Brian C. O’Meara

http://www.brianomeara.info

865-974-2804

bomeara@utk.edu

Dept. of Ecology and Evolutionary Biology

University of Tennessee, Knoxville

Research

I address questions in evolutionary biology through development, implementation, and application of new phylogenetic methods. These include approaches for examining the process of continuous trait evolution (rate, optimal values, and other factors), species delimitation, phylogeography, diversification analyses, biogeography, and more. I also collaborate extensively with empiricists, including some of my own students.

Summary

Publications 50 journal articles, including Science, Nature, Ann. Rev Ecology, Evolution & Systematics, Systematic Biology, Evolution, etc.
Teaching Approximately 2 courses per year on average, ranging from large introductory biology courses to small graduate seminars
Mentoring 6 PhD students, 16 postdocs, 3 faculty, and served on 28 graduate student committees
Service/Outreach Darwin Day TN advisor, curator of R phylogenetics task view, instructor at workshops in Sweden, Switzerland, Brazil, and various US locations (Ohio, TN, NC)
Leadership Associate Head for Dept. of Ecology & Evolutionary Biology, 2016-present; Associate Director for the National Institute for Mathematical and Biological Synthesis, 2016-2018; Code of Conduct Committee for SSE/SSB/ASN, 2018-present; Communications Director for the Society of Systematic Biologists, 2016-2017; Society of Systematic Biologists Council, 2012-2014; iEvoBio co-organizer, 2014-2016.
Funding $2.89M in external support, including 4 NSF grants (including a CAREER grant) plus funding from iPlant and Encyclopedia of Life

Education

University of California Davis: PhD (2008) in Population Biology

Harvard University: Bachelor (magna cum laude), with highest honors in Biology (2001)

Employment

2019-Present: Professor, Dept. of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN

2016-Present: Associate Head, Dept. of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN

2016-2017: Associate Director, Dept. of National Institute for Mathematical and Biological Synthesis (NIMBioS), University of Tennessee, Knoxville, TN

2015-2019: Associate Professor, Dept. of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN

2009-2015: Assistant Professor, Dept. of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN

2007-2009: Postdoc, National Evolutionary Synthesis Center, Durham, NC

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

Teaching

University Courses

I created a course on macroevolution targeted at upper level undergraduate and graduate students: we cover diversification, symbiosis, game theory, and more. I have also taught large introductory courses and small discussion seminars. Note that the “HOFF joint lab group discussion” was a collaborative lab group meeting of the Hulsey-O’Meara-Fordyce-Fitzpatrick labs.

Year Semester Course Number Topic Enrollment Percent Effort
2020 Fall EEB464 Macroevolution 36 100
2020 Spring EEB587 PhyloMeth 11 100
2019 Fall EEB464 Macroevolution 15 100
2018 Fall EEB464 Macroevolution 14 100
2018 Spring EEB603 PhyloMeth 2 100
2018 Spring EEB504 PhyloMeth 5 100
2017 Fall EEB464 Macroevolution 23 100
2017 Spring EEB603 PhyloMeth 6 100
2017 Spring EEB504 PhyloMeth 2 100
2016 Fall EEB464 Macroevolution 28 100
2016 Spring Biology150 Introductory biology 235 100
2016 Spring EEB603 PhyloMeth 9 enrolled, plus dozens online 100
2015 Fall EEB464 Macroevolution 27 100
2015 Fall EEB607 Phyloseminar discussion 10 100
2015 Spring EEB602 Phyloseminar discussion 13 100
2015 Spring EEB607 HOFF joint lab group discussion 8 100
2014 Fall EEB464 Macroevolution 28 100
2014 Fall EEB504 HOFF joint lab group discussion 9 33
2014 Fall EEB511 Graduate student core 12 50
2014 Fall EEB607 Phyloseminar discussion 15 100
2014 Spring Biology130 Introductory biology 94 100
2014 Spring EEB602 Phyloseminar discussion 24 100
2014 Spring EEB607 HOFF joint lab group discussion 6 25
2013 Fall EEB464 Macroevolution 30 100
2013 Fall EEB504 HOFF joint lab group discussion 11 25
2013 Fall EEB511 Graduate student core 19 33
2013 Spring EEB607 HOFF joint lab group discussion 8 25
2012 Fall EEB464 Macroevolution 22 100
2012 Fall EEB504 HOFF joint lab group discussion 5 25
2012 Fall EEB511 Graduate student core 14 13
2012 Spring Biology130 Introductory biology 206 100
2011 Fall EEB464 Macroevolution 24 100
2011 Fall EEB504 HOFF joint lab group discussion 7 25
2011 Fall EEB503 EEB departmental seminar 44 100
2011 Fall EEB511 Graduate student core 12 13
2011 Spring EEB503 EEB departmental seminar 35 100
2011 Spring EEB607 Speciation discussion 9 100
2010 Fall EEB511 Graduate student core 8 13
2010 Spring EEB607 Speciation discussion 13 100
2010 Spring EEB409 Macroevolution 13 100

Workshops

I organize and/or participate in numerous workshops or tutorials.

