2024

• Beaulieu, J.M., and B.C. O'Meara (2024). Navigating "tip fog": embracing uncertainty in tip measurements. bioRvix. (in review). www.biorxiv.org/content/10.1101/2024.08.19.608647v3.abstract​
• Hagen, E.R., and J.M. Beaulieu (2024). New beginnings for dead ends: polyploidy, -SSE models, and the dead-end hypothesis. Annals of Botany. In press. 
• Smith, S.A., and J.M. Beaulieu (2024). Ad fontes: divergence-time estimation and the age of angiosperms. New Phytologist, 244:760-766.
• O'Meara, B.C., and J.M. Beaulieu (2024). Noise leads to the perceived increase in evolutionary rates over short time scales. PLOS Computational Biology 20:e1012458.
• Hagen, E.R., T. Vasconcelos, J.D. Boyko, and J.M. Beaulieu (2024). Investigating historical drivers of latitudinal gradients in polyploid plant biogeography: A multiclade perspective. American Journal of Botany, 111:e16356 

2023

• Boyko, J.D., E.R. Hagen, J.M. Beaulieu, and T. Vasconcelos. (2023). The evolutionary responses of life-history strategies to climatic variability in flowering plants. New Phytologist, 240:1587-1600. ​
• Boyko, J.D., B.C. O'Meara. (2023). A novel method for jointly modeling the evolution of discrete and continuous traits. Evolution, 77:836-851.
• Boyko, J.D., and J.M. Beaulieu. (2023). Reducing the biases in false correlation between discrete characters. Systematic Biology, 72:476-488.
• Beaulieu, J.M., and B.C. O'Meara. (2023). Fossils do not substantially improve, and may even harm, estimates of diversification rate heterogeneity. Systematic Biology, 72:50-61.
• Vasconcelos, T, J.D. Boyko, and J.M. Beaulieu. (2023). Linking mode of seed dispersal and climatic niche evolution in flowering plants. Journal of Biogeography, 50:43-56.

2022

• Mortimer, S.M.E., J.D. Boyko, J.M. Beaulieu, and D.C. Tank. (2022). Synthesizing existing phylogenetic data to advance phylogenetic research in Orobanchaceae. Systematic Botany, 47:533-544.
• Vasconcelos, T., B.C. O'Meara, and J.M. Beaulieu. (2022). A flexible method for estimating tip diversification rates across a range of speciation and extinction scenarios. Evolution, 76:1420-1433.
• Vasconcelos, T., B.C. O'Meara, and J.M. Beaulieu. (2022). Retiring "cradles" and "museums" of biodiversity. The American Naturalist, 199:194-205.

2021

• O'Meara, B.C., and J.M. Beaulieu. (2021). Potential survival of some, but not all, diversification methods. EcoEvoRxiv doi: https://ecoevorxiv.org/repository/view/3912/
• Boyko, J.D., and J.M. Beaulieu. (2021). Generalized hidden Markov models for phylogenetic comparative datasets. Methods in Ecology and Evolution, 12:468-478
• Beaulieu, J.M., B.C. O'Meara, and M.A. Gilchrist. (2021). A spatially-explicit model of stabilizing selection for improving phylogenetic inference. Molecular Biology and Evolution, 38:1641-1652

2020​

• Caetano, D.S., and J.M. Beaulieu. (2020). Comparative analyses of phenotypic sequences using phylogenetic trees. The American Naturalist, 195:E38-E50.
• Howard, C.C., J.B. Landis, J.M. Beaulieu and N. Cellinese. (2020) Geophytism in monocots leads to higher rates of diversification. New Phytologist, 225:1023-1032.

