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.
CV SUMMARY
Publications
Teaching
Mentoring
Service/Outreach
Funding
32, including Science, Nature, Ann. Rev Ecology, Evolution &
Systematics, Systematic Biology, Evolution, etc. 948 citations (Web
of Science)
Biodiversity (100-level), Macroevolution (400-level), Evolution
Core class (500 level), various seminars (500/600 level)
4 PhD students, 10 postdocs
Darwin Day TN advisor, co-organizer of women in science
symposia, workshops, and other activities, co-organizer for
national meetings, curator of R phylogenetics task view,
instructor at workshops in Sweden, Switzerland, Brazil, and
various US locations (Ohio, TN, NC)
$2.3M over past six years: 5 NSF grants as PI or Co-PI
(including a CAREER grant), plus funding from iPlant and
Encyclopedia of Life
EDUCATION
University of California, Davis
Ph.D. from Population Biology Graduate Group 2008
Awarded Keizer prize for best dissertation in theoretical biology
Advisors: Michael Sanderson, Phil Ward, Michael Turelli
Harvard University
B.A., magna cum laude with highest honors in biology, June 2001
Awarded Hoopes prize for outstanding scholarly work or research
Advisor: Brian Farrell
EMPLOYMENT
2009 – present
Assistant Professor. Dept. of Ecology and Evolutionary Biology,
2007 – 2009
University of Tennessee, Knoxville
Postdoc, National Evolutionary Synthesis Center, Durham, NC
PUBLICATIONS
My papers have been highly cited (average of 39 citations per item, according to Web of Science)
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 in press. doi: 10.1093/sysbio/syv027
Beaulieu, J. M. and B. C. O'Meara. 2015. Extinction can be estimated from moderately
sized molecular phylogenies. Evolution 69:1036-1043.
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. Warman,
and J.M. Beaulieu. 2015. Zanne et al. reply (to letter by Edwards et al.). Nature
521(7552): E6-E7.
O'Meara, B. C. and J. M. Beaulieu. 2014. Modelling Stabilizing Selection: The
Attraction of Ornstein–Uhlenbeck Models. Pp. 381-393 in L. Z. Garamszegi, ed.
Modern Phylogenetic Comparative Methods and Their Application in Evolutionary
Biology. Springer-Verlag, Berlin.
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, and P. B. Reich. 2014.
Functional distinctiveness of major plant lineages. Journal of Ecology 102:345-356.
Beaulieu, J. M. and B. C. O'Meara. 2014. Hidden Markov Models for Studying the
Evolution of Binary Morphological Characters. Pp. 395-408 in L. Z. Garamszegi, ed.
Modern Phylogenetic Comparative Methods and Their Application in Evolutionary
Biology. Springer-Verlag, Berlin.
D.-C. Jhwueng, S. Huzurbazar, B. C. O’Meara, and L. Liu. 2014. Investigating the
performance of AIC in selecting phylogenetic models. Statistical Applications in
Genetics and Molecular Biology 13(4): 459-475.
J. H. Williams, M.L. Taylor, and B.C. O’Meara. 2014. Repeated evolution of tricellular
(and bicellular) pollen. American Journal of Botany 101(4): 559-571.
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. Warman,
and J.M. Beaulieu. 2014. Three keys to the radiation of angiosperms into freezing
environments. Nature 506(7486): 89-92.
Banbury, B. L. and B. C. O'Meara. 2014. Reol: R interface to the Encyclopedia of Life.
Ecology and Evolution 4:2577-2583.
Soltis, D. E., M. E. Mort, M. Latvis, E. V. Mavrodiev, B. C. O'Meara, P. S. Soltis, J. G.
Burleigh, and R. Rubio de Casas. 2013. Phylogenetic Relationships and Character
Evolution Analysis of Saxifragales Using a Supermatrix Approach. American Journal
of Botany 100:916-929.
Hulsey, C. D., B. P. Keck, H. Alamillo, and B. C. O'Meara. 2013. Mitochondrial
genome primers for Lake Malawi cichlids. Molecular Ecology Resources 13:347-353.
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.
Stoltzfus, A., B. O'Meara, J. Whitacre, R. Mounce, E. L. Gillespie, S. Kumar, D. F.
Rosauer, and R. A. Vos. 2012. Sharing and re-use of phylogenetic trees (and
associated data) to facilitate synthesis. BMC Research Notes 5:574.
Smith, S. A. and B. C. O'Meara. 2012. treePL: Divergence time estimation using
penalized likelihood for large phylogenies. Bioinformatics.
O'Meara, B. C. 2012. Phylogenetic Reconstruction. Pp. 550-557 in A. Hastings, and L.
J. Gross, eds. Encyclopedia of theoretical ecology. Univ of California Press.
O'Meara, B. C. 2012. Evolutionary Inferences from Phylogenies: A Review of
Methods. Annual Review of Ecology, Evolution, and Systematics 43.
