inst/extdata/OMearaCV.md
In bomeara/cv: Code for compiling CVs from ORCID
Brian C. O'Meara
865-974-2804
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 38 journal articles, including Science, Nature, Ann. Rev Ecology,
Evolution & Systematics, Systematic Biology, Evolution, etc.
Teaching Approximately 3 courses per year on average, ranging from large
introductory biology courses to small graduate seminars
Mentoring 4 PhD students, 15 postdocs, 3 faculty, and served on 27 graduate
student committees
Service/Outreach Darwin Day TN advisor, co-organizer of women in science symposium,
workshops, and other activities, co-organizer for scientific
meetings, 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-present; 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 \$2.67M in external support, including 5 NSF grants (including a
CAREER grant) plus funding from iPlant and Encyclopedia of Life
Altmetrics Number of citations = 3299; h-index = 20; 107 public github repos;
Erdős number = 4; papers have been tweeted about 933 times, and
have been mentioned 30 times in the news
Education
University of California Davis: PhD (2008) in Population Biology
Harvard University: Bachelor (magna cum laude), with highest honors in
Biology (2001)
Employment
2016-Present: Associate Director, Dept. of National Institute for
Mathematical and Biological Synthesis (NIMBioS), University of
Tennessee, Knoxville, TN
2016-Present: Associate Head, Dept. of Ecology and Evolutionary Biology,
University of Tennessee, Knoxville, TN
2015-Present: 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: Papers
According to Google Scholar, my work has been cited 3299 times, and my
h-index is 20. (Google Scholar tends to overestimate citations,
however). 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.
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". In: American Journal of
Botany 105.3, pp. 417-432.
Jackson, N. D, A. E. Morales, B. C. Carstens and B. C. O'Meara
(2017). "PHRAPL: Phylogeographic Inference Using Approximate
Likelihoods". In: Systematic Biology 66.6, pp. 1045-1053.
Carstens, B. C, A. E. Morales, N. D. Jackson and B. C. O'Meara
(2017). "Objective choice of phylogeographic models". In: Molecular
Phylogenetics and Evolution 116, pp. 136-140.
Bosco, J. M, S. E. Riechert and B. C. O'Meara (2017). "The ontogeny
of personality traits in the desert funnel-web spider, Agelenopsis lisa
(Araneae: Agelenidae)". In: Ethology 123.9. Ed. by E. Hebets,
pp. 648-658.
Schwery, O. and B. C. O'Meara (2016). "MonoPhy: a simple R package
to find and visualize monophyly issues". In: PeerJ Computer Science 2,
p. e56.
O'Meara, B. C, S. D. Smith, W. S. Armbruster, L. D. Harder, C. R.
Hardy, L. C. Hileman, L. Hufford, A. Litt, S. Magallón, S. A. Smith, P.
F. Stevens, C. B. Fenster and P. K. Diggle (2016). "Non-equilibrium
dynamics and floral trait interactions shape extant angiosperm
diversity". In: Proceedings of the Royal Society B: Biological
Sciences 283.1830, p. 20152304.
O'Meara, B. C. and J. M. Beaulieu (2016). "Past, future, and present
of state-dependent models of diversification". In: American Journal of
Botany 103.5, pp. 792-795.
Morales, A. E, N. D. Jackson, T. A. Dewey, B. C. O'Meara and B. C.
Carstens (2016). "Speciation with Gene Flow in North
AmericanMyotisBats". In: Systematic Biology, p. syw100.
Jackson, N. D, B. C. Carstens, A. E. Morales and B. C. O'Meara
(2016). "Species Delimitation with Gene Flow". In: Systematic Biology,
p. syw117.
Beaulieu, J. M. and B. C. O'Meara (2016). "Detecting Hidden
Diversification Shifts in Models of Trait-Dependent Speciation and
Extinction". In: Systematic Biology 65.4, pp. 583-601.
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 (2015a). "Zanne et al. reply". In: Nature 521.7552,
pp. E6-E7.
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 (2015b). "Corrigendum: Three keys to the radiation of
angiosperms into freezing environments". In: Nature 521.7552,
pp. 380-380.
