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

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM069801-09
Application #
8372388
Study Section
Genetic Variation and Evolution Study Section (GVE)
Program Officer
Eckstrand, Irene A
Project Start
2004-08-01
Project End
2014-11-30
Budget Start
2012-12-01
Budget End
2014-11-30
Support Year
9
Fiscal Year
2013
Total Cost
$280,138
Indirect Cost
$89,068
Name
University of California Berkeley
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
124726725
City
Berkeley
State
CA
Country
United States
Zip Code
94704
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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
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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

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