Year Location Topic Role
2018 Friday Harbor, WA Evolutionary Quantitative Genetics workshop Instructor
2017 Friday Harbor, WA Evolutionary Quantitative Genetics workshop Instructor
2017 Baton Rouge, LA PHRAPL Organizer/instructor
2016 Knoxville, TN Evolutionary Quantitative Genetics workshop at NIMBioS Instructor
2015 Ann Arbor, MI Comparative methods in R, SSB satellite meeting Organizer/instructor
2015 Knoxville, TN Evolutionary Quantitative Genetics workshop at NIMBioS Instructor
2015 Guaruja, Brazil SSB-sponsored phylogeography workshop at Evolution meetings Instructor
2014 Knoxville, TN Evolutionary Quantitative Genetics workshop at NIMBioS Instructor
2014 Knoxville, TN Computing in the Cloud NIMBioS Tutorial Co-organizer/instructor
2014 Columbus, OH PHRAPL workshop Co-organizer/Instructor
2013 Lausanne, Switzerland Markov processes in phylogenetics Instructor
2013 Vienna, Austria eFlower Summer School Remote instructor
2013 Knoxville, TN Evolutionary Quantitative Genetics workshop at NESCent Instructor
2010 Knoxville, TN Fast, Free Phylogenies: HPC for Phylogenetics NIMBioS Tutorial Organizer/instructor
2010 Gothenberg, Sweden Species delimitation Remote instructor
2008 Durham, NC Computational phyloinformatics at NESCent Instructor
2008 Bodega Bay, CA Bodega Bay Workshop in Applied Phylogenetics Instructor
2007 Bodega Bay, CA Bodega Bay Workshop in Applied Phylogenetics Instructor
2007 Davis, CA Paleontology and its relevance to neontologists Instructor
2006 Bodega Bay, CA Bodega Bay Workshop in Applied Phylogenetics Instructor
2006 Davis, CA Model selection workshop Organizer
2005 Bodega Bay, CA Bodega Bay Workshop in Applied Phylogenetics Instructor

Funding

This is all in addition to other funding my students have gotten (NSF EAPSI grant, fellowships from NIMBioS and PEER (an NIH-funded program at UTK), Google Summer of Code funding), funding for workshops or working groups (from NIMBioS and the Society for Systematic Biologists), and funding I got before my faculty position (NESCent postdoctoral fellowship, NSF DDIG, NSF GRF, and various internal grants at UC Davis). Total external funding, so far, as a faculty member is $2,887,182.

Year Title Funder Amount
2019 Collaborative Research: Novel framework for estimating continuously-varying diversification rates Directorate for Biological Sciences $193,401
2018 Phylotastic subaward University of Maryland $165,492
2017 DISSERTATION RESEARCH: Morphological consequences of trophic evolution Directorate for Biological Sciences $19,630
2015 CAREER: Reducing barriers for comparative methods Directorate for Biological Sciences $738,297
2015 Collaborative Research: ABI Development: An open infrastructure to disseminate phylogenetic knowledge NSF $148,101
2014 Population genetics-based codon models NSF $470,000
2013 R interface to Encyclopedia of Life (Rubenstein Fellowship) Encyclopedia of Life $50,000
2013 Collaborative Research: Phylogeographic Inference Using Approximated Likelihoods NSF $340,000
2012 rPlant iPlant $98,252
2012 Historical naming traditions and cryptic speciation bias biodiversity estimates in transatlantic agaric fungi NSF $393,074
2011 iPlant: Trait evolution group, year 2 iPlant $138,590
2010 iPlant: Trait evolution group, year 1 iPlant $132,345

Presentations

Bold indicates presentation was delivered by me; otherwise, I was a coauthor. Also see various workshops under teaching.

June 2018: Talk on DateLife project for getting chronograms for the tree of life. Presented at the Society of Systematic Biologists meeting in Columbus, OH. Luna Sanchez Garcia & Brian O’Meara.

June 2017: Poster on inference of amino acid functionality from DNA sequences using a novel phylogenetic approach at the Society for Molecular Biology and Evolution meeting in Austin, TX. Cedric Landerer, Jeremy Beaulieu, Brian O’Meara, Mike Gilchrist.

June 2017: Symposium talk on phylogenetic networks at Evolution 2017 meeting: co-lead author was Tony Jhwueng.