O'Meara, B. C, K. L. Graham, S. M. Pellis and G. M. Burghardt
(2015a). "Evolutionary models for the retention of
adult\textendashadult social play in primates: The roles of diet and
other factors associated with resource acquisition". In: Adaptive
Behavior 23.6, pp. 381-391.
O'Meara, B. C, K. L. Graham, S. M. Pellis and G. M. Burghardt
(2015b). "Evolutionary models for the retention of
adult\textendashadult social play in primates: The roles of diet and
other factors associated with resource acquisition". In: Adaptive
Behavior 23.6, pp. 381-391.
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". In: Systematic
Biology 64.5, pp. 869-878.
Beaulieu, J. M. and B. C. O'Meara (2015). "Extinction can be
estimated from moderately sized molecular phylogenies". In: Evolution
69.4, pp. 1036-1043.
Aldrovandi, M. S. P, J. E. Johnson, B. OMeara, R. H. Petersen and K. W.
Hughes (2015). "The Xeromphalina campanella/kauffmanii complex: species
delineation and biogeographical patterns of speciation". In: Mycologia
107.6, pp. 1270-1284.
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). "Corrigendum: Three keys to the radiation of
angiosperms into freezing environments". In: Nature 514.7522,
pp. 394-394.
Williams, J. H, M. L. Taylor and B. C. O'Meara (2014). "Repeated
evolution of tricellular (and bicellular) pollen". In: American Journal
of Botany 101.4, pp. 559-571.
Jhwueng, D, S. Huzurbazar, B. C. O'Meara and L. Liu (2014).
"Investigating the performance of AIC in selecting phylogenetic models".
In: Statistical Applications in Genetics and Molecular Biology 13.4.
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, Ü. Niinemets, J. Oleksyn, A.
Ordonez, D. L. Royer, S. A. Smith, P. F. Stevens, L. Warman, P. Wilf and
A. E. Zanne (2014). "Functional distinctiveness of major plant
lineages". In: Journal of Ecology 102.2. Ed. by A. Austin,
pp. 345-356.
Banbury, B. L. and B. C. O'Meara (2014). "Reol: R interface to the
Encyclopedia of Life". In: Ecology and Evolution 4.12, pp. 2577-2583.
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 (2013). "Three keys to the radiation of angiosperms into
freezing environments". In: Nature 506.7486, pp. 89-92.
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 (2013). "Phylotastic! Making tree-of-life knowledge accessible,
reusable and convenient". In: BMC Bioinformatics 14.1, p. 158.
Soltis, D. E, M. E. Mort, M. Latvis, E. V. Mavrodiev, B. C. O'Meara,
P. S. Soltis, J. G. Burleigh and R. R. de Casas (2013). "Phylogenetic
relationships and character evolution analysis of Saxifragales using a
supermatrix approach". In: American Journal of Botany 100.5,
pp. 916-929.
Hulsey, C. D, B. P. Keck, H. Alamillo and B. C. O'Meara (2013).
"Mitochondrial genome primers for Lake Malawi cichlids". In: Molecular
Ecology Resources 13.3, pp. 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". In: Systematic Biology 62.5, pp. 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". In:
BMC Research Notes 5.1, p. 574.
Smith, S. A. and B. C. O'Meara (2012). "treePL: divergence time
estimation using penalized likelihood for large phylogenies". In:
Bioinformatics 28.20, pp. 2689-2690.
O'Meara, B. C. (2012). "Evolutionary Inferences from Phylogenies: A
Review of Methods". In: Annual Review of Ecology, Evolution, and
Systematics 43.1, pp. 267-285.
Beaulieu, J. M, D. Jhwueng, C. Boettiger and B. C. O'Meara (2012).
"MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN-UHLENBECK MODEL
OF ADAPTIVE EVOLUTION". In: Evolution 66.8, pp. 2369-2383.
Stack, J. C, L. J. Harmon and B. O'Meara (2011). "RBrownie: an R
package for testing hypotheses about rates of evolutionary change". In:
Methods in Ecology and Evolution 2.6, pp. 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. 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". In: Frontiers in Plant Science 2.
