Publications

I would recommend reading a few of my best papers to get a sense of my work; good examples are O’Meara, Smith, et al. (2016) and Beaulieu & O’Meara (2016). Metrics are not as great (for example, my work with software might get cited than someone else’s work on a new discovery about evolution, but it is not clear that the former is ‘better’) , but I know some people find them useful, so: According to Google Scholar, my work has been cited 5279 times, and my h-index is 28. (Google Scholar tends to overestimate citations, however). If there were a journal of just my papers, its 2019 impact factor would be 7.545. Also note that I work under a very stringent criterion for when I get authorship – I have to actively make a significant contribution to the research and writing to merit authorship. For example, in 2015-6, three lab members had papers in Science (grad student Sam Borstein, postdoc Nick Matzke, and postdoc Sandy Kawano) but I am, appropriately to my mind, not an author on any of these.

Papers

Authors Year Title, Journal DOI Citations
Dwueng-Chwuan Jhwueng, Brian C O’Meara 2020 “On the Matrix Condition of Phylogenetic Tree” Evolutionary Bioinformatics 16, 1176934320901721 10.1177/1176934320901721 0
Van D Nguyen, Thanh H Nguyen, Abu Saleh Md Tayeen, H Dail Laughinghouse, Luna L Sánchez-Reyes, Jodie Wiggins, Enrico Pontelli, Dmitry Mozzherin, Brian O’Meara, Arlin Stoltzfus 2020 “Phylotastic: Improving Access to Tree-of-Life Knowledge With Flexible, on-the-Fly Delivery of Trees” Evolutionary Bioinformatics 16, 1176934319899384 10.1177/1176934319899384 0
Cedric Landerer, Brian C. O’Meara, Russell Zaretzki, Michael A. Gilchrist 2020 “Unlocking a signal of introgression from codons in Lachancea kluyveri using a mutation-selection model” BMC Evolutionary Biology 539148 10.1186/s12862-020-01649-w 0
Alexander L. Cope, Brian C. O’Meara, Michael A. Gilchrist 2020 “Gene expression of functionally-related genes coevolves across fungal species: Detecting coevolution of gene expression using phylogenetic comparative methods” BMC Genomics 21, 1-17 10.1186/s12864-020-6761-3 0
José Eduardo Meireles, Jeannine Cavender-Bares, Philip A. Townsend, Susan Ustin, John A. Gamon, Anna K. Schweiger, Michael E. Schaepman, Gregory P. Asner, Roberta E. Martin, Aditya Singh, Franziska Schrodt, Adam Chlus, Brian C. O’Meara 2020 “Leaf reflectance spectra capture the evolutionary history of seed plants” New Phytologist 10.1111/nph.16771 1
Matthew D. McGee, Samuel R. Borstein, Joana I. Meier, David A. Marques, Salome Mwaiko, Anthony Taabu, Mary A. Kishe, Brian O’Meara, Rémy Bruggmann, Laurent Excoffier, Ole Seehausen 2020 “The ecological and genomic basis of explosive adaptive radiation” Nature 1-5 10.1038/s41586-020-2652-7 1
Jeremy M. Beaulieu, Brian C. O’Meara 2019 “Diversity and skepticism are vital for comparative biology: a response to Donoghue and Edwards (2019)” American Journal of Botany 106 (5), 613-617 10.1002/ajb2.1278 4
Jeremy M Beaulieu, Brian C O’Meara, Russell Zaretzki, Cedric Landerer, Juanjuan Chai, Michael 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 (4), 834-851 10.1093/molbev/msy222 7
Samuel R. Borstein, Brian C. O’Meara 2018 “AnnotationBustR: An R package to extract subsequences from GenBank annotations” PeerJ 6, e5179 10.7717/peerj.5179 3
Jeremy M. Beaulieu, Brian 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 (3), 417-432 10.1002/ajb2.1020 21
