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Assistant Professor R. Thane Papke
Education: Ph.D.: Department of Microbiology, Montana State University, Bozeman, MT; Postdoctoral Training: Department of Biochemistry and Molecular Biology, Dalhousie University Halifax, Nova Scotia
Research Interests: Although we recognize names of microorganisms like Escherichia coli and Bacillus subtilis, our ability to classify strains into “natural kinds” is rigorously tested by the observation that genetic variation is frequently shuttled across so-called species boundaries. Also, much of what we know about species comes from well-studied pathogenic bacteria, which are often classified by the disease that they cause (e.g., Bacillus anthracis or Neisseria gonorrhoeae). This is important to doctors and their patients but the Earth’s biomass and diversity is comprised mainly of prokaryotes, the vast majority of which do not cause disease. Combined, these observations suggest that our understanding of species evolution is relatively shallow and that our current standards of classification are biased and difficult to apply to most microbes. The main goal of our research is to use evolution and ecology theory in combination with approaches like genomics, metagenomics and population genetics to investigate intra and inter species variation, gene flow and genetic relationships for non-pathogenic (e.g., environmental) prokaryotes. We concentrate on hypersaline adapted Archea (Haloarchaea) as model organisms because they live in island-like habits which aid in simplifying or sorting the evolutionary forces that effect their distributions, adaptations and variation.
Selected Publications:
Papke, R.T., Zhaxybayeva, O., Feil, E., Sommerfeld, K., Muise, D. and Doolittle, W.F. (2007) Searching for species in haloarchaea. PNAS. 104:14092-14097.
Cuadros-Orellana, S., Legault, B., Martin-Cuadorado, A.-B., D’Auria, G., Zhaxybayeva, O., Papke, R.T. and Rodriguez-Valera, F. (2007) Genomic plasticity in Prokaryotes; the case of the square haloarchaeon. ISME Journal. 1:235-245.
Sharma, A.K., Walsh, D.A., Bapteste, E., Rodriguez-Valera, F., Doolittle, W.F. and Papke, R.T. (2007) Evolution of rhodopsin ion pumps in haloarchaea. BMC Evolutionary Biology. 7:79.
Doolittle, W.F. and Papke, R.T. (2006). Genomics and the bacterial species problem. Genome Biology. 7:116.
Zhaxybayeva, O., Gogarten, J.P., Charlebois, R.L., Doolittle, W.F. and Papke, R.T. (2006). Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Research. 16:1099-1108.
Legault, B., López-López A., Alba-Casado, J.C., Doolittle, W.F., Bolhuis, H., Rodríguez-Valera F. and Papke, R.T. (2006) Environmental genomics of Haloquadratum walsbyi in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics. 7:171
Mongodin, E.F., Legault, B., Walsh, D.A., Daugherty, S., Nesbř, C.L., Papke, R.T. Shanchez-Perez, G., Sharma, A.K., Charlebois, R.L., Bapteste, E., Nelson, K.E., Doolittle, W.F., and Rodríguez-Valera, F. (2005). The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc. Natl. Acad. Sci. U.S.A. 102:18147-18152.
Walsh, D.A., Papke, R.T. and Doolittle, W.F. (2005) Archaeal diversity along a soil salinity gradient prone to disturbance. Environ. Microbiol. 7:1655-1666.
Papke, R.T., Koenig, J.E., Rodríguez-Valera, F. and Doolittle, W.F. (2004) Frequent recombination in a saltern population of Halorubrum. Science. 306: 1928-1929.
Papke, R.T. and Ward, D.M. (2004) Minireview: The importance of physical isolation to microbial diversification. FEMS Microbiol. Ecol. 48:293-303.
Papke, R.T., Ramsing, N.B., Bateson, M.M. and Ward, D.M. (2003) Geographic isolation in thermophilic cyanobacteria. Environ. Microbiol. 5:650-659.
Papke, R.T., Douady, C.J., Doolittle, W.F. and Rodríguez-Valera, F. (2003) Diversity of bacteriorhodopsins in different hypersaline waters from a single Spanish saltern. Environ. Microbiol. 5:1039-1045.
Papke, R.T. and Doolittle, W.F. (2003) Phage evolution: new worlds of genomic diversity. Curr. Biol. 13:R606-R607.
Boucher, Y., Douady, C.J., Papke, R.T., Walsh, D.A., Boudreau, M.E.R., Nesbř, C.L., Case, R.J. and Doolittle, W.F. (2003) Lateral gene transfer, adaptation and the origins of prokaryotic groups. Annu. Rev. Genet. 37:283-328
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