2019

• Nakov, T., J.M. Beaulieu, and A.J. Alverson. (2019). Diatoms diversify and turn over faster in freshwater than marine environments. Evolution, 73:2497-2511
• Beaulieu, J.M., and B.C. O'Meara. (2019) Diversity and skepticism are vital for comparative biology: a response to Donoghue and Edwards. American Journal of Botany, 106:613-617. 
• Howard, C.C., R.A. Folk, J.M. Beaulieu and N. Cellinese. (2019) The monocotyledonous underground: global climatic and phylogenetic patterns of geophyte diversity. American Journal of Botany, 106:850-863.
• Beaulieu, J.M., B.C. O'Meara, R. Zaretzki, C. Landerer, J.J. Chai, M.A. Gilchrist. (2019) Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach. Molecular Biology and Evolution, 36:834-851. ​

2018

• Caetano, D.S., B.C. O'Meara, and J.M. Beaulieu. (2018). Hidden state models improve the adequacy of state-dependent diversification, including biogeographical models. Evolution 72:2308-2324.
• Beaulieu, J.M., and B.C. O'Meara. (2018). Can we build it? Yes we can, but should we use it? Assessing the quality and value of a very large phylogeny of campanulid angiosperms. American Journal of Botany 105: 417-432.
• Welch, J.N., and J.M. Beaulieu. (2018). Predicting extinction risk for data-deficient bats. Diversity 10:63.
• Nakov, T, J.M. Beaulieu, and A.J. Alverson. (2018). Insights into global planktonic diatom diversity: The importance of comparisons between phylogenetically equivalent units that account for time. The ISME Journal 12:2807–2810.
• Nakov, T., J.M. Beaulieu, and A.J. Alverson. (2018). Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta). New Phytologist 219: 462:473.
• Gitzendanner, M.A., Y. Yang, N.J. Wickett, M. McKain, and J.M. Beaulieu. (2018). Methods for exploring the plant tree of life. Applications in Plant Sciences 6: e1039.​
• Leslie, A.B, J.M. Beaulieu, G. Holman, C.S. Campbell, W. Mei, L.R. Raubeson, S. Mathews. (2018). An overview of extant conifer evolution from the perspective of the fossil record. American Journal of Botany 105: 1531-1544.

2017

• Nakov, T., J.D. Boyko, A.J. Alverson, and J.M. Beaulieu. (2017). Models with unequal transition rates favor marine origins of cyanobacteria and photosynthetic eukaryotes. Proceedings of the National Academy of Sciences of the USA 114: E10606-E10607.
• Siepielski, A.M, and J.M. Beaulieu. (2017). Adaptive evolution to novel predators facilitates the evolution of damselfly species range. Evolution 71: 974-984.
• Leslie, A.B., J.M. Beaulieu, and S. Matthews. (2017). Variation in seed size is structured by dispersal syndrome and cone morphology in conifers and other nonflowering seed plants. New Phytologist 216: 429-437.

2016

• O'Meara, B.C., and J.M. Beaulieu. (2016). Past, future, and present of state-dependent models of diversification. American Journal of Botany 103: 1-4.
• Beaulieu, J.M., and B.C. O'Meara. (2016). Detecting hidden diversification shifts in models of trait-dependent speciation and extinction. Systematic Biology 65: 583-601.​

2015

• Beaulieu, J.M., B.C. O'Meara, P. Crane, and M.J. Donoghue. (2015). Heterogeneous rates of molecular evolution and diversification could explain the Triassic age estimate for angiosperms. Systematic Biology 64:869-878. 
• Near, T.J., A. Dornburg, R.C. Harrington, C. Oliveira, T.W. Pietsch, C.E. Thacker, T.P. Satoh, E. Katayama, P.C. Wainwright, J.T. Eastman, and J.M. Beaulieu. (2015) Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation. BMC Evolutionary Biology 15:109.
• Leslie, A.B., J.M. Beaulieu, P.R. Crane, P. Knopf, and M.J. Donoghue. (2015). Trait integration and macroevolutionary patterns in the pollination biology of conifers. Evolution 69:1573-1583.
• Beaulieu, J.M., and B.C. O’Meara. (2015). Extinction can be estimated from moderately sized molecular phylogenies. Evolution 69:1036-1043.
• Dornburg A., J. Moore, J.M. Beaulieu, R.I. Eytan, and T.J. Near. (2015). The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from Holocentridae (squirrelfishes and soldierfishes). Evolution 69:146-161.