Jeremy M. Beaulieu, Brian 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 (3), 417-432 10.1002/ajb2.1020 21
Daniel S. Caetano, Brian C. O’Meara, Jeremy M. Beaulieu 2018 “Hidden state models improve state-dependent diversification approaches, including biogeographical models” Evolution 72 (11), 2308-2324 10.1111/evo.13602 41
Nathan D. Jackson, Ariadna E. Morales, Bryan C. Carstens, Brian C. O’Meara 2017 “PHRAPL: Phylogeographic Inference Using Approximate Likelihoods” Systematic Biology 66 (6), 1045-1053 10.1093/sysbio/syx001 34
Bryan C. Carstens, Ariadna E. Morales, Nathan D. Jackson, Brian C. O’Meara 2017 “Objective choice of phylogeographic models” Molecular Phylogenetics and Evolution 116, 136-140 10.1016/j.ympev.2017.08.018 7
Ariadna E. Morales, Nathan D. Jackson, Tanya A. Dewey, Brian C. O’Meara, Bryan C. Carstens 2017 “Speciation with gene flow in North American Myotis bats” Systematic Biology 66 (3), 440-452 10.1093/sysbio/syw100 42
Nathan D. Jackson, Bryan C. Carstens, Ariadna E. Morales, Brian C. O’Meara 2017 “Species delimitation with gene flow” Systematic Biology 66 (5), 799-812 10.1093/sysbio/syw117 88
Jennifer M. Bosco, Susan E. Riechert, Brian C. O’Meara 2017 “The ontogeny of personality traits in the desert funnel-web spider, Agelenopsis lisa (Araneae: Agelenidae)” Ethology 123 (9), 648-658 10.1111/eth.12639 2
Orlando Schwery, Brian C. O’Meara 2016 “MonoPhy : a simple R package to find and visualize monophyly issues” PeerJ Computer Science 2, e56 10.7717/peerj-cs.56 16
Orlando Schwery, Brian C. O’Meara 2016 “MonoPhy: A simple R package to find and visualize monophyly issues” PeerJ Computer Science 2, e56 10.7717/peerj-cs.56 16
Jeremy M. Beaulieu, Brian C. O’Meara 2016 “Detecting hidden diversification shifts in models of trait-dependent speciation and extinction” Systematic Biology 65 (4), 583-601 10.1093/sysbio/syw022 238
Brian C. O’Meara, Stacey D. Smith, W. Scott Armbruster, Lawrence D. Harder, Christopher R. Hardy, Lena C. Hileman, Larry Hufford, Amy Litt, Susana Magallón, Stephen A. Smith, Peter F. Stevens, Charles B. Fenster, Pamela K. Diggle 2016 “Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity” Proceedings of the Royal Society of London B: Biological Sciences 283 (1830), 20152304 10.1098/rspb.2015.2304 50
Brian C. O’Meara, Jeremy M. Beaulieu 2016 “Past, future, and present of state-dependent models of diversification” American Journal of Botany 103 (5), 792-795 10.3732/ajb.1600012 28
Amy E. Zanne, David C. Tank, William K. Cornwell, Jonathan M. Eastman, Stephen A. Smith, Richard G. FitzJohn, Daniel J. McGlinn, Brian C. O’Meara, Angela T. Moles, Peter B. Reich, Dana L. Royer, Douglas E. Soltis, Peter F. Stevens, Mark Westoby, Ian J. Wright, Lonnie Aarssen, Robert I. Bertin, Andre Calaminus, Rafaël Govaerts, Frank Hemmings, Michelle R. Leishman, Jacek Oleksyn, Pamela S. Soltis, Nathan G. Swenson, Laura Warman, Jeremy M. Beaulieu 2015 “Erratum: Three keys to the radiation of angiosperms into freezing environments (Nature (2014) 506 (89-92) (Doi:10.1038/nature12872))” Nature 10.1038/nature12872 NA
Brian C O’Meara, Kerrie Lewis Graham, Sergio M Pellis, Gordon M Burghardt 2015 “Evolutionary models for the retention of adult–adult social play in primates: The roles of diet and other factors associated with resource acquisition” Adaptive Behavior 23 (6), 381-391 10.1177/1059712315611733 11
