Area of Interest

Every living thing on Earth shares at least two qualities. First, they contain genomes that influence their physical and behavioral interactions with the rest of the world. Second, they are the products of long evolutionary histories that have molded their genomes in very particular ways.   I develop, test, and apply computational tools to understand how evolution shapes genomes. Our ability to gather genome sequence data has increased dramatically in recent years. The limiting step in testing evolutionary hypotheses is now often analytical. The need for computational biologists has never been greater and will only increase in the future.   My work involves both reconstructing patterns of relatedness (phylogenies) between species, populations, individuals, and genes, as well as understanding what evolutionary forces (e.g., selection, drift, etc.) have acted on different branches of the tree of life. I work across a wide breadth of organisms and time scales. Some recent empirical work has involved:  
- Inferring HIV transmission dynamics in criminal cases (Scaduto, Brown, etal. 2010. PNAS)
- Describing the most anciently diverging lineage of living ants (Rabeling, Brown, and Verhaagh. 2008. PNAS)
- Testing the role of non-adaptive processes in genome size evolution (Boussau, Brown, and Fujita. 2011. Evolution)
- Understanding the causes of variation in molecular evolutionary rate (Brown and Pauly. 2005. Evolution)  
Much of my work also involves developing statistical and computational tools to analyze genomic data:
- Assessing the adequacy of current models of sequence evolution (Brown, 2012, In Prep.)
- Accurately inferring levels of sequence divergence (Brown et al., 2009, Syst. Biol.) - Understanding the effects of missing data (Lemmon, Brown, et al., 2008, Syst. Biol.; Brown and Lemmon, In Review)
- Incorporating heterogeneity in evolutionary processes into models of sequence evolution (Brown and Lemmon, 2007, Syst. Biol.)  
If you're interested in working with me, please send me an email. Programming experience is helpful, but not required. A passion for understanding the forces that shape the living world is required.

Awards & Honors

Ernst Mayr Award, 2010, Society of Systematic Biologists

Selected Publications

Publication tracking:  Researcher ID , Google Scholar

Leitner, T., M.L. Metzker, D. Zwickl, J.M. Brown, A.M. Geretti, A. Vandamme, J. Albert, and D.M. Hillis. 2011. Guidelines for HIV in court cases. Nature. 473: 284 [Correspondence]

Boussau, B., J.M. Brown, and M.K. Fujita. 2011. Nonadaptive evolution of mitochondrial genome size. Evolution. 65: 2706-2711.

Brown, J.M., K. Savidge*, and E. McTavish. 2011. DIM SUM: Demography and Individual Migration Simulated Using a Markov chain. Molecular Ecology Resources. 11: 358-363.

Brown, J.M. 2010. Ensuring the adequacy of phylogenetic inferences. In Prep.

Scaduto, D.I., J.M. Brown, W.C. Haaland, D.J. Zwickl, D.M. Hillis, and M.L. Metzker. 2010. Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences. Proceedings of the National Academy of Sciences USA. 107: 21242-21247.

Brown, J.M., K. Savidge*, and E.J.B. McTavish. 2010. DIM SUM: Demography and Individual Migration simulated using a Markov chain. Molecular Ecology Resources. In Press.

Brown, J.M., S.M. Hedtke, A.R. Lemmon, and E.M. Lemmon. 2009. When trees grow too long: investigating the causes of highly inaccurate Bayesian branch-length estimates. Systematic Biology. 59: 145-161.

Brown, J.M., and R. ElDabaje*. 2009. PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy. Bioinformatics. 25: 537-538.

Lemmon, A.R., J.M. Brown, K. Stanger-Hall, and E.M. Lemmon. 2009. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Systematic Biology. 58: 130-145.

Rabeling, C., J.M. Brown, and M. Verhaagh. 2008. Newly discovered sister lineage sheds light on early ant evolution. Proceedings of the National Academy of Sciences USA. 105: 14913-14917.

Brown, J.M. and A.R. Lemmon. 2007. The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Systematic Biology. 56: 643-655.

Brown, J.M. and G.B. Pauly. 2005. Increasted rates of molecular evolution in an equatorial plant clade: an effect of environment or phylogenetic nonindependence? Evolution. 59: 238-242.

* Undergraduates