Brief Biography

I am a Research Associate in the Department of Scientific Computing, Director of FSU's High Performance Computing facility and manage the Technical Support Group in the Department of Scientific Computing. In addition to my management responsibilities, I coordinate the development and user support of PAUP* and maintain research activities in the study and implementation of models and search algorithms used in phylogenetic inference. 

Prior to coming to FSU in 2001, I worked at the Smithsonian Institution's Laboratory of Molecular Systematics (now the Laboratories of Analytical Biology) and the Division of Amphibians and Reptiles. While at the division of Amphibians and Reptiles I employed molecular techniques to obtain DNA sequences for several groups of lizards in order to learn about their evolutionary history. At the LMS I worked with David Swofford on the support and development of PAUP*, a widely used program for phylogenetic inference. 

I also have a passion for the outdoors, even though I currently spend most of my time behind a computer. After completing my undergraduate degree in Biology, I was an Associate Director of George Mason University's (GMU) Center for Experiential Education in Fairfax, Virginia. During my tenure at the Center I managed the opening of Bull Run Marina under a joint management agreement between GMU and the Northern Virginia Regional Park Authority

Academic Training

  • 2000. Ph.D., Environmental Science and Public Policy, George Mason University. Advisor: Dr. Carl H. Ernst
  • 1994. M.S., Biology, George Mason University
  • 1991. B.S., Biology, George Mason University
  • 1991. Certificate, Environmental Resource Management, George Mason University

Workshops and Teaching

  • 2007, 2002, and 2004. Lecturer, Recent Advances in Conservation Genetics course sponsored by the American Genetic Association, Laboratory of Genomic Diversity/National Cancer Institute, and The Smithsonian Institution's Conservation & Research Center. Font Royal, Virginia and Hawaii Institute of Marine Biology, Oahu, Hawaii.
  • 2003. Faculty, Phylogenetic Methods, 5-day intensive course. Department of Biochemistry, Faculty of Medicine, Srinakharinwirot University, Bangkok, Thailand.
  • 2001 and 2003. Lecturer, Molecular Evolution II: Methods, Models, and Reliability In An introduction to Bioinformatics, Florida State University, Tallahassee, Florida.
  • 2000. Faculty, Molecular Taxonomy for the exploration of biodiversity: principles and methods in phylogenetic analyses, 2-week intensive course. Museum of Natural Science, Universidad Nacional de La Plata, Argentina.

Selected Publications and Presentations

  • Swofford, D. L., J. C. Wilgenbusch, and C. Bell. (In Prep.) PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods), Manual. Sinauer, Sunderland, Massachusetts.
  • Nylander, J. A., J.C. Wilgenbusch, D. L. Warren, D. L. Swofford. 2008. AWTY (Are We There Yet): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24:581-583. 
  • Nylander, AA., J. C. Wilgenbusch, D.L. Swofford. 2006. AWTY: A system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. University of Florida and Florida State University Phylogenetic Symposium, Cedar Key, FL. 
  • Jackson, V., D. L. Swofford, M. Holder, and J. C. Wilgenbusch. 2004. A computer simulation study of the accuracy of phylogenetic methods for estimating ancestral states. Evolution Meeting, Fort Collins, CO.
  • Kelchner, S. A., D. L. Swofford, J. C. Wilgenbusch. 2004 Evaluating partitioned models for phylogenetic analysis of combined data. Botany Conference, Snowbird, UT. 
  • Wilgenbusch, J. C. and D. L. Swofford. 2003. Inferring Evolutionary Trees with PAUP*. Pages 6.4.1-6.4.28 in A. D. Baxevanis, D. B. Davison, R. D. M. Page, G. A. Petsko, L. D. Stein, and G. D. Stormo (eds.) Current Protocols in Bioinformatics, Wiley and Sons, New York.
  • Wilgenbusch, J. C. and K. de Queiroz. 2000. Phylogenetic relationships among the phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes. Systematic Biology 49:592-612.
  • Wilgenbusch, J. C. and D. P. Gantz. 2000. The effects of hormonally induced oviposition on egg viability in the common snapping turtle (Chelydra serpentina). Herpetilogica 56:1-7.
  • Ernst, C. H., J. C. Wilgenbusch, T. P. Boucher, and S. W. Sekcienski. 1998. Growth, allometry, and sexual dimorphism in the Florida box turtle, Terrapene carolina bauri. The Herpetological Journal 8:72-78.
  • Ernst C. H., J. C. Wilgenbusch, T. P. Boucher, and S. W. Sekscienski. 1998. Morphometrics of the fossil box turtle, Terrapene innoxia Hay 1916, from Florida. Chelonian Conservation and Biology 3:99-102.
  • Ernst, C. H., J. C. Wilgenbusch, D. R. Morgan, T. P. Boucher, and M. Sommerfield. 1996. Fishes of Fort Belvoir, Virginia. Maryland Naturalist 39:1-60.
  • Ernst, C. H., T. P. Boucher, S. W. Sekscienski, and J. C. Wilgenbusch. 1995. Fire ecology of the Florida Box Turtle, Terrapene carolina bauri. Herpetological Review 26:185-187.


  • Editorial Board Member, Systematic Biology.
  • Panelist, Ad hoc Reviewer National Science Foundation.