W F Doolittle

Summary

Affiliation: Dalhousie University
Country: Canada

Publications

  1. ncbi request reprint Lateral genomics
    W F Doolittle
    Canadian Institute for Advanced Research, Dept of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Trends Cell Biol 9:M5-8. 1999
  2. pmc How big is the iceberg of which organellar genes in nuclear genomes are but the tip?
    W F Doolittle
    Genome Atlantic, Dalhousie University, 5850 College Street, Halifax, Nova Scotia B3H 1X5, Canada
    Philos Trans R Soc Lond B Biol Sci 358:39-57; discussion 57-8. 2003
  3. ncbi request reprint The nature of the universal ancestor and the evolution of the proteome
    W F Doolittle
    Department of Biochemistry and Molecular Biology, Canadian Institute for Advanced Research, Dalhousie University, Halifax, B3H 4H7, Canada
    Curr Opin Struct Biol 10:355-8. 2000
  4. ncbi request reprint Archaeal genomics: do archaea have a mixed heritage?
    W F Doolittle
    Canadian Institute for Advanced Research, Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
    Curr Biol 8:R209-11. 1998
  5. ncbi request reprint Phylogenetic classification and the universal tree
    W F Doolittle
    Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Science 284:2124-9. 1999
  6. ncbi request reprint You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes
    W F Doolittle
    Department of Biochemistry, Dalhousie University, Nova Scotia, Canada
    Trends Genet 14:307-11. 1998
  7. ncbi request reprint Reconstructing/deconstructing the earliest eukaryotes: how comparative genomics can help
    J B Dacks
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Cell 107:419-25. 2001
  8. pmc Origin and evolution of the slime molds (Mycetozoa)
    S L Baldauf
    Canadian Institute for Advanced Research and Department of Biochemistry, Dalhousie University, Halifax, NS, Canada B3H 4H7
    Proc Natl Acad Sci U S A 94:12007-12. 1997
  9. ncbi request reprint Origin and evolution of eukaryotic chaperonins: phylogenetic evidence for ancient duplications in CCT genes
    J M Archibald
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 17:1456-66. 2000
  10. ncbi request reprint Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny
    E Bapteste
    Canadian Institute for Advanced Research and Genome Atlantic, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 25:83-91. 2008

