Doolittle Laboratory Publications

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(4), 1024-1038.

Sharma, A.K., Zhaxybayeva, O., Papke, R.T. & Doolittle, W.F. (2008) Actinorhodopsins: Proteorhodopsin-like gene sequences found predominantly in non-marine environments. (Environmental Microbiology: 10(4), 1039-1056.)

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.

Boucher, Y., Labbate, M., Koenig, J.E. & Stokes, H.W. (2007) Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends in Microbiology 15: 301-309.

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.

Sharma, AK, Walsh, DA, Bapteste, E, Rodriguez-Valera, F, Doolittle W.F., Papke, RT. (2007) Evolution of rhodopsin ion pumps in haloarchaea. BMC Evol Biol. 7: 79.

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.

Zhaxybayeva, O., Gogarten, J.P., and Doolittle, W.F. (2007) A hyperconserved protein in Prochlorococcus and marine Synechococcus. FEMS Microbiol Lett. 274: 30-34.

Doolittle, W.F. and Zhaxybayeva, O. (2007) Evolution: reducible complexity -- the case for bacterial flagella. Current Biology 17: R510-512.

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. [Open Access]

Sharma, A.K., Walsh, D.A., Bapteste, E. Rodríguez-Valera, F., Doolittle, W.F. and Papke, R.T. (In press) Evolution of rhodopsin ion pumps in haloarchaea. BMC Evolutionary Biology .

Case RJ, Boucher Y, Dahllof I, Holmstrom C, Doolittle WF, Kjelleberg S. (2007) The 16S rRNA and rpoB genes as molecular markers for microbial ecology. Applied and Environmental Microbiology 73: 278-288.

Doolittle, W.F. and Bapteste, E. (2007) Pattern pluralism and the Tree of Life hypothesis. PNAS 104: 2043-2049.

Doolittle, W.F. and Papke, R.T. (2006) Genomics and the bacterial species problem. Genome Biology 7: 1161-1167.

Doolittle, W.F. (2006) Species. Microbiology Today (SGM) 33: 148-151.

Sharma, A.K., Spudich, J.L. and Doolittle, W.F. (2006) Microbial rhodopsins: functional versatility and genetic mobility. Trends in Microbiology 14: 463-469.

Nesbø, 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 Environmental Microbiology 72: 5061-5068.

Zhaxybayeva, O., Gogarten, J.P., Charlebois, R.L., Doolittle, W. Ford & Papke, R.T. (2006) Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Research 16: 1099-1108.

Nesbø, C.L., Dlutek, M., & Doolittle, W.F. (2006) Recombination in Thermotoga: implications for species concepts and biogeography. Genetics 172: 759-769.

Nesbø, C.L., Doolittle, W.F., Mongodin, E.F. and Nelson, K.E. (2006) Outside forces helped shape the Thermotoga metagenome. Microbe 1: 235-241.

Legault, B.A., Lopez-Lopez A., Alba-Casado, J.C., Doolittle, W.F., Bolhuis, H., Rodriguez-Valera, F. & Papke, T.R. (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.

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. Journal of Clinical Microbiology 44: 4136-4141.

Gophna, U., Thompson, J.R., Boucher, Y., and Doolittle, W.F. (2006) Complex histories of genes encoding 3-hydroxy-3-methylglutaryl-CoenzymeA reductase. Mol. Biol. Evol. 23: 168-178.

Susko, E., Leigh, J., Doolittle, W.F. & 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.

Gophna, U., Charlebois, R.L. and Doolittle, W.F. (2006). Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus. Trends in Microbiology 14: 64-69.

Boucher, Y., Nesbo, C.L., Joss, M.J., Robinson, A., Mabbutt, B.C., Gillings, 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.

Doolittle, W.F. (2005) Some thoughts on the tree of life. Harvey Lectures Series 99: 111-128.

Gophna, U., Doolittle,W.F. and Charlebois, R.L. (2005) Weighted genome trees: refinements and applications. Journal of Bacteriology 187: 1305-1316.

Gophna, U., Bapteste, E., Doolittle, W.F., Biran, D. & Ron, E.Z. (2005) Evolutionary plasticity of methionine biosynthesis. GENE, 355: 48-57.

Bapeste, E., Susko, E., Leigh, J., MacLeod, D., Charlebois, R.L. and Doolittle, W.F. (2005) Do orthologous gene phylogenies really support tree-thinking? BMC Evolutionary Biology 5: 33.

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 Evolutionary Biology 5: 27.