Beaulieu, J. M. and B. O'Meara. 2012. OUwie: analysis of evolutionary rates in an OU
framework. R package version 1.
Beaulieu, J. M., D.-C. Jhwueng, C. Boettiger, and B. C. O'Meara. 2012. Modeling
Stabilizing Selection: Expanding the Ornstein-Uhlenbeck Model of Adaptive
Evolution. Evolution 66:2369-2383.
Stoltzfus, A., B. O'Meara, J. Whitacre, R. Mounce, D. Rosauer, and R. Vos. 2011.
Publishing re-usable phylogenetic trees, in theory and practice. iEvoBio 2011.
Stack, J. C., L. J. Harmon, and B. O'Meara. 2011. RBrownie: an R package for testing
hypotheses about rates of evolutionary change. Methods in Ecology and Evolution
2:660-662.
Goff, S. A., M. Vaughn, S. McKay, E. Lyons, A. E. Stapleton, D. Gessler, N. Matasci, L.
Wang, M. Hanlon, A. Lenards, A. Muir, N. Merchant, S. Lowry, S. Mock, M.
Helmke, A. Kubach, M. Narro, N. Hopkins, D. Micklos, U. Hilgert, M. Gonzales, C.
Jordan, E. Skidmore, R. Dooley, J. Cazes, R. McLay, Z. Lu, S. Pasternak, L.
Koesterke, W. H. Piel, R. Grene, C. Noutsos, K. Gendler, X. Feng, C. Tang, M.
Lent, S.-J. Kim, K. Kvilekval, B. S. Manjunath, V. Tannen, A. Stamatakis, M.
Sanderson, S. M. Welch, K. A. Cranston, P. Soltis, D. Soltis, B. O'Meara, C. Ane, T.
Brutnell, D. J. Kleibenstein, J. W. White, J. Leebens-Mack, M. J. Donoghue, E. P.
Spalding, T. J. Vision, C. R. Myers, D. Lowenthal, B. J. Enquist, B. Boyle, A. Akoglu,
G. Andrews, S. Ram, D. Ware, L. Stein, and D. Stanzione. 2011. The iPlant
Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in plant science 2:3434.
Abercrombie, J. M., B. C. O'Meara, A. R. Moffatt, and J. H. Williams. 2011.
Developmental evolution of flowering plant pollen tube cell walls: callose synthase
(CalS) gene expression patterns. EvoDevo 2:14.
O'Meara, B. C. 2010. New Heuristic Methods for Joint Species Delimitation and
Species Tree Inference. Systematic Biology 59:59-73.
Collar, D. C., J. A. Schulte, B. C. O'Meara, and J. B. Losos. 2010. Habitat use affects
morphological diversification in dragon lizards. Journal of Evolutionary Biology
23:1033-1049.
Smith, S. A. and B. C. O'Meara. 2009. Morphogenera, monophyly, and macroevolution.
Proceedings of the National Academy of Sciences of the United States of America
106:E97-E98.
O'Meara, B. C. 2009. New heuristic methods for joint species delimitation and species
tree inference. Systematic Biology:syp077.
Collar, D. C., B. C. O'Meara, P. C. Wainwright, and T. J. Near. 2009. Piscivory Limits
Diversification of Feeding Morphology in Centrarchid Fishes. Evolution 63:15571573.
O'Meara, B. C. 2007. Estimating Different Rates of Gene Loss on a Tree. Genetics
177:1415-1416.
O'Meara, B. C., C. Ane, M. J. Sanderson, and P. C. Wainwright. 2006. Testing for
different rates of continuous trait evolution using likelihood. Evolution 60:922-933.
Driskell, A. C., C. Ané, J. G. Burleigh, M. M. McMahon, B. C. O'Meara, and M. J.
Sanderson. 2004. Prospects for building the tree of life from large sequence
databases. Science 306:1172-1174.
Farrell, B. D., A. S. Sequeira, B. C. O'Meara, B. B. Normark, J. H. Chung, and B. H.
Jordal. 2001. The evolution of agriculture in beetles (Curculionidae : Scolytinae and
Platypodinae). Evolution 55:2011-2027.
TEACHING
Macroevolution, EEB464. Fall 2015, 2014, 2013, 2012, 2011, 2010. New course designed
by me, run as EEB409 in 2010
HOFF, EEB602/EEB504. Fall 2014, Spring 2014, 2012
Graduate Core course, EEB511. Fall 2014, 2013, 2012, 2011, 2010, 2009
Biodiversity, Biology130. Spring 2014, 2012
Speciation, EEB607. Fall 2014, Spring 2014, Spring 2011, Spring 2010
Instructor in Arnold and Felsenstein’s Evolutionary Genetics workshop, Summer 2014
(NIMBioS), Summer 2013 (NESCent)
Phrapl workshop, Summer 2014
Instructor in R basic and advanced tracks of Computational Phyloinformatics summer
course, 2008. http://www.nescent.org/courses/2008/comphy/
Instructor in Bodega Bay Workshop in Applied Phylogenetics: 2008, 2007, 2006, 2005.