Jeremy M. Beaulieu, Brian C. O’Meara 2015 “Extinction can be estimated from moderately sized molecular phylogenies” Evolution 69 (4), 1036-1043 10.1111/evo.12614 81
Jeremy M. Beaulieu, Brian C. O’Meara, Peter Crane, Michael J. Donoghue 2015 “Heterogeneous rates of molecular evolution and diversification could explain the triassic age estimate for angiosperms” Systematic Biology 64 (5), 869-878 10.1093/sysbio/syv027 82
M. S. P. Aldrovandi, J. E. Johnson, B. OMeara, R. H. Petersen, K. W. Hughes 2015 “The Xeromphalina campanella/kauffmanii complex: Species delineation and biogeographical patterns of speciation” Mycologia 107 (6), 1270-1284 10.3852/15-087 11
Amy E. Zanne, David C. Tank, William K. Cornwell, Jonathan M. Eastman, Stephen A. Smith, Richard G. FitzJohn, Daniel J. McGlinn, Brian C. O’Meara, Angela T. Moles, Peter B. Reich, Dana L. Royer, Douglas E. Soltis, Peter F. Stevens, Mark Westoby, Ian J. Wright, Lonnie Aarssen, Robert I. Bertin, Andre Calaminus, Rafaël Govaerts, Frank Hemmings, Michelle R. Leishman, Jacek Oleksyn, Pamela S. Soltis, Nathan G. Swenson, Laura Warman, Jeremy M. Beaulieu 2015 “Zanne et al. reply” Nature 521 (7552), E6-E7 10.1038/nature14394 3
Amy E. Zanne, David C. Tank, William K. Cornwell, Jonathan M. Eastman, Stephen A. Smith, Richard G. FitzJohn, Daniel J. McGlinn, Brian C. O’Meara, Angela T. Moles, Peter B. Reich, Dana L. Royer, Douglas E. Soltis, Peter F. Stevens, Mark Westoby, Ian J. Wright, Lonnie Aarssen, Robert I. Bertin, Andre Calaminus, Rafaël Govaerts, Frank Hemmings, Michelle R. Leishman, Jacek Oleksyn, Pamela S. Soltis, Nathan G. Swenson, Laura Warman, Jeremy M. Beaulieu 2014 “Erratum: Three keys to the radiation of angiosperms into freezing environments (Nature (2014) 506 (89-92) DOI:10.1038/nature12872)” Nature 10.1038/nature12872 NA
William K. Cornwell, Mark Westoby, Daniel S. Falster, Richard G. FitzJohn, Brian C. O’Meara, Matthew W. Pennell, Daniel J. McGlinn, Jonathan M. Eastman, Angela T. Moles, Peter B. Reich, David C. Tank, Ian J. Wright, Lonnie Aarssen, Jeremy M. Beaulieu, Robert M. Kooyman, Michelle R. Leishman, Eliot T. Miller, Ülo Niinemets, Jacek Oleksyn, Alejandro Ordonez, Dana L. Royer, Stephen A. Smith, Peter F. Stevens, Laura Warman, Peter Wilf, Amy E. Zanne 2014 “Functional distinctiveness of major plant lineages” Journal of Ecology 102 (2), 345-356 10.1111/1365-2745.12208 100
Dwueng-Chwuan Jhwueng, Snehalata Huzurbazar, Brian C. O’Meara, Liang Liu 2014 “Investigating the performance of AIC in selecting phylogenetic models” Statistical Applications in Genetics and Molecular Biology 13 (4), 459-475 10.1515/sagmb-2013-0048 6
Barbara L. Banbury, Brian C. O’Meara 2014 “Reol: R interface to the encyclopedia of life” Ecology and Evolution 4 (12), 2577-2583 10.1002/ece3.1109 3
Joseph H. Williams, Mackenzie L. Taylor, Brian C. O’Meara 2014 “Repeated evolution of tricellular (and bicellular) pollen” American Journal of Botany 101 (4), 559-571 10.3732/ajb.1300423 35
Amy E. Zanne, David C. Tank, William K. Cornwell, Jonathan M. Eastman, Stephen A. Smith, Richard G. FitzJohn, Daniel J. McGlinn, Brian C. O’Meara, Angela T. Moles, Peter B. Reich, Dana L. Royer, Douglas E. Soltis, Peter F. Stevens, Mark Westoby, Ian J. Wright, Lonnie Aarssen, Robert I. Bertin, Andre Calaminus, Rafaël Govaerts, Frank Hemmings, Michelle R. Leishman, Jacek Oleksyn, Pamela S. Soltis, Nathan G. Swenson, Laura Warman, Jeremy M. Beaulieu 2014 “Three keys to the radiation of angiosperms into freezing environments” Nature 506 (7486), 89-92 10.1038/nature12872 786