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". In: EvoDevo
2.1, p. 14.
COLLAR, D. C, J. A. SCHULTE, B. C. O'MEARA and J. B. LOSOS (2010).
"Habitat use affects morphological diversification in dragon lizards".
In: Journal of Evolutionary Biology 23.5, pp. 1033-1049.
Smith, S. A. and B. C. O'Meara (2009). "Morphogenera, monophyly, and
macroevolution". In: Proceedings of the National Academy of Sciences
106.36, pp. E97-E98.
O'Meara, B. C. (2009). "New Heuristic Methods for Joint Species
Delimitation and Species Tree Inference". In: Systematic Biology 59.1,
pp. 59-73.
Collar, D. C, B. C. O'Meara, P. C. Wainwright and T. J. Near (2009).
"PISCIVORY LIMITS DIVERSIFICATION OF FEEDING MORPHOLOGY IN CENTRARCHID
FISHES". In: Evolution 63.6, pp. 1557-1573.
O'Meara, B. C, C. A. é, M. J. Sanderson and P. C. Wainwright (2006).
"TESTING FOR DIFFERENT RATES OF CONTINUOUS TRAIT EVOLUTION USING
LIKELIHOOD". In: Evolution 60.5, p. 922.
Driskell, A. C. (2004). "Prospects for Building the Tree of Life from
Large Sequence Databases". In: Science 306.5699, pp. 1172-1174.
Publications: Books or Book Chapters
Caetano, D, B. O'Meara and J. Beaulieu (2018). "Hidden state models
improve the adequacy of state-dependent diversification approaches using
empirical trees, including biogeographical models". In: bioRxiv.
O'Meara, B. C. and J. M. Beaulieu (2014). "Modelling Stabilizing
Selection: The Attraction of Ornstein-Uhlenbeck Models". In: Modern
Phylogenetic Comparative Methods and Their Application in Evolutionary
Biology: Concepts and Practice. Ed. by L. Z. Garamszegi. Berlin,
Heidelberg: Springer Berlin Heidelberg, pp. 381-393. ISBN:
978-3-662-43550-2.
Beaulieu, J. M. and B. C. O'Meara (2014). "Hidden Markov Models for
Studying the Evolution of Binary Morphological Characters". In: Modern
Phylogenetic Comparative Methods and Their Application in Evolutionary
Biology: Concepts and Practice. Ed. by L. Z. Garamszegi. Berlin,
Heidelberg: Springer Berlin Heidelberg, pp. 395-408. ISBN:
978-3-662-43550-2.
O'Meara, B. C. (2012). "Phylogenetic Reconstruction". In:
Encyclopedia of Theoretical Ecology. Ed. by A. Hastings and L. Gross.
4. Univ of California Press. ISBN: 0520269659.
O'Meara, B. (2008). "PhD Dissertation: Using Trees: Myrmecocystus
Phylogeny and Character Evolution and New Methods for Investigating
Trait Evolution and Species Delimitation". In: Nature Precedings.
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
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 Evolutionary Quantitative Genetics Instructor
Harbor, WA workshop
2017 Friday Evolutionary Quantitative Genetics Instructor
Harbor, WA workshop
2017 Baton Rouge, PHRAPL Organizer/instructor
LA
2016 Knoxville, TN Evolutionary Quantitative Genetics Instructor
workshop at NIMBioS
2015 Ann Arbor, MI Comparative methods in R, SSB Organizer/instructor
satellite meeting
2015 Knoxville, TN Evolutionary Quantitative Genetics Instructor
workshop at NIMBioS
2015 Guaruja, SSB-sponsored phylogeography workshop Instructor
Brazil at Evolution meetings
2014 Knoxville, TN Evolutionary Quantitative Genetics Instructor
workshop at NIMBioS
2014 Knoxville, TN Computing in the Cloud NIMBioS Co-organizer/instructor
Tutorial
2014 Columbus, OH PHRAPL workshop Co-organizer/Instructor
2013 Lausanne, Markov processes in phylogenetics Instructor
Switzerland
2013 Vienna, eFlower Summer School Remote instructor
Austria
2013 Knoxville, TN Evolutionary Quantitative Genetics Instructor
workshop at NESCent
2010 Knoxville, TN Fast, Free Phylogenies: HPC for Organizer/instructor
Phylogenetics NIMBioS Tutorial
2010 Gothenberg, Species delimitation Remote instructor
Sweden
2008 Durham, NC Computational phyloinformatics at Instructor
NESCent
2008 Bodega Bay, Bodega Bay Workshop in Applied Instructor
CA Phylogenetics
2007 Bodega Bay, Bodega Bay Workshop in Applied Instructor
CA Phylogenetics
2007 Davis, CA Paleontology and its relevance to Instructor
neontologists
2006 Bodega Bay, Bodega Bay Workshop in Applied Instructor
CA Phylogenetics
2006 Davis, CA Model selection workshop Organizer
2005 Bodega Bay, Bodega Bay Workshop in Applied Instructor
CA Phylogenetics
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
\$2,673,854.
