. Feschotte, G. Formenti, G.H. Garcia, L. de Gennaro, D. Gilbert, R.E. Green, A. Guarracino, I. Gupta, D. Haddad, J. Han, R.S. Harris, G.A. Hartley, W.T. Harvey, M. Hiller, K. Hoekzema, M.L. Houck, H. Jeong, K. Kamali, M. Kellis, B. Kille, C. Lee, Y. Lee, W. Lees, A.P. Lewis, Q. Li, M. Loftus, Y.H.E. Loh, H. Loucks, J. Ma, Y. Mao, J.F.I. Martinez, P. Masterson, R.C. McCoy, B. McGrath, S. McKinney, B.S. Meyer, K.H. Miga, S.K. Mohanty, K.M. Munson, K. Pal, M. Pennell, P.A. Pevzner, D. Porubsky, T. Potapova, F.R. Ringeling, J.L. Rocha, O.A. Ryder, S. Sacco, S. Saha, T. Sasaki, M.C. Schatz, N.J. Schork, C. Shanks, L. Smeds, D.R. Son, C. Steiner, A.P. Sweeten, M.G. Tassia, F. Thibaud-Nissen, E. Torres-González, M. Trivedi, W. Wei, J. Wertz, M. Yang, P. Zhang, S. Zhang, Y. Zhang, Z. Zhang, S.A. Zhao, Y. Zhu, E.D. Jarvis, J.L. Gerton, I. Rivas-González, B. Paten, Z.A. Szpiech, C.D. Huber, T.L. Lenz, M.K. Konkel, S.V. Yi, S. Canzar, C.T. Watson, P.H. Sudmant, E. Molloy, E. Garrison, C.B. Lowe, M. Ventura, R.J. O’Neill, S. Koren, K.D. Makova, A.M. Phillippy, E.E. Eichler. Complete sequencing of ape genomes. Nature. [doi] [pdf]

2024

Schraiber, J.G., M.D. Edge, and M. Pennell. 2024. Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations. PLoS Biology. [doi]

Voss, K., K.M. Kaur, R. Banerjee, F. Breden, and M. Pennell. Applying phylogenetic methods for species delimitation to distinguish B-cell clonal families. Frontiers in Immunology. [doi]

David, K.T., M.-C. Harrison, D.A. Opulente, A.L. LaBella, J.F. Wolters, X. Zhou, X.-X. Shen, M. Groenewald, M. Pennell, C.T. Hittinger, and A. Rokas. Saccharomycotina yeasts defy longstanding macroecological patterns. Proceedings of the National Academy of Sciences. [doi]

Mull, C.M, M. Pennell, K.E. Yopak, and N.K. Dulvy. Maternal investment evolves with larger body size and higher diversification rates in sharks and rays. Current Biology. [doi]

Jiang, D. and M. Pennell. The macroevolutionary adaptive landscape: more than a metaphor? Evolution. [doi]

T.S. Kalbfleisch, S.D. McKay, B.M. Murdoch, D.L. Adelson, D. Almansa-Villa, G. Becker, L.M. Beckett, M.J. Benítez-Galeano, F. Biase, T. Casey, E. Chuong, E. Clark, S. Clarke, N. Cockett, C. Couldrey, B.W. Davis, C.G. Elsik, T. Faraut, Y. Gao, C. Genet, P. Grady, J. Green, R. Green, D. Guan, D. Hagen, G.A. Hartley, M. Heaton, S.J. Hoyt, W. Huang, E. Jarvis, J. Kalleberg, H. Khatib, K-P. Koepfi, J. Koltes, S. Koren, C. Kuehn, T. Leeb, A. Leonard, G.E. Liu, W.Y. Low, H. McConnell, K. McRae, K. Miga, M. Mousel, H. Neibergs, T. Olagunju, M. Pennell, B. Petry, M. Pewsner, A.M. Phillippy, B.D. Pickett, P. Pineda, T. Potapova, S. Rachagani, A. Rhie, M. Rijnkels, A. Robic, N. Rodriguez Osorio, Y. Safonova, G. Schettini, R.D. Schnabel, N. Sirpu Natesh, M. Stegemiller, J. Storer, P. Stothard, C. Stull, G. Tosser-Klopp, G.M. Traglia, C.K. Tuggle, C.P. Van Tassell, C. Watson, R. Weikard, K. Wimmers, S. Xie, L. Yang, T.P.L. Smith, R.J. O’Neill, B.D. Rosen. The Ruminant Telomere-to-Telomere (R2T2) Consortium. Nature Genetics. [doi]

2023

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]

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

Jiang, D., A.L. Cope, J. Zhang, and M. Pennell. 2023. On the decoupling of evolutionary changes in mRNA and protein levels. Molecular Biology and Evolution. [doi]

Kaur, K.M. and M. Pennell. Synthesizing the phylogenetic evidence for mutualism-associated diversification. Evolution. [doi]

Henao-Diaz, L.F. and M. Pennell. The Major Features of Macroevolution. Systematic Biology. [doi]

Pennell, M. Genes are often uninformative for dating species origins. Nature. [doi]

Rolland, J., L.F. Henao-Diaz, M. Doebeli, R. Germain, L.J. Harmon, L.L. Knowles, L.H. Low, J.E. Mank, A. Machac, S.P. Otto, M. Pennell, N. Salamin, D. Silvestro, M. Sugawara, J. Uyeda, C.E. Wagner, and D. Schluter. Conceptual and empirical bridges between micro- and macro-evolution. Nature Ecology and Evolution. [doi]

2022

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]

2021

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]

2020

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 ]

2019

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 ]

2018

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 ]

2017

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]

2016

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 ]

2015

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 ]

2014

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]

2013

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 ]

2012

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 ]

2011

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]

the applied phylogenetics lab at cornell

publications