http://bodegaphylo.wikispot.org/
Invited guest lectures on phylogenetics in UC Davis Ecology Core Class (graduate level),
UC Davis Population Biology Core Class (graduate level), UC Davis Geology course
260 (graduate level) and San Francisco State University computer science course 858
(undergraduate level), 2005-2006
Co-organizer of workshop on paleontology and its relevance to neontologists, 2007
Co-organizer of a graduate seminar on when to use phylogenetic trees, 2006
Co-organizer of a two-day workshop on model selection, 2006
Teaching assistant for Evolution and Ecology 103, “Phylogeny and Macroevolution”,
2006
Grader, Evolution and Ecology 100, “Introduction to Evolution”, 2004
GRANTS/AWARDS
To date, over $2.3M in external grants over past six years as a faculty member, including five NSF
grants
2015
NSF CAREER: Reducing barriers for comparative
$738,000
methods (PI, 5 yr)
2015
NSF: Collaborative Research: ABI Development: An
$148,000
open infrastructure to disseminate phylogenetic
knowledge (Co-PI, 3 yr)
2013
NSF: Population genetics based codon models (PI, 3 yr)
$520,000
2013
Encyclopedia of Life Rubenstein fellows, Barb Banbury
$50,000
PI, O’Meara subcontractor (two months)
2013
NSF: Phylogeographic Inference using Approximate
$340,000
Likelihoods (PI, 3 yr)
2012
iPlant: rPlant project (1 yr)
$98,252
2012
NSF: Historical naming traditions and cryptic speciation
$141,143
bias biodiversity estimates (Co-PI, 3 yr)
2012
Google Summer of Code funding to student to work on
$5000
TreEvo project (3 months)
2011
iPlant: Trait evolution group (1 yr)
$138,590
2010
iPlant: Trait evolution group (1 yr)
$132,345
2010
Google Summer of Code funding to student to work on R
$5000
version of Brownie (3 months)
I have received internal funding for a 20 laptop cart for teaching and an interdisciplinary
series of workshops on women in science.
This is in addition to many grants and fellowships dating from before I started my
faculty job: NESCent postdoctoral fellowship, Google Summer of Code funding for
project for database graphical interface, NSF Dissertation Improvement Grant, NSF
Graduate Research Fellowship, UCD Center for Biosystematics Research Grant,
UCD Center for Population Biology Research Award, UCD Jastro-Shields Graduate
Research Scholarship, UCD Population Biology First Year Fellowship.
SERVICE
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 (and incoming group lead for 2015)
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, National Science Foundation, and Proceedings of the
Royal Society: Biological Sciences, and others.
MENTORING, POSTDOCS
Barb Banbury, 2010-2012
Jeremy Beaulieu, NIMBioS. 2012-present
JJ Chai, NIMBioS. 2011-2013
Nathan Jackson, 2013-present
Sandy Kawano, NIMBioS, 2014-present
Michelle Lawing, NIMBioS. 2012-2014
Ryan Martin, NIMBioS, 2012-2013
Nick Matzke, NIMBioS, 2013-2015
Tony Jhwueng, NIMBioS, 2009-2011
Hugo Alamillo, 2011-2012
MENTORING, GRAD STUDENT ADVISEES
Sam Borstein, EEB, 2014-present
Jenn Bosco, EEB, 2012-present (co-advisor)
Katie Massana, EEB, 2012-present
Orlando Schwery, EEB, 2014-present
MENTORING, GRAD STUDENT COMMITTEES
Will Atwood, Geology
Jeremy Blaschke, Entomology and Plant Pathology
Sharon Clemmensen, EEB
Troy Fadiga, Geology
Maurio Gonzalez-Forero, EEB
Phillip Hollingsworth, EEB
Will Howell, EEB
Ivan Juric, EEB
Brian Looney, EEB
Ryan Rooney, Geology
Max Rupp, EEB
Geetha Saaruyna S, Genome Sciences and Technology
Leonidas Salichos, Vanderbilt
Marisol Sanchez, EEB
Jordan Utley, Genome Sciences and Technology
Jess Welch, EEB
SOFTWARE
phrapl: Phylogeographic model evaluation
OUWie: Fit a variety of Ornstein-Uhlenbeck and Brownian motion models
Brownie: Estimate rates of continuous and discrete character evolution and compare
different models; perform species delimitation
MrFisher: Modification of MrBayes to do maximum likelihood tree inference
phylobase: An R package for dealing with phylogenetic trees and databases
ModelPartition: Web application to generate partitioned searches in MrBayes
TreEvo: An assortment of methods for understanding evolution using R
Research Tools: Software for managing a phylogenetic project, including realtime display
of sequencing and collection information to the web.
Cluster software: Perl and bash scripts for SGE job submission and user-specific
queuing
PRESENTATIONS
June 2014: Talk on floral evolution at Evolution 2014 meeting; coauthors were S Smith,
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