For genomic analyses of bacterial genomes, horizontal gene transfer is a complicating factor, causing different genes to have discordant histories. I plan to develop methods for estimating bacterial species phylogeny in the face of this horizontal gene transfer. I will also develop methods that allow the biologist to uncover patterns in the data, by grouping together genes that have similar realized values of evolutionary parameters. Finally, I will develop more realistic models of protein evolution that take advantage of the most cutting-edge work for the ab initio prediction of protein structure. Using the same statistical framework, I will attempt to predict RNA secondary structure by combining information on the Gibb's free energy with comparative sequence information. The methods developed in the course of this research will be implemented in the next generation of the MrBayes software. 1

Public Health Relevance

The comparison of DNA sequences from different organisms allows scientists to learn about the processes that shape genomes. For example, by comparing the DNA sequences of deferent genes, we can learn about how natural selection has acted. This proposal develops improved methods for the analysis of DNA sequences. 1

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Genetic Variation and Evolution Study Section (GVE)
Program Officer
Eckstrand, Irene A
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California Berkeley
Schools of Arts and Sciences
United States
Zip Code
Höhna, Sebastian; Heath, Tracy A; Boussau, Bastien et al. (2014) Probabilistic graphical model representation in phylogenetics. Syst Biol 63:753-71
Landis, Michael J; Bedford, Trevor (2014) Phylowood: interactive web-based animations of biogeographic and phylogeographic histories. Bioinformatics 30:123-4
Heath, Tracy A; Huelsenbeck, John P; Stadler, Tanja (2014) The fossilized birth-death process for coherent calibration of divergence-time estimates. Proc Natl Acad Sci U S A 111:E2957-66
Boussau, Bastien; Walton, Zaak; Delgado, Juan A et al. (2014) Strepsiptera, phylogenomics and the long branch attraction problem. PLoS One 9:e107709
Landis, Michael J; Schraiber, Joshua G; Liang, Mason (2013) Phylogenetic analysis using Levy processes: finding jumps in the evolution of continuous traits. Syst Biol 62:193-204
Nasrallah, Chris A; Huelsenbeck, John P (2013) A phylogenetic model for the detection of epistatic interactions. Mol Biol Evol 30:2197-208
Landis, Michael J; Matzke, Nicholas J; Moore, Brian R et al. (2013) Bayesian analysis of biogeography when the number of areas is large. Syst Biol 62:789-804
Ronquist, Fredrik; Teslenko, Maxim; van der Mark, Paul et al. (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539-42
Heath, Tracy A; Holder, Mark T; Huelsenbeck, John P (2012) A dirichlet process prior for estimating lineage-specific substitution rates. Mol Biol Evol 29:939-55
Ayres, Daniel L; Darling, Aaron; Zwickl, Derrick J et al. (2012) BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst Biol 61:170-3

Showing the most recent 10 out of 25 publications