Jeremy Brown

Assistant Professor


A243 Life Science Annex

Baton Rouge, LA

email address:

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Biological Sciences

Current Research

Evolutionary biologists are driven by a desire to understand the staggering diversity of life on Earth, its history of change through time and the processes that have driven such change. DNA sequences are the fundamental material upon which evolutionary change is wrought and each organism’s genome carries the legacies of its evolutionary history. By sequencing the genomes of different organisms, we can use the information they contain to reconstruct their historical relationships and test hypotheses about their evolutionary past. Organismal histories can be depicted as branching diagrams known as phylogenetic trees. Phylogenies are of fundamental importance to all of comparative biology, including fields as diverse as conservation, forensics, agriculture, and medicine. My research focuses on the development of statistical methods for inferring phylogenies, the use of these methods to answer questions of fundamental importance in evolution, and the development of software to perform such inference.


  • 2014, Finalist, NIH Early Innovator Award
  • 2013, Finalist, NIH Early Innovator Award
  • 2010, Ernst Mayr Award, Society of Systematic Biologists


    National Science FoundationCollaborative Research: ABI Innovation: Quantifying and Exploiting the Structure of Phylogenetic Tree Space Through Network Analyses

    The major goals of this project are to provide new statistical and computational tools for characterizing massive sets of phylogenetic trees and to use these tools to investigate levels of phylogenetic concordance and conflict across genomes. These tools will provide new visualization techniques and new approaches for handling phylogenetic 'big data'. PI: J.M. Brown. co-PIs: J. Wilgenbusch (Univ. of Minnesota) and K. Gallivan (Florida State University)

    Amount: $446345

    National Science FoundationCollaborative Research: Bayesian Model Checking for Phylogenetics in the Post-Genomic Era

    Diagrams of evolutionary relationships (phylogenetic trees) for species and genes are widely employed in biological research, including the fields of medicine, epidemiology, forensics, conservation, evolutionary biology and agriculture. This research project will explore new ideas and develop new software tools to improve the accuracy by which phylogenetic relationships are determined; in this way the research will contribute to improved understanding and decision-making for a broad range of scientific disciplines and practical applications. PI: J.M. Brown co-PI: R.C. Thomson (Univ. of Hawaii)

    Amount: $600208

Student Assistants

    Genevieve Mount,


    David Morris,




    Nelson, B.J., J.J. Andersen, and J.M. Brown (2015) Deflating Trees: Improving Bayesian Branch-Length Estimates using Informed Priors In: Systematic Biology

    Couturier, J., J.W. Suliburk, J.M. Brown, D.J. Luke, N. Agarwal, X. Yu, C. Nguyen, D. Iyer, C. Kozinetz, P.A. Overbeek, M.L. Metzker, A. Balasubramanyam, and D.E. Lewis (2015) Human adipose tissue as a reservoir for memory CD4+ T cells and HIV In: AIDS

    Doyle, V.P., J.J. Andersen, B.J. Nelson, M.L. Metzker, and J.M. Brown (2014) Untangling the influences of unmodeled evolutionary processes on phylogenetic signal in a forensically important HIV-1 transmission cluster. In: Molecular Phylogenetics and Evolution

    Brown, Jeremy M. (2014) Predictive approaches to assessing the fit of evolutionary models In: Systematic Biology

    Brown, Jeremy M. (2014) Detection of implausible phylogenetic inferences using posterior predictive assessment of model fit In: Systematic Biology

    Reid, N.M., S.M. Hird, J.M. Brown, T.A. Pelletier, J.D. McVay, J.D. Satler, and B.C. Carstens (2013) Poor fit to the coalescent is widely detectable in empirical data In: Systematic Biology

    Fong, J.J., J.M. Brown, M.K. Fujita, and B. Boussau (2012) A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia In: PLoS ONE

    Boussau, B., J.M. Brown, and M.K. Fujita (2011) Nonadaptive evolution of mitochondrial genome size In: Evolution

    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 In: Proceedings of the National Academy of Sciences USA