2014

• Beaulieu, J.M., and B.C. O’Meara. (2014). Hidden Markov models for studying the evolution of binary morphological character. In Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology - Concepts and Practice edited by L. Z. Garamszegi.
• O'Meara, B.C., and J.M. Beaulieu. (2014). Modeling stabilising selection: the attraction of Ornstein-Uhlenbeck models. In Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology - Concepts and Practice edited by L. Z. Garamszegi.
• Leslie, A.B., J.M. Beaulieu, P.R. Crane, and M.J. Donoghue. (2014). Cone size is related to branching architecture in conifers. New Phytologist 203:119-1127
• Zanne, A.E., D.C. Tank, W.K. Cornwell, J.M. Eastman, S.A. Smith, R.G. FitzJohn, D.J. McGlinn, B.C. O’Meara, A.T. Moles, P.B. Reich, D.L. Royer, D.E. Soltis, P.F. Stevens, M. Westoby, I.J. Wright, L. Aarssen, R.I. Bertin, A. Calaminus, R. Govaerts, F. Hemmings, M.R. Leishman, J. Oleksyn, P.S. Soltis, N.G. Swenson, L. Warmon, and J.M. Beaulieu. (2014). Into the cold: three keys to the radiation of angiosperms into freezing environments. Nature 506: 89-92.
• Cornwell, W.K., M. Westoby, D.S. Falster, R.G. FitzJohn, B.C. O'Meara, 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, U. Niinemets, J. Oleksyn, A. Ordonez, M.W. Pennell, D.L. Royer, S.A. Smith, P.F. Stevens, L. Warman, P. Wilf, E.T. Miller, and A.E. Zanne. (2014). Functional distinctiveness of major plant lineages. Journal of Ecology 102: 345-356.
• Oliver, J.C., J.M. Beaulieu, L.F. Gall, W.H. Piel, and A. Monteiro. (2014) Nymphalid eyespot serial homologues originate as a few individualized modules. Proceedings of the Royal Society B. 281: 20133262

2013

• Leslie, A.B., J.M. Beaulieu, P.R. Crane, and M.J. Donoghue. (2013). Explaining the distribution of breeding and dispersal syndromes in conifers. Proceedings of the Royal Society B. 280: 20131812.
• Beaulieu, J.M., and M.J. Donoghue. (2013). Fruit evolution and diversification in campanulid angiosperms. Evolution. 67: 3132-3144.
• Beaulieu, J.M., D.C. Tank, and M.J. Donoghue. (2013). A Southern Hemisphere origin for campanulid angiosperms, with traces of the break-up of Gondwana. BMC Evolutionary Biology 13: 80
• Beaulieu, J.M., B.C. O’Meara, and M.J. Donoghue. (2013). Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms. Systematic Biology 62: 725-737.
• Bossu, C.M., J.M. Beaulieu, P.A. Ceas, and T.J. Near. (2013). Explicit tests of paleodrainage connections of southeastern North America and the historical biogeography of Orangethroat Darters (Percidae: Etheostoma: Ceasia). Molecular Ecology 22:5397-5417.
• Lapiedra, O, D. Sol, S. Carranza, and J.M. Beaulieu. (2013). Behavioural changes and the adaptive diversification of pigeons and doves. Proceedings of the Royal Society B 280: 2012-2893

2012

• Beaulieu, J.M., D-J. Jhueng, and B.C. O’Meara. (2012). Modeling stabilizing selection: Expanding the Ornstein-Uhlenbeck model of adaptive evolution. Evolution. 66: 2369-2383
• Beaulieu, J.M., R.H. Ree, J. Cavender-Bares, G.D. Weiblen, and M.J. Donoghue. (2012). Synthesizing phylogenetic knowledge for ecological research. Ecology 93: S4-S13.
• Leslie, A.B., J.M. Beaulieu, H. Rai, P.R. Crane, M.J. Donoghue, and S. Matthews. (2012). Hemisphere-scale differences in conifer evolutionary dynamics. Proceedings of the National Academy of Sciences of the USA 109: 16217-16221.
• Schmerler, S., W.L. Clement, J.M. Beaulieu, D. Chatelet, L. Sack, M.J. Donoghue, and E.J. Edwards. (2012). Evolution of leaf form correlates with tropical-temperate transitions in Viburnum (Adoxaceae). Proceedings of the Royal Society B 279: 3905–3913.
• Avolio, M.L, J.M. Beaulieu, E. Lo, and M.D. Smith. (2012). Measuring genetic diversity in ecological studies. Plant Ecology 213: 1105-1115.
• Avolio, M.L., J.M. Beaulieu, M.D. Smith. (2012). Genetic diversity of a dominant C4 grass is altered with increased precipitation variability. Oecologia. 171: 437-442.
• Franks, P.J., R.P. Freckleton, J.M. Beaulieu, I.J. Leitch, and D.J. Beerling. (2012). Megacycles of atmospheric CO2 concentration correlate with fossil plant genome size. Philosophical Transactions of the Royal Society, B. 367: 556-564.