March 2017: Invited talk on three projects at U. of Idaho, Moscow.

September 2016: Symposium talk on Approximate Bayesian computation for trait evolution on phylogenies at Geological Society of America annual meeting.

August 2016: Talk on linking leaf spectra to phylogenies at Ecological Society of America 2016 annual meeting. Jose Eduardo Meireles, Brian O’Meara, Anna Schweiger, Aditya Singh, Phil Townsend, Susan Ustin, Michael Schaepman, Franziska Schrodt, John Gamon, and Jeannine Cavender-Bares.

July 2016: Talk on Moving beyond black box, GTR models in phyogenetic analyses through the use of mechanistic models of sequence evolution at the Genetics Society of America: The Allied Genetics Conference in Orlando, FL. Mike Gilchrist, Russ Zaretzki, Cedric Landerer, Jeremy Beaulieu, and Brian O’Meara

November 2015: Talk on Improving Phylogenetics via Population Genetics at the Society for the Study of Molecular Evolution Satellite Meeting on Mechanisms of Protein Evolution in Denver, CO. Mike Gilchrist, Jeremy Beaulieu, JJ Chai, and Brian O’Meara.

September 2015: Talk on heterogeneity at Texas A&M

July 2015: Talk on Moving beyond black box, GTR models in phyogenetic analyses through the use of mechanistic models of sequence evolution at the Annual Meeting of the Society for Molecular Biology & Evolution in Vienna, Austria. Mike Gilchrist, Jeremy Beaulieu, and Brian O’Meara

June 2014: Talk on floral evolution at Evolution 2014 meeting; co-lead author was Stacey Smith, coauthors were W SArmbruster, L Harder, C Hardy, L Hileman, L Hufford, A Litt, S Magallon, S Smith, P Stevens, C Fenster, P Diggle.

June 2014: Talk on phylogeography at Evolution 2014 meeting; lead author and speaker was Nathan Jackson, other authors were A. Garcia, B. Carstens, and B. O’Meara.

June 2014: Talk on biogeography at Evolution 2014; lead author and speaker was Katie Massana (grad student), coauthors were J. Beaulieu, B. O’Meara, and N. Matzke.

June 2014: Talk on Hawaiian island plant immigration at Evolution 2014; lead author and speaker was Jeremy Beaulieu, coauthor was Brian O’Meara.

May 2014: Smithsonian Phylopizza

June, 2013: Symposium talk on species delimitation, Evolution meetings

Aug. 2012: Invited talk on comparative methods, Institute of Bioinformatics, U. of Georgia

June, 2012: Symposium talk on ABC and comparative methods, Evolution meetings

March, 2011: Phyloseminar talk on ABC and comparative methods. Apple Keynote and PDF.

May, 2010: Talk on phylogenetics and iPToL at iPlant meeting in Las Vegas

April, 2010: Invited talk on species delimitation at Louisiana State University

Nov., 2009: Talk at NIMBios about species delimitation and species tree inference

Mar., 2009: Talk to UT Knoxville EEB

June, 2008: Talk at Evolution 2008 in Minnesota

June, 2008: Poster at Evolution 2008 in Minnesota

June, 2008: Invited Joel Keizer Prize in Theoretical Biology lecture at University of California, Davis

May, 2008: Invited symposium talk at Interface 2008 [statistics conference] in NC

April, 2008: Invited talk to the Organismic and Evolutionary Biology department at Harvard U.

Jan., 2008: Invited symposium talk at Society for Integrative and Comparative Biology meeting in TX

Oct., 2007: Invited talk at Duke Systematics Discussion Group

Oct., 2007: Talk at NESCent brown bag lunch series

June, 2007: Exit seminar

June, 2006: Talk at Evolution 2006 in NY

Feb., 2006: Poster at CIPRES all hands meeting in TX

July, 2005: Talk at CIPRES-funded graduate student meeting in NM

June, 2005: Talk on Brownie at Evolution meetings in Alaska.

Dec, 2004: Presentation at the Bay Area Biosystematists meeting

Dec., 2001: Talk at Entomology Society of America national meeting in CA

June, 2001: Poster at Evolution 2001 in TN

Dec., 2000: Poster at the Entomology Society of America national meeting in Canada

Mentoring, Postdocs

I have mentored numerous postdocs off of my own grants and/or as one of their chosen NIMBioS mentors. Note that NIMBioS postdocs pursue independent research projects but choose one faculty member to mentor them in math and another to mentor them in biology (I have served in both roles).