Walsh, D.A. and Doolittle, W.F. (2005) The real 'domains' of life. Current Biology 15: R237-R240.

Walsh, D.A., Papke, R.T. & Doolittle, W.F. (2005) Archaeal diversity along a soil salinity gradient prone to disturbance. Environmental Microbiology 7: 1655-1666.

Nesbø, 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.

Mongodin, E.F., Nelson, K.E., Daugherty, S., DeBoy, R.T., Wister, J., Khouri, H., Weidman, J., Walsh, D.A., Papke, R.T., Sanchez-Perez, G., Sharma, A.K., Nesbø, C.L., MacLeod, D., Bapteste, E., Doolittle, W.F., Charlebois, R.L., Legault, B. & Rodriguez-Valera, F. (2005) The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. PNAS 102: 18147-18152.

Papke, R.T., Koenig, J.E., Rodriguez-Valera, F. and Doolittle, W.F. (2004) Frequent recombination in a saltern population of Halorubrum. Science 306: 1928-29.

Boucher, Y., Kamekura, M. and Doolittle, W. F. (2004) Origins and evolution of isoprenoid lipid biosynthesis in archaea. Molecular Microbiology 52: 515-527.

Dacks, J.B. and Doolittle, W.F. (2004) Molecular and phylogenetic characterization of syntaxin genes from parasitic protozoa. Molecular & Biochemical Parasitology, 136: 123-136.

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.

Walsh, D.A., Bapteste, E., Kamekura, M. & Doolittle, W. F. (2004) Evolution of the RNA polymerase B' subunit gene (rpoB') in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. Mol. Biol. Evol. 21: 2340-2351.

Doolittle, W.F. (2004) Q&A, Current Biology 14: R176-177.

Gophna, U., Charlebois, R.L. and Doolittle, W.F. (2004) Have archaeal genes contributed to bacterial virulence? Trends in Microbiology 12: 213-219.

Bapteste, E., Boucher, Y., Leigh, J. and Doolittle, W.F. (2004) Phylogenetic reconstruction and lateral gene transfer. Trends in Microbiology 12: 406-411.

Charlebois, R.L. and Doolittle, W.F. (2004) Computing prokaryotic gene ubiquity: Rescuing the core from extinction. Genome Research 14: 2469-2477.

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.

Nesbø, C.L. and Doolittle, W. Ford (2003). Active self-splicing group I introns in the 23S rRNA genes of hyperthermophilic bacteria, denved hom introns in eukaryotic organelles. PNAS, 100: 10806 - 10811.

Papke, R.T. and Doolittle, W. Ford (2003). Phage evolution: new worlds of genomic diversity. Current Biology, 13: R 606-607.

Papke, R.T., Douady, C.J., Doolittle, W.F. and Rodriguez-Valera, F. (2003). Diversity of bacteriorhodopsins in different hypersaline waters from a single Spanish saltern. Environmental Microbiology, 5: 1039 - 1045.

Nesbo, C.L. and Doolittle, W. Ford (2003). Targeting clusters of transferred genes in Thermotoga maritima. Environmental Microbiology, 5: 1144 - 1154.

Boucher, Y., Douady, C.J., Papke, R.T., Walsh, D.A., Boudreau, M.E.R., Nesbo, C.L., Case, R.J., and Doolittle, W.F. (2003). Lateral gene transfer and the origins of prokaryotic groups. Ann. Rev. Genetics 37: 283 - 328.

Moriya, S., Dacks, J.B., Takagi, A., Noda, S., Ohkuma, M., Doolittle, W.F. and Kudo, T. (2003). Molecular phylogeny of three oxymonad genera: Pyrsonympha, Dinenympha and Oxymonas. J Euk. Microbiol., 50: 190-197.

O'Malley, M.A., Roger, A.J. and Doolittle, W.F. (2002). Can commercial protection be good for science? Nature 419: 111. (Commentary on Nature, 2002, 417: 589-590).

Dacks, J.B., Davis, L.A.M., Sjogren, A.M., Andersson, J.O., Roger, A.J. and Doolittle, W.F. (2003). Evidence for Golgi bodies in proposed 'Golgi-lacking' lineages. Proc. Royal Soc. Lond. B (Suppl.), 270: S168 - S171.

Douady, C.J., Delsuc, F., Boucher, Y., Doolittle, W.F. and Douzery, E.J.P. (2003). Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20: 248-254.

Doolittle, W.F. (2004). Bacteria and archaea. In Assembling the Tree of Life, J. Cracraft & M.J. Donoghue, Eds. (from Tree Life Symposium, American Museum of Natural History, June 2002), Oxford University Press, NY.