2011

• Smith, S.A., J.M. Beaulieu, A. Stamatakis, and M.J. Donoghue. (2011). Understanding angiosperm diversification using small and large phylogenetic trees. American Journal of Botany 98: 404-414.
• Dornburg, A., J.M. Beaulieu, J.C. Oliver, and T.J. Near. (2011). Integrating fossil preservation biases in the selection of calibration for molecular divergence time estimation. Systematic Biology 60: 519-527.

2010

• Smith, S.A., J.M. Beaulieu, and M.J. Donoghue. (2010). An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants. Proceedings of the National Academy of Sciences of the USA 107: 5897-5902.
• Beaulieu, J.M. (2010). The right stuff: evidence for an ‘optimal’ genome size in a wild grass population. New Phytologist 187: 883-885.
• Leitch I.J., J.M. Beaulieu, M.W. Chase, A.R. Leitch, and M.F. Fay. (2010). Genome size dynamics and evolution in monocots. Journal of Botany doi:10.1155/2010/862516.
• Beaulieu, J.M., S.A. Smith, and I.J. Leitch. (2010). On the tempo of genome size evolution in angiosperms. Journal of Botany doi:10.1155/2010/989152.
• Knight, C.A., R.B. Clancy, L. Gotzenberger, L. Dann, and J.M. Beaulieu. (2010). On the relationship between pollen size and genome size. Journal of Botany doi:10.1155/2010/612017.

2009

• Smith, S.A. and J.M. Beaulieu. (2009). Life history influences rates of climatic niche evolution in flowering plants. Proceedings of the Royal Society B. 276: 4345-4352. 
• Smith, S.A., J.M. Beaulieu, and M.J. Donoghue. (2009). Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evolutionary Biology 9: 37.
• Lysak, M.A., M.A. Koch, J.M. Beaulieu, A. Meister, and I.J. Leitch.  (2009). The dynamic ups and downs of genome size evolution in Brassicaceae. Molecular Biology and Evolution 26: 85-98.

2008

• Beaulieu, J.M., I.J. Leitch, S. Patel, A. Pendharkar, and C.A. Knight. (2008). Genome size is a strong predictor of cell size and stomatal density in angiosperms. New Phytologist 179: 975-986.
• Knight, C.A. and J.M. Beaulieu. (2008). Genome size scaling through phenotype space. Annals of Botany 6: 759-766.
• Connolly, J.A., M.J. Oliver, J.M. Beaulieu, C.A. Knight, L. Tomanek, and M.A. Moline. (2008). The correlated evolution of genome size and cell volume in diatoms (Bacillariophyceae). Journal of Phycology 44: 124-131.

2007

• Beaulieu, J.M., A.T. Moles, I.J. Leitch, M.D. Bennett, J.B. Dickie, and C.A. Knight. (2007). Correlated evolution of genome size and seed mass.  New Phytologist. 173: 422-437.
• Beaulieu, J.M., I.J. Leitch, and C.A. Knight. (2007). Genome size evolution in relation to leaf strategy and metabolic rates revisited. Annals of Botany 99: 495-505.
• Leitch, I.J., J.M. Beaulieu, L. Hansen, K. Cheung, M. Lysak, and M.F. Fay. (2007). Punctuated genome size evolution in Liliaceae. Journal of Evolutionary Biology 20: 2296-2308.