Jeremy M. Beaulieu, Brian C. O’Meara, Michael 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 (5), 725-737 10.1093/sysbio/syt034 185
C. Darrin Hulsey, Benjamin P. Keck, Hugo Alamillo, Brian C. O’Meara 2013 “Mitochondrial genome primers for Lake Malawi cichlids” Molecular Ecology Resources 13 (3), 347-353 10.1111/1755-0998.12066 14
D. E. Soltis, M. E. Mort, M. Latvis, E. V. Mavrodiev, B. C. O’Meara, P. S. Soltis, J. G. Burleigh, R. Rubio de Casas 2013 “Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach” American Journal of Botany 100 (5), 916-929 10.3732/ajb.1300044 64
Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena Deus, Brian Sidlauskas, Christian M Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger Vos, Campbell O Webb, Luke J Harmon, Megan Pirrung, Brian O’Meara, Matthew W Pennell, Siavash Mirarab, Michael S Rosenberg, James P Balhoff, Holly M Bik, Tracy A Heath, Peter E Midford, Joseph W Brown, Emily Jane McTavish, Jeet Sukumaran, Mark Westneat, Michael E Alfaro, Aaron Steele, Greg Jordan 2013 “Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient” BMC Bioinformatics 14 (1), 1-17 10.1186/1471-2105-14-158 36
Brian C. O’Meara 2012 “Evolutionary inferences from phylogenies: a review of methods” Annual Review of Ecology, Evolution, and Systematics 43, 267-285 10.1146/annurev-ecolsys-110411-160331 175
Jeremy M. Beaulieu, Dwueng-Chwuan Jhwueng, Carl Boettiger, Brian C. O’Meara 2012 “Modeling stabilizing selection: Expanding the Ornstein-Uhlenbeck model of adaptive evolution” Evolution 66 (8), 2369-2383 10.1111/j.1558-5646.2012.01619.x 396
Arlin Stoltzfus, Brian O’Meara, Jamie Whitacre, Ross Mounce, Emily L Gillespie, Sudhir Kumar, Dan F Rosauer, Rutger A Vos 2012 “Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis” BMC Research Notes 5 (1), 574 10.1186/1756-0500-5-574 42
Stephen A. Smith, Brian C. O’Meara 2012 “TreePL: Divergence time estimation using penalized likelihood for large phylogenies” Bioinformatics 28 (20), 2689-2690 10.1093/bioinformatics/bts492 238
J. Conrad Stack, Luke J. Harmon, Brian O’Meara 2011 “RBrownie: an R package for testing hypotheses about rates of evolutionary change” Methods in Ecology and Evolution 2 (6), 660-662 10.1111/j.2041-210x.2011.00112.x 12
Jason M Abercrombie, Brian C O’Meara, Andrew R Moffatt, Joseph H Williams 2011 “Developmental evolution of flowering plant pollen tube cell walls: Callose synthase (CalS) gene expression patterns” EvoDevo 2 (1), 14 10.1186/2041-9139-2-14 31
Stephen A. Goff, Matthew Vaughn, Sheldon McKay, Eric Lyons, Ann E. Stapleton, Damian Gessler, Naim Matasci, Liya Wang, Matthew Hanlon, Andrew Lenards, Andy Muir, Nirav Merchant, Sonya Lowry, Stephen Mock, Matthew Helmke, Adam Kubach, Martha Narro, Nicole Hopkins, David Micklos, Uwe Hilgert, Michael Gonzales, Chris Jordan, Edwin Skidmore, Rion Dooley, John Cazes, Robert McLay, Zhenyuan Lu, Shiran Pasternak, Lars Koesterke, William H. Piel, Ruth Grene, Christos Noutsos, Karla Gendler, Xin Feng, Chunlao Tang, Monica Lent, Seung-Jin Kim, Kristian Kvilekval, B. S. Manjunath, Val Tannen, Alexandros Stamatakis, Michael Sanderson, Stephen M. Welch, Karen A. Cranston, Pamela Soltis, Doug Soltis, Brian O’Meara, Cecile Ane, Tom Brutnell, Daniel J. Kleibenstein, Jeffery W. White, James Leebens-Mack, Michael J. Donoghue, Edgar P. Spalding, Todd J. Vision, Christopher R. Myers, David Lowenthal, Brian J. Enquist, Brad Boyle, Ali Akoglu, Greg Andrews, Sudha Ram, Doreen Ware, Lincoln Stein, Dan Stanzione 2011 “The iPlant collaborative: Cyberinfrastructure for plant biology” Frontiers in Plant Science 2, 34 10.3389/fpls.2011.00034 427