Doolittle, W.F., Boucher, Y., Nesbo, C.L., Douady, C.J., Andersson, J., and Roger, A.J. (2003). How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Phil. Trans. Roy. Soc. Lond. B. 358: 39-58.

O'Malley, M., Roger, A.J. and Doolittle, W.F. (submitted). Evolutionary accounts of scientific change: the case of genomics and data disclosure. Studies in the History and Philosophy of Science, Cambridge, U.K.

O'Malley, M., McOuat, G. and Doolittle, W.F. (submitted). The triple helix account of scientific innovation: a critical appraisal. Science, Technology and Human Values.

Dacks, J.B., Marinets, A., Doolittle, W.F., Cavalier-Smith, T. and Logsdon, J.M. (2002). Analyses of RNA polymerase II genes from free-living protists: phylogeny, long branch attraction and the eukaryotic big bang. Mol. Biol. Evol., 19(6): 830-840

Nesbø:, C.L., Nelson, K.E. and Doolittle, W.F. (2002). Suppressive substractive hybridization detects extensive genome diversity in Thermotoga maritima. Journal of Bacteriology, 184: 4475-4488

Boucher, Y. and Doolittle, W.F. (2002). Something new under the sea. Nature, 417: 27-28

Inagaki, Y., Doolittle, W.F., Baldauf, S.L. and Roger, A.J. (2002) Lateral transfer of gene encoding EF-1a: origin and evolution of the large subunit of ATP sulfurylase in eubacteria. Current Biology, 12(9): 772-776.

Doolittle, W.F. (2002). Diversity squared. Environmental Microbiology, 4: 10-12.

Dacks, J.B. and Doolitttle, W.F. (2002). Novel syntaxin gene sequences from Giardia, Trypanosoma and algae: implications for the ancient evolution of the eukaryotic endomembrane system. J. of Cell Science, 115 (8) : 1635-1642.

Gogarten, P., Doolittle, W.F. and Lawrence, J. (2002). Prokaryotic evolution in light of gene transfer. PNAS, 19: 2226-2238.

Simpson, A.G.B., Radek, R., Dacks, J.B. and O'Kelly, C.J. (2002). How oxymonads lost their groove: An ultrastructural comparison of Monocercomonoides and excavate taxa, J. Euk Micro., 49(3): 23-248.

Inagaki, Y., Blouin, C., Doolittle, W.F. and Roger, A.J. (2002). Convergence and constraint in eRF1 domain 1: the evolution of stop codon recognition. Nucleic Acid Research, 30: 532-544.

Archibald, J.M., O'Kelly, C.J. and Dolittle, W.F. (2002). The chaperonin genes of jakobid and jacobid-like flagellates: implications for eukaryotic evolution., Mol. Biol. Evol., 19: 422-431.

Dacks, J.B., (2002). Malaria, Amoebae and You: Recent advances in eukaryotic relationships., Actionbioscience.org, online article

Dacks, J.B. and Doolittle, W.F. (2001). Reconstructing/deconstructing the earliest eukaryotes: How comparative genomics can help., Cell, 107: 419-425

She, Q., Singh, R.K., Confalonieri, F., Zivanovic, Y., allard, G., Awayez, M.J., Chan-Weiher, C.C.-Y., Clausen, I.B., Curtis, B.A., De Moors, A., Erauso, G., Fletcher, C., Gordon, P.M.K., Heikamp-de Jong, I., Jeffries, A.C., Kozera, C.J., Medina, N., Peng, X., Thi-Ngoc, H.P., Redder, P., Schenk, M.E., Theriault, C., Tolstrup, N., Charlebois, R.L., Doolittle, W.F., Duguet, M., Gaasterland, T., Garret, R.A., sensen, C.W. and Van der Oost, J. (2001). The complete genome of the crenarchaeon Sulfolobus solfataricus P2. PNAS, 98(14): 7835-7840.

Andersson, J.O., Doolittle, W.F. and Nesbø:, C.L. (2001). Are there bugs in our genome? Science, 292(5523): 1848-1850.

Doolittle, W.F. (in press, 2001). Reconstructing/Deconstructing the tree of life. CFI Publication: Why We Need to Know: Essays by Leading Canadian Researchers on their Work.

Archibald, J.M., Blouin, C. and Doolittle, W.F. (2001). Gene duplication and the evolution of group II chaperonins: implications for structure and function. J. of Structural Biology, 135: 157-169.

