Postdoctoral Research Fellowship in Biological Informatics FY 2006

Darling Aaron E, Madison WI

Investigators

Abstract

This project is awarded under the Postdoctoral Research Fellowships in Biological Informatics Program for 2006. As microbes evolve they are known to periodically exchange genetic material with each other. Such exchange can contribute to successful adaptation to new environments and appears to be relatively frequent between members of the same species but less frequent between distantly related microbes. This research project will develop and apply computational tools to investigate the role of homologous recombination and lateral genetic transfer during the process of microbial speciation. Advances in DNA sequencing technology have provided whole genome fequences for a large number of closely-related microbes, while corresponding advances in genome alignment enable accurate identification of regions conserved among multiple genomes. Specifically, genomes of closely-related /Enterobacteriacae/ and /Streptococci/ will be analyzed to better understand how the rate of recombination and genetic exchange decayed during the process of speciation. Towards this end, Markov-chain Monte-Carlo sampling methods will be developed to model genealogies as a coalescent process with separate recombination rate parameters for cross-species lateral transfer and intraspecific recombination. Local phylogenetic signals will be combined to infer robust estimates of species phylogenies and divergence times. Application of these analytic methods to sequenced microbial genomes will illuminate the role of recombination during speciation, in addition to providing historical information about natural selection and adaptation of microbial genomes. The scientific training objectives fall into two general categories: informatic and biological. Informatic training will be carried out at the Institute for Molecular Bioscience at the University of Queensland. The informatic training will foster growth in the Fellow's understanding of population genetics, statistical models for phylogenetics, and computational methods such as Markov-chain Monte-Carlo. Biological training will take place in the lab of Dr. Jonathan Eisen at UC-Davis and includes topics such as molecular mechanisms of DNA repair and recombination. Professional training goals such as developing the abilities to mentor graduate students, write fundable grants, and deliver informative, enjoyable scientific talks will take place at both locations of study over the duration of the fellowship period. The Fellow's research at the University of Queensland will provide the opportunity to network with leading international researchers in phylogenetics and molecular evolution. Study at UC-Davis will prepare the Fellow for future career opportunities through interaction with researchers at both UC-Davis and neighboring institutions such as UC-Berkeley, LBL, and the DOE Joint Genome Institute.