_______________ Dr. W. Ford Doolittle, Ph.D. (Stanford) Professor Canada Research Chair in Comparative Microbial Genomics (902) 494-3569 Link to Email Lab Homepage _______________

Research Areas:

Our research focuses on the evolution of genes and genomes. We use standard methods of molecular genetics and sophisticated computer algorithms to reconstruct phylogenies from gene sequences and to understand genome evolution as a process. Questions of recent interest include the following. (1) Introns -- are they relics of precellular gene assembly or quasi-transposable elements? (2) Origins of eukaryotic genomes -- to what extent are eukaryotic nuclear genomes chimeric, made up of genes of bacterial and archaeal origin, and what processes were involved in their creation? (3) Early events (gene duplications) in eukaryotic nuclear genome evolution -- can we use these to determine branching order among eukaryotes, and do they suggest a rapid "radiation" at the base of the eukaryotes? (4) Role of lateral gene transfer in evolution -- is this process so pervasive, among prokaryotes, that it is impossible to define phylogenetic relationships at the highest level? (5) Neutral models for the evolution of molecular complexity -- can we understand many complex molecular mechanisms as an unavoidable cellular "bureaucracy"? In the last year, we have also begun to focus on questions and methods in environmental microbiology, looking at gene transfer in natural systems.

Postdoctoral Fellows

Lab Personnel

Recent Publications:

1. Doolittle, W. F., Nesbo, C.L., Bapteste, E. and Zhaxybayeva, O. (2008) Lateral gene transfer. Evolutionary Genomics and Proteonomics, M. Pagel and A. Pomiankowski (eds.) Sinauer:45-79
2. Bapteste, E., Susko, E., Leigh, J., Ruiz-Trillo, I., Bucknam, J. & Doolittle, W.F. (2008) Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny. Mol. Biol. Evol. 25:83-91
3. Sharma, A.K., Zhaxybayeva, O., Papke, R.T. & Doolittle, W.F. (2008) Actinorhodopsins: Proteorhodopsin-like gene sequences found predominantly in non-marine environments. Env. Microbiol. in press: xx
4. Koenig, J.E., Boucher, Y., Charlebois, R.L., Nesbo, C., Zhaxybayeva, O., Bapteste, E., Spencer, M., Joss, M.J., Stokes, H.W. and Doolittle, W.F. (2008) Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments. Env. Microbiol. in press: xx
5. Walsh, D.A., Boudreau, M.E., Bapteste, E. and Doolittle, W.F. (2007) The root of the tree: lateral gene transfer and the nature of the domains. Archaea: Evolution, Physiology and Molecular Biology. Blackwell Publishing:29-37
6. Case, R.J., Boucher, Y., Dahllof, I., Holmstrom, C., Doolittle, W. F. and Kjelleberg, S. (2007) Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Applied and Environmental Microbiology 73:278-288
7. Doolittle, W. F. and Bapteste, E. (2007) Pattern pluralism and the Tree of Life hypothesis. PNAS 104:2043-2049
8. Doolittle, W. F. and Zhaxybayeva, O. (2007) Evolution: reducible complexity -- the case for bacterial flagella. Current Biology 17:R510-512
9. Zhaxybayeva, O., Nesbo, C.L. and Doolittle, W. F. (2007) Systematic overestimation of gene gain through false diagnosis of gene absence. Genome Biology 8:402
10. Zhaxybayeva,O., Gogarten, J.P. and Doolittle, W.F. (2007) A hyperconserved protein in Prochlorococcus and marine Synechococcus. FEMS Microbiol. Lett. 274:30-34
11. Papke, R.T., Zhaxybayeva, O., Feil, E.J., Sommerfeld, K., Muise, D. and Doolittle, W.F. (2007) Searching for species in haloarchaea. PNAS 104:14092-14097
12. Cullen, J.J., Doolittle, W.F., Levin, S.A. and Li, W.K.W. (2007) Patterns and prediction in microbial oceanography. Oceanography 20:34-46
13. 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 Evol. Biol. 7:79
14. Boucher, Y., Labbate, M., Koenig, J.E. & Stokes, H.W. (2007) Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends Microbiol. 15:301-309
15. Gophna, U., Thompson, J.R., Boucher, Y. and Doolittle, W.F. (2006) Complex historiesof genes encoding 3-hydroxy-3-methylglutaryl-CoenymeA reductase. Molecular Biology and Evolution 23:168-178
16. 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
17. Nesbo, C.L., Dlutek, M., Zhaxybayeva, O. and Doolittle, W.F. (2006) Evidence for existence of "Mesotogas", members of the order Thermotogales adapted to low-temperature environments. Applied and Env. Microbiol. 72:5061-5068
18. Nesbo, C.L., Doolittle, W.F., Mongodin, E.F. and Nelson, K.E. (2006) Outside forces helped shape the Thermotoga metagenome. Microbe 1:235-241
19. Susko, E., Leigh, J., Doolittle, W.F. and Bapteste, E. (2006) Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the (gamma)-proteobacteria. Mol. Biol. Evol. 23:1019-1030
20. Legault, B.A., Lopez-Lopez, A., Alba-Casado, J.C., Doolittle, W.F., Bolhuis, H., Rodriguez-Valera, F. and Papke, T.R. (2006) Environmental genomics of Haloquadratum walsbyi in a saltern crystallizer indicates a large pool of accessory genes in an outside coherent species. BMC Genomics 7:171
21. Boucher, Y., Nesbo, C.L., Joss, M.J., Robinson, A., Mabbutt, B.C., Gilllings, M.R., Doolittle, W. F. and Stokes, H.W. (2006) Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio. BMC Evol. Biol. 6:3
22. Gophna, U., Charlebois, R.L. and Doolittle, W. F. (2006) Lateral gene transfer in the evolution of Bdellovibrio bacteriovorus. Trends in Microbiology 14:64-69
23. Doolittle, W.F. and Papke, R.T. (2006) Genomics and the bacterial species problem. Genome Biology 7:116.1-116.7
24. Doolittle, W.F. (2006) Species. Microbiology Today 33:148-151
25. Sharma, A.K., Spudich, J.L. and Doolittle, W. F. (2006) Microbial rhodopsins: functional versatility and genetic mobility. Trends Microbiol. 14:463-469
26. Gophna, U., Sommerfeld, K., Gophna, S., Doolittle, W. F. and van Zanten, S.J.O.V. (2006) Differences between Crohn's disease and ulcerative colitis patients in tissue-associated intestinal microflora. J. Clin. Microbiol. 44:4136-4141
27. Nesbo,C.L., Dlutek, M. and Doolittle, W.F. (2006) Recombination in Thermotoga: implications for species concepts and biogeography. Genetics 172:759-769
28. Doolittle, W.F. (2005) Some thoughts on the Tree of Life. The Harvey Lectures 2003-2004:99:111-128
29. Nesbo, C.L., Boucher, Y., Dlutek, M. and Doolittle, W.F. (2005) Lateral gene transfer and phylogenetic assignment of environmental fosmid clones. Environmental Microbiology 7:2011-2026
30. Gophna, U., Doolittle, W.F. and Charlebois, R.L. (2005) Weighted genome trees: refinements and applications. Journal of Bacteriology 187:1305-1316
31. MacLeod, D., Charlebois, R.L., Doolittle, W.F. and Bapteste, E. (2005) Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evol. Biol. 5:27
32. Walsh, D.A., Papke, R.T. and Doolittle, W.F. (2005) Archaeal diversity along a soil salinity gradient prone to disturbance. Environmental Microbiology 7:1655-1666
33. Walsh, D.A. and Doolittle, W.F. (2005) The real domains of life. Current Biology 15:R237-R240
34. Bapteste, E., Susko, E., Leigh, J., MacLeod, D., Charlebois, R.L. and Doolittle, W.F. (2005) Do orthologous gene phylogenies really support tree-thining? BMC Evol. Biol. 5:33
35. Gophna, U., Bapteste, E., Doolittle, W.F., Biran, D. and Ron, E.Z. (2005) Evolutionary plasticity of methionine biosynthesis. Gene 355:48-57
36. Doolittle, W. F. (2005) The origin and early evolution of life. Evolutionary Science and Society: Educating a New Generation, J. Cracraft and R.W. Bybee (eds.) American Institute of Biological Sciences, Washington:35-42
37. Doolittle, W.F. (+17 authors) (2005) The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc. Natl. Acad. Sci. USA 102:18147-18152
38. Walsh, D.A., Bapteste, E., Kamekura, M. and Doolittle, W.F. (2004) Evolution of RNA polymerase B' subunit gene (rpoB') in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. Mol. Biol. Evol. 21:2340-2351
39. Papke, R.T., Koenig, J.E., Rodriguez-Valera, F. and Doolittle, W.F. (2004) Frequent recombination in a saltern populationof Halorubrum. Science 306:1928-1929
40. Doolittle, W.F. (2004) Q & A Current Biology 14(5):R176-177
41. Boucher, Y., Kamekura, M. and Doolittle, W.F. (2004) Origins and evolution of isoprenoid lipid biosynthesis in archaea. Molecular Microbiology 52:515-527
42. Bapteste, E., Boucher, Y., Leigh, J. and Doolittle, W.F. (2004) Phylogenetic reconstruction and lateral gene transfer. Trends in Microbiology 12:406-411
43. Gophna, U., Charlebois, R.L. and Doolittle, W.F. (2004) Have archaeal genes contributed to bacterial virulence? Trends in Microbiology 12:213-219
44. Boucher, Y., Douady, C.J., Sharma, A.K., Kamekura, M. and Doolittle, W.F. (2004) Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. Journal of Bacteriology 186:3980-3990
45. Charlebois, R.L. and Doolittle, W.F. (2004) Computing prokaryotic gene ubiquity: Rescuing the core from extinction. Genome Research 14:2469-2477
46. Dacks, J.B. and Doolittle, W.F. (2004) Molecular and phylogenetic characterization of syntaxin genes from parasitic protozoa. Molecular & Biochemical Parasitology 136:123-136
47. Doolittle, W.F. (2004) Bacteria and archaea. In Assembling the Tree of Life J. Cracraft & M.J. Donoghue, eds. (from Tree of Life Symposium, American Museum of Natural History, June 2002) Oxford University Press, New York:
48. Doolittle, W.F. (2004) If the Tree of Life fell, would we recognize the sound? In J. Sapp (Ed.), Microbial Evolution: Concepts and controversies Oxford University Press, USA:119-133