Kasinsky, H.E., Lewis, J.D., Dacks, J.B. and Ausio, J. (2001). Origin of H1 Linker Histones, FASEB J., 15: 34-42.

Doolittle, W.F. (2001). Fascination of the Third Domain. Review of The Surprising Archaea (by John Howland, Oxford University Press, 2000). Science, 291(5509): 1707

Boucher, Y., Nesbø:, C.L. and Doolittle, W.F. (2001). Microbial genomes: dealing with diversity. Current Opinion in Microbiology, 4(3): 285-289.

Dacks,J.B., Silberman, J.D., Simpson, A.G.B., Moriya, S., Kudo, T., Ohkuma, M., and Redfield, R.J. (2001). Oxymonads are closely related to the excavate taxon Trimastix", M.B.E., 18(6): 1034-1044

Noel, C., Gerbod, D., Fast, N.M., Wintjens, R., Delgado-Viscogliosi, P., Doolittle, W.F. and Viscogliosi, E. (2001). Tubulins in Trichomonas vaginalis. I. Molecular characterization of the tubulin dimer. J. of Eukaryotic Microbiology.

Boucher, Y., Huber, H., L'Haridon, S., Stetter, K.O. and Doolittle, W.F. (2001). Bacterial origin for the isoprenoid biosynthesis enzyme HMG-CoA reductase of the archaeal orders Thermoplasmatales and Archaeoglobales. Mol. Biol. Evol., 18: 1378-1388

Inagaki, Y. and Doolittle, W.F. (2001) Class 1 release factors in ciliates with variant genetic codes. Nucleic Acids Res. 29(4):921-927.

Nesbø:, C.L., L'Haridon, S., Stetter, K.O. and Doolittle, W.F. (2001). Phylogenetic analyses of two "archaeal" genes in Thermotoga maritima reveal multiple transfers between archaea and bacteria. Mol. Biol. Evol. 18(3):362-375.

Nesbø:, C.L., Boucher, Y. and Doolittle, W.F. (2001). Defining the core of nontransferable procaryotic genes: The euryarchaeal core. J. Mol. Evol., 53(4/5), 340-350.

Doolittle, W.F. (2000) Another branch of the family. A review of The Variety of Life: A Survey and a Celebration of all the Creatures that Have Ever Lived, by Colin Tudge. The New York Times (June 18, 2000), Sunday Book Review Section

Archibald, J.M., Logsdon, J.M. and Doolittle (2000) Origin and evolution of eukaryotic chaperonins: phylogenetic evidence for ancient duplications in CCT genes. Mol. Biol. Evol. 17(10): 1456-1466.

Baldauf, S.L., Roger, A.J., Wenk-Siefert, I. and Doolittle, W.F. (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290: 972-977.

Boucher, Y. and Doolittle, W.F. (2000) The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways. Mol. Microbiol. 37(4): 703-716.

Charlebois, R.L., Singh, R., Chan-Weiher, C. C. -Y., Allard, G., Chow, C., Confalonieri, B.,Curtis, B., Duget, M., Faguy, D., Gaasterland, T., Garrett, R.A., Jeffries, A., Kozera, C.,Kushwaha, N., Lafleur, E., Medina, N., Peng, X., Penny, S.L., She, Q., St. Jean, A., van der Oost, J., Young, F., Zivanovic, Y., Doolittle, W.F., Ragan, M.A. and Sensen, C.W.(2000) Gene content and organization of a 281-kbp contig from the genome of the extremely thermophilic archaeon, Sulfolobus solfataricus P2. Genome 43: 116-136.

Doolittle, W.F. (2000) The nature of the universal ancestor and the evolution of the proteome. Curr. Op. Struct. Biol. 10(3): 355-358.

Faguy, D.M. and Doolittle, W.F. (2000) Horizontal transfer of catalase-peroxidase genes between archaea and pathogenic bacteria. Trends Genet. 16(5):196-197.

Inagaki, Y. and Doolittle, W.F. (2000) Evolution of the eukaryotic translation termination system: origins of release factors. Mol. Biol. Evol. 17(6): 882-889.

Inagaki, Y., Dacks, J.B., Doolittle, W.F., Watanabe, K.I. and Ohama, T. (2000) Evolutionary relationship between dinoflagellates bearing olbigate diatom endosymbionts: insight into tertiary endosymbiosis. Int. J. Syst. Evol. Microbiol. 50: 2075-2081.

Van de Peer, Y., Baldauf, S.L., Doolittle, W.F. and Myer, A. (2000) An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances. J. Mol. Evol. 51:565-576.