Year Title Funder Amount
2018 Phylotastic subaward University of \$165,492
Maryland
2015 CAREER: Reducing barriers for comparative NSF \$738,000
methods (PI)
2015 Collaborative Research: ABI Development: An NSF \$148,101
open infrastructure to disseminate
phylogenetic knowledge
2014 Population genetics-based codon models NSF \$470,000
2013 R interface to Encyclopedia of Life Encyclopedia \$50,000
(Rubenstein Fellowship) of Life
2013 Collaborative Research: Phylogeographic NSF \$340,000
Inference Using Approximated Likelihoods
2012 rPlant iPlant \$98,252
2012 Historical naming traditions and cryptic NSF \$393,074
speciation bias biodiversity estimates in
transatlantic agaric fungi
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.
September 2015: Talk on heterogeneity at Texas A&M
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, Faculty
Our department now has faculty mentored by a committee of later career
faculty. I have served on several
Name Department
Liz Derryberry EEB
Stephanie Kivlin EEB
Kimberly Sheldon EEB
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 2011-2012 N Assistant Professor North
Alamillo 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 2011-2013 Y Quantitative Analyst at
Chai) Quantamental Technologies
LLC
Dominic Evangelista 2018-present 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-present N
Sergei 2016-present Y NIMBioS postdoc
Tarasov
Mentoring, Grad students in my lab
Name Stage Time in Lab Note
Sam Borstein PhD student 2014-present
Jenn Bosco PhD student 2012-2017 Co-advised with Susan Riechert
Katie Massana PhD student 2012-2017
Orlando Schwery PhD student 2014-present
Mentoring, Undergrad students in my lab
Name Stage Time in Lab Note
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
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
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.
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Brian C. O'Meara
865-974-2804
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 38 journal articles, including Science, Nature, Ann. Rev Ecology, Evolution & Systematics, Systematic Biology, Evolution, etc.
Teaching Approximately 3 courses per year on average, ranging from large introductory biology courses to small graduate seminars
Mentoring 4 PhD students, 15 postdocs, 3 faculty, and served on 27 graduate student committees
Service/Outreach Darwin Day TN advisor, co-organizer of women in science symposium, workshops, and other activities, co-organizer for scientific meetings, 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-present; 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 \$2.67M in external support, including 5 NSF grants (including a CAREER grant) plus funding from iPlant and Encyclopedia of Life
Altmetrics Number of citations = 3299; h-index = 20; 107 public github repos; Erdős number = 4; papers have been tweeted about 933 times, and have been mentioned 30 times in the news
Education
University of California Davis: PhD (2008) in Population Biology
Harvard University: Bachelor (magna cum laude), with highest honors in Biology (2001)
Employment
2016-Present: Associate Director, Dept. of National Institute for Mathematical and Biological Synthesis (NIMBioS), University of Tennessee, Knoxville, TN
2016-Present: Associate Head, Dept. of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN
2015-Present: 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: Papers
According to Google Scholar, my work has been cited 3299 times, and my h-index is 20. (Google Scholar tends to overestimate citations, however). 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.
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". In: American Journal of Botany 105.3, pp. 417-432.
