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W. Ford Doolittle

PhD (Stanford), FRSC

Professor Emeritus

Member, U.S. National Academy of Sciences
Department member since 1971

Tupper 8-A2
Lab Homepage


Genomics, Molecular Phylogeny, Gene Transfer

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.

Lab Personnel

Wanda Danilchuk Research Assistant


  1. TDP Brunet, WF Doolittle, (2015) Multilevel selection theory and the evolutionary functions of transposable elements Genome Biology and Evolution 7 (8):2445-2457 [Article]
  2. WF Doolittle, TDP Brunet, S Linquist, TR Gregory, (2014) Distinguishing between “function” and “effect” in genome biology Genome Biology and Evolution 6 (5):1234-1237 [Article]
  3. TDP Brunet, WF Doolittle, (2014) Getting “function” right Proceedings of the National Academy of Sciences 111 (33):E3365-E3365 [Article]
  4. Zhaxybayeva, O. and Doolittle, W.F. , (2011) Lateral gene transfer (Primer). Curr. Biol. 21:R242-R246
  5. Koenig, J.E., Bourne, D.G., Curtis, B., Dlutek, M., Stokes, H.W., Doolittle, W.F. and Boucher, Y. , (2011) Coral-mucus-associated Vibrio integrons in the Great Barrier Reef: genomic hotspots for environmental adaptation. ISME J. 5(6):962-972 [PubMed]
  6. Doolittle, W.F., Lukes, J., Archibald, J.M., Keeling, P.J. and Gray, M.W. , (2011) Comment on “Does constructive neutral evolution play an important role in the origin of cellular complexity?” Bioessays 33(6):427-429 [PubMed]
  7. Lukes, J., Archibald, J.M., Keeling, P.J., Doolittle, W.F. and Gray, M.W., (2011) How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 63:528-537
  8. Doolittle, W.F., Lukeš, J., Archibald, J.M.. Keeling, P.J. and Gray, M.W., (2011) Comment on “Does constructive neutral evolution play an important role in the origin of cellular complexity?” Bioessays 33:427-429 [PubMed]
  9. Gray, M.W., Lukes, J., Archibald, J.M., Keeling, P.J. and Doolittle, W.F. , (2010) Irremediable complexity? Science 330:920-921
  10. Nesbo, C.L., Kumaraswamy, R., Dlutek, M., Doolittle, W.F. and Foght, J. , (2010) Searching for mesophilic Thermotogales bacteria: “mesotogas” in the wild. App. Env. Microbiol. 76:4896-4900
  11. Doolittle, W.F. and Zhaxybayeva, O. , (2010) Metagenomics and the units of biological organization. Bioscience 60:102-112
  12. Koenig, J.E., Sharp, C., Dlutek, M., Curtis, B., Joss, M., Boucher, Y. and Doolittle, W.F. , (2009) Integron Gene Cassettes and Degradation of Compounds Associated with Industrial Waste: The Case of the Sydney Tar Ponds. PLoS One 4:e5276
  13. Joss MJ, Koenig JE, Labbate M, Polz MF, Gillings MR, Stokes HW, Doolittle WF, Boucher Y., (2009) ACID: annotation of cassette and integron data. BMC Bioinformatics 21:118
  14. Doolittle, W. F., (2009) The attempt on the life of the Tree of Life: science, philosophy and politics. Philosophy and Biology 25:455-473
  15. Zhaxybayeva, O., Doolittle, W.F., Papke, R.T. and Gogarten, J.P., (2009) Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus. Genome Biol. Evol. 2009:325-339
  16. Doolittle, W.F., (2009) Eradicating typological thinking in prokaryotic systematics and evolution. Cold Spring Harbor Symposia, Quantitative Biology 74:197-204
  17. Sharma, A.K., Sommerfeld, K., Bullerjahn, G.S., Matteson, A.R., Wilhelm, S.W., Jezbera, J., Brandt, U., Doolittle, W.F. and Hahn, M.W. , (2009) Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria. ISME J. 3:726-37
  18. Zhaxybayeva, O., Swithers, K., Lapierre, P., Fournier, G., Bickhard, D., DeBoy, R.T., Nelson, K.E., Nesbo, C.L., Doolittle, W.F., Gogarten, J.P. and Noll, K.M. , (2009) On the Chimeric Nature, Thermophilic Origin and Phylogenetic Placement of the Thermotogales. PNAS 106:5865-70
  19. Doolittle, W.F. and Zhaxybayeva, O. , (2009) On the origin of prokaryotic species. Genome Res. 19:744-756.
  20. Jezbera, J., Sharma, A.K., Brandt, U., Doolittle, W.F. and Hahn, M.W. , (2009) Candidatus Planktophila limnetica', an Actinobacterium representing one of the most numerically important taxa in freshwater bacterioplankton. IJSEM 59:2864-2869.
  21. Doolittle, W. F., (2009) The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them. Phil. Trans. Roy. Soc. Lond., Series B 364:2221-2228
  22. DiPPo, J.L., Nesbo, C.L., Dahle, H., Doolittle, W.F., Birkland, N.-K. and Noll, K.M. , (2009) Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerobic heterotroph isolated from an oil production fluid. Int J Syst Evol Microbiol. 59:2991-3000.
  23. Nesbo CL, Bapteste E, Curtis B, Dahle H, Lopez P, Macleod D, Dlutek M, Bowman S, Zhaxybayeva O, Birkeland NK, and Doolittle WF , (2009) The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. J Bacteriol. 191:1974-78.