D. C. COLLAR, J. A. SCHULTE, B. C. O’MEARA, J. B. LOSOS 2010 “Habitat use affects morphological diversification in dragon lizards” Journal of Evolutionary Biology 23 (5), 1033-1049 10.1111/j.1420-9101.2010.01971.x 78
Brian C. O’Meara 2010 “New heuristic methods for joint species delimitation and species tree inference” Systematic Biology 59 (1), 59-73 10.1093/sysbio/syp077 262
S. A. Smith, B. C. O’Meara 2009 “Morphogenera, monophyly, and macroevolution” Proceedings of the National Academy of Sciences of the United States of America 106 (36), E97-E98 10.1073/pnas.0906918106 4
David C. Collar, Brian C. O’Meara, Peter C. Wainwright, Thomas J. Near 2009 “Piscivory limits diversification of feeding morphology in centrarchid fishes” Evolution 63 (6), 1557-1573 10.1111/j.1558-5646.2009.00626.x 140
Brian C. O’Meara, Cécile Ané, Michael J. Sanderson, Peter C. Wainwright 2006 “Testing for different rates of continuous trait evolution using likelihood” Evolution 60 (5), 922-933 10.1554/05-130.1 591
A. C. Driskell 2004 “Prospects for building the tree of life from large sequence databases” Science 306 (5699), 1172-1174 10.1126/science.1102036 258
Farrell, B.D., Sequeira, A.S., O’Meara, B.C., Normark, B.B., Chung, J.H., Jordal, B.H. 2001 “The evolution of agriculture in beetles (Curculionidae: Scolytinae and Platypodinae)” Evolution 55 (10), 2011-2027 NA 395

Publications: Books or Book Chapters

Authors Year Title Book
Jeremy M. Beaulieu, Brian C. O’Meara 2014 “Hidden Markov Models for Studying the Evolution of Binary Morphological Characters” Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology: Concepts and Practice
Brian C. O’Meara, Jeremy M. Beaulieu 2014 “Modelling Stabilizing Selection: The Attraction of Ornstein–Uhlenbeck Models” Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology: Concepts and Practice
B. O’Meara 2012 “Phylogenetic Reconstruction” Encyclopedia of Theoretical Ecology

Packages

Software developed in R (often associated with a publication, but not always)

Package Authors Description Downloads
AnnotationBustR Samuel R. Borstein , Brian O’Meara Extract Subsequences from GenBank Annotations 18009
corHMM Jeremy Beaulieu, Brian O’Meara, Jeffrey Oliver, James Boyko Hidden Markov Models of Character Evolution 49921
hisse Jeremy Beaulieu, Brian O’Meara, Daniel Caetano, James Boyko Hidden State Speciation and Extinction 40598
OUwie Jeremy M. Beaulieu , Brian O’Meara Analysis of Evolutionary Rates in an OU Framework 54503
phylobase R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut, Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O’Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl) Base Package for Phylogenetic Structures and Comparative Data 166159
rncl Francois Michonneau, (https://orcid.org/0000-0002-9092-966X), Ben Bolker (https://orcid.org/0000-0002-2127-0443), Mark Holder (https://orcid.org/0000-0001-5575-0536), Paul Lewis (https://orcid.org/0000-0001-9852-8759), Brian O’Meara (https://orcid.org/0000-0002-0337-5997) An Interface to the Nexus Class Library 181273
selac Jeremy Beaulieu, JJ Chai, Mike Gilchrist, Cedric Landerer, Graham Derryberry, Brian O’Meara Selection Models for Amino Acid and/or Codon Evolution 5992