Jackson, N. D, A. E. Morales, B. C. Carstens and B. C. O'Meara (2017). "PHRAPL: Phylogeographic Inference Using Approximate Likelihoods". In: Systematic Biology 66.6, pp. 1045-1053.
Carstens, B. C, A. E. Morales, N. D. Jackson and B. C. O'Meara (2017). "Objective choice of phylogeographic models". In: Molecular Phylogenetics and Evolution 116, pp. 136-140.
Bosco, J. M, S. E. Riechert and B. C. O'Meara (2017). "The ontogeny of personality traits in the desert funnel-web spider, Agelenopsis lisa (Araneae: Agelenidae)". In: Ethology 123.9. Ed. by E. Hebets, pp. 648-658.
Schwery, O. and B. C. O'Meara (2016). "MonoPhy: a simple R package to find and visualize monophyly issues". In: PeerJ Computer Science 2, p. e56.
O'Meara, B. C, S. D. Smith, W. S. Armbruster, L. D. Harder, C. R. Hardy, L. C. Hileman, L. Hufford, A. Litt, S. Magallón, S. A. Smith, P. F. Stevens, C. B. Fenster and P. K. Diggle (2016). "Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity". In: Proceedings of the Royal Society B: Biological Sciences 283.1830, p. 20152304.
O'Meara, B. C. and J. M. Beaulieu (2016). "Past, future, and present of state-dependent models of diversification". In: American Journal of Botany 103.5, pp. 792-795.
Morales, A. E, N. D. Jackson, T. A. Dewey, B. C. O'Meara and B. C. Carstens (2016). "Speciation with Gene Flow in North AmericanMyotisBats". In: Systematic Biology, p. syw100.
Jackson, N. D, B. C. Carstens, A. E. Morales and B. C. O'Meara (2016). "Species Delimitation with Gene Flow". In: Systematic Biology, p. syw117.
Beaulieu, J. M. and B. C. O'Meara (2016). "Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction". In: Systematic Biology 65.4, pp. 583-601.
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 (2015a). "Zanne et al. reply". In: Nature 521.7552, pp. E6-E7.
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 (2015b). "Corrigendum: Three keys to the radiation of angiosperms into freezing environments". In: Nature 521.7552, pp. 380-380.
O'Meara, B. C, K. L. Graham, S. M. Pellis and G. M. Burghardt (2015a). "Evolutionary models for the retention of adult\textendashadult social play in primates: The roles of diet and other factors associated with resource acquisition". In: Adaptive Behavior 23.6, pp. 381-391.
O'Meara, B. C, K. L. Graham, S. M. Pellis and G. M. Burghardt (2015b). "Evolutionary models for the retention of adult\textendashadult social play in primates: The roles of diet and other factors associated with resource acquisition". In: Adaptive Behavior 23.6, pp. 381-391.
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". In: Systematic Biology 64.5, pp. 869-878.
Beaulieu, J. M. and B. C. O'Meara (2015). "Extinction can be estimated from moderately sized molecular phylogenies". In: Evolution 69.4, pp. 1036-1043.
Aldrovandi, M. S. P, J. E. Johnson, B. OMeara, R. H. Petersen and K. W. Hughes (2015). "The Xeromphalina campanella/kauffmanii complex: species delineation and biogeographical patterns of speciation". In: Mycologia 107.6, pp. 1270-1284.
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). "Corrigendum: Three keys to the radiation of angiosperms into freezing environments". In: Nature 514.7522, pp. 394-394.
Williams, J. H, M. L. Taylor and B. C. O'Meara (2014). "Repeated evolution of tricellular (and bicellular) pollen". In: American Journal of Botany 101.4, pp. 559-571.
Jhwueng, D, S. Huzurbazar, B. C. O'Meara and L. Liu (2014). "Investigating the performance of AIC in selecting phylogenetic models". In: Statistical Applications in Genetics and Molecular Biology 13.4.
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, Ü. Niinemets, J. Oleksyn, A. Ordonez, D. L. Royer, S. A. Smith, P. F. Stevens, L. Warman, P. Wilf and A. E. Zanne (2014). "Functional distinctiveness of major plant lineages". In: Journal of Ecology 102.2. Ed. by A. Austin, pp. 345-356.