Name Duration NIMBioS Current Position
Hugo Alamillo 2011-2012 N Assistant Professor North Seattle College
Barb Banbury 2010-2012 N Statistical Analyst at Fred Hutch
David Bapst 2017-present N
Jeremy Beaulieu 2012-2016 Both Assistant Professor at U. of Arkansas
Juanjuan (JJ) Crosskey (formerly Chai) 2011-2013 Y Quantitative Analyst at Quantamental Technologies LLC
Dominic Evangelista 2018-2018 Y
Nathan Jackson 2013-2016 N Researcher at National Jewish Health
Tony Jhwueng 2009-2011 Y Assistant Professor Feng-Chia U., Taiwan
Sandy Kawano 2014-2016 Y Starting as Assistant Professor at CSU Long Beach in Aug. 2017
Michelle Lawing 2012-2014 Y Assistant Professor Texas A&M
Ryan Martin 2012-2013 Y Assistant Professor Case Western U
Nick Matzke 2013-2015 Y DECRA Fellow at The Australian National University in Canberra
Megan Rua 2015-2016 Y Assistant Professor Wright State U
Luna Sanchez Reyes 2017-2019 N
Sergei Tarasov 2016-2018 Y NIMBioS postdoc
Jodie Wiggins 2018-2019 N

Mentoring, Grad students in my lab

Name Stage Time in Lab Note
Sam Borstein PhD student 2014-2019
Jenn Bosco PhD student 2012-2017 Co-advised with Susan Riechert
Krista De Cooke PhD student 2020-present Co-advised with Dan Simberloff
Katie Massana PhD student 2012-2017
Orlando Schwery PhD student 2014-2020
Jenn Summers PhD student 2020-2021

Mentoring, Undergrad students in my lab

Name Stage Time in Lab Note
Tyler-Christian Daniels Undergrad 2019-2020
Stephen Ray Undergrad 2019-2020
Zach Tharpe Undergrad 2019-2020
Christian Yarber Undergrad 2015-2016

Mentoring, Grad student committees

In addition to my own students, of course.

Name Department
Will Atwood Geology
Jen Bauer Geology
Sharon Clemmensen EEB
Troy Fadiga Geology
Aaron Floden EEB
Nicholas Gladstone Geology
Mauricio Gonzalez-Forero EEB
Alannie-Grace Grant EEB
Phillip Hollingsworth EEB
Whitaker Hoskins EEB
Will Howell EEB
Ivan Juric EEB
Cedric Landerer EEB
Jasper Lee Microbiology
Sara Lipshutz EEB
Bryan Looney EEB
Liam Mueller EEB
Tyson Paulson EEB
Todd Pierson EEB
Ryan Rooney Geology
Max Rupp EEB
Geetha Saarunya S GST
Leonidas Salichos Vanderbilt
Marisol Sanchez-Garcia EEB
Sarah Sheffield Geology
Jordan Utley GST
Jess Welch EEB
Rachel Wooliver EEB

Mentoring, Faculty

Our department now has faculty mentored by a committee of later career faculty. I have served on committees for folks hired after me.

Name Department
Liz Derryberry EEB
Stephanie Kivlin EEB
Kimberly Sheldon EEB

Service

  • Joint Code of Conduct committee for Society for the Study of Evolution, Society of Systematic Biologists, and American Society of Naturalists, 2018-present
  • Communications Director for the Society of Systematic Biologists (SSB), 2016-2017
  • Co-organizer of iEvoBio meeting, 2016
  • Co-organizer of SSB symposium on Breaking Barriers: Empirical, Theoretical, and Gender Issues in Phylogenetics for Evolution meetings in Brazil, 2015
  • Co-organizer of SSB satellite meeting in May, 2015
  • Co-organizer of iEvoBio meeting (met with SSB) May 2015
  • Co-organizer of Evolution meetings, 2014, including sole organizer for lightning talks
  • Co-organizer of iEvoBio meeting, 2014
  • Member of Phylotastic leadership team (group arranging hackathons for making trees more reusable), 2012-present
  • Organizer of lighting talks for Evolution meetings, 2013
  • UTK Faculty advisor for Darwin Day Tennessee, 2012-present
  • UTK Department representative on Dean’s advisory council, 2012-2014
  • UTK EEB Undergraduate affairs committee, 2012-2013
  • UTK EEB Graduate admissions committee, 2013-present
  • Chair, UTK EEB Web committee, 2011-present
  • Co-organizer of Comparative Methods in R hackathon, 2007
  • Bay Area Biosystematists Steering Committee: 2004-2007
  • Secretary Cambridge Entomological Club, 2001-2002
  • Reviewer for Science, Heredity, Molecular Phylogenetics and Evolution, Systematic Biology, Evolution, Systematic Entomology, Proceedings of the Royal Society: Biological Sciences, US National Science Foundation, and others.