  24. 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
  25. 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
  26. Sharma, A.K., Zhaxybayeva, O., Papke, R.T. and Doolittle, W.F. , (2008) Actinorhodopsins: Proteorhodopsin-like gene sequences found predominantly in non-marine environments. Env. Microbiol. 10:1039-1056
  27. 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. 10:1024-1038
  28. Beiko, R.G., Doolittle, W.F. and Charlebois, R.L. , (2008) The impact of reticulate evolution on genome phylogeny. Systematic Biol. 57:844-56.
  29. Doolittle, W. F., (2008) Microbial evolution: stalking the wild bacterial species. Current Biology 18:R565-567
  30. 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. Environmental Microbiology 10:1024-1038.
  31. 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
  32. 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
  33. Doolittle, W. F. and Bapteste, E., (2007) Pattern pluralism and the Tree of Life hypothesis. PNAS 104:2043-2049
  34. Doolittle, W. F. and Zhaxybayeva, O., (2007) Evolution: reducible complexity -- the case for bacterial flagella. Current Biology 17:R510-512
  35. 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
  36. Zhaxybayeva,O., Gogarten, J.P. and Doolittle, W.F., (2007) A hyperconserved protein in Prochlorococcus and marine Synechococcus. FEMS Microbiol. Lett. 274:30-34
  37. 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
  38. 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
  39. 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
  40. Gophna, U., Thompson, J.R., Boucher, Y. and Doolittle, W.F., (2006) Complex historiesof genes encoding 3-hydroxy-3-methylglutaryl-CoenymeA reductase. Mol. Biol. Evol. 23:168-178
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. Doolittle, W.F. and Papke, R.T., (2006) Genomics and the bacterial species problem. Genome Biology 7:116.1-116.7
  49. Doolittle, W.F., (2006) Species. Microbiology Today 33:148-151
  50. Sharma, A.K., Spudich, J.L. and Doolittle, W. F., (2006) Microbial rhodopsins: functional versatility and genetic mobility. Trends Microbiol. 14:463-469
  51. 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
  52. Nesbo,C.L., Dlutek, M. and Doolittle, W.F., (2006) Recombination in Thermotoga: implications for species concepts and biogeography. Genetics 172:759-769
  53. Doolittle, W.F., (2005) Some thoughts on the Tree of Life. The Harvey Lectures 2003-2004:99:111-128
  54. 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
  55. Gophna, U., Doolittle, W.F. and Charlebois, R.L., (2005) Weighted genome trees: refinements and applications. Journal of Bacteriology 187:1305-1316
  56. 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
  57. 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
  58. Walsh, D.A. and Doolittle, W.F., (2005) The real domains of life. Current Biology 15:R237-R240
  59. 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
  60. Gophna, U., Bapteste, E., Doolittle, W.F., Biran, D. and Ron, E.Z., (2005) Evolutionary plasticity of methionine biosynthesis. Gene 355:48-57
  61. 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
  62. 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
  63. 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
  64. 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
  65. Doolittle, W.F., (2004) Q & A Current Biology 14(5):R176-177
  66. Boucher, Y., Kamekura, M. and Doolittle, W.F., (2004) Origins and evolution of isoprenoid lipid biosynthesis in archaea. Molecular Microbiology 52:515-527
  67. Bapteste, E., Boucher, Y., Leigh, J. and Doolittle, W.F., (2004) Phylogenetic reconstruction and lateral gene transfer. Trends in Microbiology 12:406-411
  68. Gophna, U., Charlebois, R.L. and Doolittle, W.F., (2004) Have archaeal genes contributed to bacterial virulence? Trends in Microbiology 12:213-219
  69. Boucher, Y., Douady, C.J., Sharma, A.K., Kamekura, M. and Doolittle, W.F., (2004) Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. J. Bacteriol. 186:3980-3990
  70. Charlebois, R.L. and Doolittle, W.F., (2004) Computing prokaryotic gene ubiquity: Rescuing the core from extinction. Genome Research 14:2469-2477
  71. Dacks, J.B. and Doolittle, W.F., (2004) Molecular and phylogenetic characterization of syntaxin genes from parasitic protozoa. Molecular & Biochemical Parasitology 136:123-136
  72. 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:
  73. 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