Banbury, B. L. and B. C. O'Meara (2014). "Reol: R interface to the Encyclopedia of Life". In: Ecology and Evolution 4.12, pp. 2577-2583.
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 (2013). "Three keys to the radiation of angiosperms into freezing environments". In: Nature 506.7486, pp. 89-92.
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 (2013). "Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient". In: BMC Bioinformatics 14.1, p. 158.
Soltis, D. E, M. E. Mort, M. Latvis, E. V. Mavrodiev, B. C. O'Meara, P. S. Soltis, J. G. Burleigh and R. R. de Casas (2013). "Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach". In: American Journal of Botany 100.5, pp. 916-929.
Hulsey, C. D, B. P. Keck, H. Alamillo and B. C. O'Meara (2013). "Mitochondrial genome primers for Lake Malawi cichlids". In: Molecular Ecology Resources 13.3, pp. 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". In: Systematic Biology 62.5, pp. 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". In: BMC Research Notes 5.1, p. 574.
Smith, S. A. and B. C. O'Meara (2012). "treePL: divergence time estimation using penalized likelihood for large phylogenies". In: Bioinformatics 28.20, pp. 2689-2690.
O'Meara, B. C. (2012). "Evolutionary Inferences from Phylogenies: A Review of Methods". In: Annual Review of Ecology, Evolution, and Systematics 43.1, pp. 267-285.
Beaulieu, J. M, D. Jhwueng, C. Boettiger and B. C. O'Meara (2012). "MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN-UHLENBECK MODEL OF ADAPTIVE EVOLUTION". In: Evolution 66.8, pp. 2369-2383.
Stack, J. C, L. J. Harmon and B. O'Meara (2011). "RBrownie: an R package for testing hypotheses about rates of evolutionary change". In: Methods in Ecology and Evolution 2.6, pp. 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. 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". In: Frontiers in Plant Science 2.
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". In: EvoDevo 2.1, p. 14.
COLLAR, D. C, J. A. SCHULTE, B. C. O'MEARA and J. B. LOSOS (2010). "Habitat use affects morphological diversification in dragon lizards". In: Journal of Evolutionary Biology 23.5, pp. 1033-1049.
Smith, S. A. and B. C. O'Meara (2009). "Morphogenera, monophyly, and macroevolution". In: Proceedings of the National Academy of Sciences 106.36, pp. E97-E98.
O'Meara, B. C. (2009). "New Heuristic Methods for Joint Species Delimitation and Species Tree Inference". In: Systematic Biology 59.1, pp. 59-73.
Collar, D. C, B. C. O'Meara, P. C. Wainwright and T. J. Near (2009). "PISCIVORY LIMITS DIVERSIFICATION OF FEEDING MORPHOLOGY IN CENTRARCHID FISHES". In: Evolution 63.6, pp. 1557-1573.
O'Meara, B. C, C. A. é, M. J. Sanderson and P. C. Wainwright (2006). "TESTING FOR DIFFERENT RATES OF CONTINUOUS TRAIT EVOLUTION USING LIKELIHOOD". In: Evolution 60.5, p. 922.
Driskell, A. C. (2004). "Prospects for Building the Tree of Life from Large Sequence Databases". In: Science 306.5699, pp. 1172-1174.
Publications: Books or Book Chapters
Caetano, D, B. O'Meara and J. Beaulieu (2018). "Hidden state models improve the adequacy of state-dependent diversification approaches using empirical trees, including biogeographical models". In: bioRxiv.
O'Meara, B. C. and J. M. Beaulieu (2014). "Modelling Stabilizing Selection: The Attraction of Ornstein-Uhlenbeck Models". In: Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology: Concepts and Practice. Ed. by L. Z. Garamszegi. Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 381-393. ISBN: 978-3-662-43550-2.
Beaulieu, J. M. and B. C. O'Meara (2014). "Hidden Markov Models for Studying the Evolution of Binary Morphological Characters". In: Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology: Concepts and Practice. Ed. by L. Z. Garamszegi. Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 395-408. ISBN: 978-3-662-43550-2.
O'Meara, B. C. (2012). "Phylogenetic Reconstruction". In: Encyclopedia of Theoretical Ecology. Ed. by A. Hastings and L. Gross. 4. Univ of California Press. ISBN: 0520269659.
O'Meara, B. (2008). "PhD Dissertation: Using Trees: Myrmecocystus Phylogeny and Character Evolution and New Methods for Investigating Trait Evolution and Species Delimitation". In: Nature Precedings.
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
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 Evolutionary Quantitative Genetics Instructor Harbor, WA workshop
2017 Friday Evolutionary Quantitative Genetics Instructor Harbor, WA workshop
2017 Baton Rouge, PHRAPL Organizer/instructor LA
2016 Knoxville, TN Evolutionary Quantitative Genetics Instructor workshop at NIMBioS
2015 Ann Arbor, MI Comparative methods in R, SSB Organizer/instructor satellite meeting
2015 Knoxville, TN Evolutionary Quantitative Genetics Instructor workshop at NIMBioS
2015 Guaruja, SSB-sponsored phylogeography workshop Instructor Brazil at Evolution meetings
2014 Knoxville, TN Evolutionary Quantitative Genetics Instructor workshop at NIMBioS
2014 Knoxville, TN Computing in the Cloud NIMBioS Co-organizer/instructor Tutorial
2014 Columbus, OH PHRAPL workshop Co-organizer/Instructor
2013 Lausanne, Markov processes in phylogenetics Instructor Switzerland
2013 Vienna, eFlower Summer School Remote instructor Austria
2013 Knoxville, TN Evolutionary Quantitative Genetics Instructor workshop at NESCent
2010 Knoxville, TN Fast, Free Phylogenies: HPC for Organizer/instructor Phylogenetics NIMBioS Tutorial
2010 Gothenberg, Species delimitation Remote instructor Sweden
2008 Durham, NC Computational phyloinformatics at Instructor NESCent
2008 Bodega Bay, Bodega Bay Workshop in Applied Instructor CA Phylogenetics
2007 Bodega Bay, Bodega Bay Workshop in Applied Instructor CA Phylogenetics
2007 Davis, CA Paleontology and its relevance to Instructor neontologists
2006 Bodega Bay, Bodega Bay Workshop in Applied Instructor CA Phylogenetics
2006 Davis, CA Model selection workshop Organizer
2005 Bodega Bay, Bodega Bay Workshop in Applied Instructor CA Phylogenetics
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 \$2,673,854.
Year Title Funder Amount
2018 Phylotastic subaward University of \$165,492 Maryland
2015 CAREER: Reducing barriers for comparative NSF \$738,000 methods (PI)
2015 Collaborative Research: ABI Development: An NSF \$148,101 open infrastructure to disseminate phylogenetic knowledge
2014 Population genetics-based codon models NSF \$470,000
2013 R interface to Encyclopedia of Life Encyclopedia \$50,000 (Rubenstein Fellowship) of Life
2013 Collaborative Research: Phylogeographic NSF \$340,000 Inference Using Approximated Likelihoods
2012 rPlant iPlant \$98,252
2012 Historical naming traditions and cryptic NSF \$393,074 speciation bias biodiversity estimates in transatlantic agaric fungi
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.
September 2015: Talk on heterogeneity at Texas A&M
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, Faculty
Our department now has faculty mentored by a committee of later career faculty. I have served on several
Name Department
Liz Derryberry EEB Stephanie Kivlin EEB Kimberly Sheldon EEB
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 2011-2012 N Assistant Professor North Alamillo 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 2011-2013 Y Quantitative Analyst at Chai) Quantamental Technologies LLC
Dominic Evangelista 2018-present 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-present N
Sergei 2016-present Y NIMBioS postdoc Tarasov
Mentoring, Grad students in my lab
Name Stage Time in Lab Note
Sam Borstein PhD student 2014-present Jenn Bosco PhD student 2012-2017 Co-advised with Susan Riechert Katie Massana PhD student 2012-2017 Orlando Schwery PhD student 2014-present
Mentoring, Undergrad students in my lab
Name Stage Time in Lab Note
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 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
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.
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