Collaborators

Detail Information

Publications50

  1. ncbi request reprint Lateral genomics
    W F Doolittle
    Canadian Institute for Advanced Research, Dept of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Trends Cell Biol 9:M5-8. 1999
    ..Here, I ask whether this way of thinking is really justified, and explore its implications...
  2. pmc How big is the iceberg of which organellar genes in nuclear genomes are but the tip?
    W F Doolittle
    Genome Atlantic, Dalhousie University, 5850 College Street, Halifax, Nova Scotia B3H 1X5, Canada
    Philos Trans R Soc Lond B Biol Sci 358:39-57; discussion 57-8. 2003
    ..We also consider evidence for, and implications of, LGT between prokaryotes and phagocytic eukaryotes...
  3. ncbi request reprint The nature of the universal ancestor and the evolution of the proteome
    W F Doolittle
    Department of Biochemistry and Molecular Biology, Canadian Institute for Advanced Research, Dalhousie University, Halifax, B3H 4H7, Canada
    Curr Opin Struct Biol 10:355-8. 2000
    ..However, increasing evidence for lateral gene transfer could mean that such attempts are based on an incorrect understanding of evolution...
  4. ncbi request reprint Archaeal genomics: do archaea have a mixed heritage?
    W F Doolittle
    Canadian Institute for Advanced Research, Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
    Curr Biol 8:R209-11. 1998
    ..The sequence also shows bacteria-like features. It is time to come to grips with this evidence for a mixed heritage...
  5. ncbi request reprint Phylogenetic classification and the universal tree
    W F Doolittle
    Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Science 284:2124-9. 1999
    ..However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished...
  6. ncbi request reprint You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes
    W F Doolittle
    Department of Biochemistry, Dalhousie University, Nova Scotia, Canada
    Trends Genet 14:307-11. 1998
    ..The operation of a gene transfer ratchet would inevitably result in the replacement of nuclear genes of early eukaryotes by genes from the bacteria taken by them as food...
  7. ncbi request reprint Reconstructing/deconstructing the earliest eukaryotes: how comparative genomics can help
    J B Dacks
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Cell 107:419-25. 2001
    ..It's not clear that either is the case, but the expanding protist genomic database could help us in several ways...
  8. pmc Origin and evolution of the slime molds (Mycetozoa)
    S L Baldauf
    Canadian Institute for Advanced Research and Department of Biochemistry, Dalhousie University, Halifax, NS, Canada B3H 4H7
    Proc Natl Acad Sci U S A 94:12007-12. 1997
    ..We suggest that ribosomal RNA data should be more closely examined with regard to these questions, and we emphasize the importance of developing multiple sequence data sets...
  9. ncbi request reprint Origin and evolution of eukaryotic chaperonins: phylogenetic evidence for ancient duplications in CCT genes
    J M Archibald
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 17:1456-66. 2000
    ..We discuss these results in light of current views on the origin, evolution, and function of CCT complexes...
  10. ncbi request reprint Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny
    E Bapteste
    Canadian Institute for Advanced Research and Genome Atlantic, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 25:83-91. 2008
    ..Using concatenated core genes as a valid framework to classify uncharacterized environmental sequences can thus be misleading...
  11. ncbi request reprint Evidence of independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases
    D R Edgell
    Canadian Institute for Advanced Research, Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 15:1207-17. 1998
    ....
  12. ncbi request reprint Bacterial origin for the isoprenoid biosynthesis enzyme HMG-CoA reductase of the archaeal orders Thermoplasmatales and Archaeoglobales
    Y Boucher
    Canadian Institute for Advanced Research, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 18:1378-88. 2001
    ..Their presence in two divergent archaeal lineages suggests an important adaptive role for these laterally transferred genes...
  13. ncbi request reprint Defining the core of nontransferable prokaryotic genes: the euryarchaeal core
    C L Nesbø
    Department of Biochemistry and Molecular Biology, Dalhousie University, 5859 University Avenue, Halifax, Nova Scotia, B3H 4H7 Canada
    J Mol Evol 53:340-50. 2001
    ....
  14. pmc Gene duplications in evolution of archaeal family B DNA polymerases
    D R Edgell
    Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
    J Bacteriol 179:2632-40. 1997
    ..Archaeal family B DNA polymerases together constitute a monophyletic subfamily whose evolution has been characterized by a number of gene duplication events...
  15. pmc Characterization of pHV2 from Halobacterium volcanii and its use in demonstrating transformation of an archaebacterium
    R L Charlebois
    Department of Biochemistry, Dalhousie University, Halifax, NS, Canada
    Proc Natl Acad Sci U S A 84:8530-4. 1987
    ..We describe PEG-mediated transformation of H. volcanii WFD11 with intact pHV2 and with a form of pHV2 marked by a 93-base-pair deletion generated in vitro...
  16. ncbi request reprint Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria
    E Susko
    Genome Atlantic, Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 23:1019-30. 2006
    ..Instead of an organismal tree, we propose that these core genes could be used to define a more subtle and partially reticulated pattern of relationships...
  17. pmc Do orthologous gene phylogenies really support tree-thinking?
    E Bapteste
    GenomeAtlantic, 1721 Lower Water Street, Suite 401, Halifax, NS, B3J 1S5, Canada
    BMC Evol Biol 5:33. 2005
    ..The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes...
  18. ncbi request reprint Completing the sequence of the Sulfolobus solfataricus P2 genome
    C W Sensen
    National Research Council of Canada, Institute for Marine Biosciences, Halifax, NS, Canada
    Extremophiles 2:305-12. 1998
    ..After an overview of the general sequence features, metabolic pathway studies are explained, using sugar metabolism as an example. The paper closes with an overview of repetitive elements in S. solfataricus...
  19. ncbi request reprint Methods for evaluating exon-protein correspondences
    A Stoltzfus
    Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
    Comput Appl Biosci 11:509-15. 1995
    ..The likely effects of deletion and putative displacement ('sliding') of introns on the ability to detect correlations are also examined...
  20. ncbi request reprint An archaebacterial homolog of pelota, a meiotic cell division protein in eukaryotes
    M A Ragan
    Program in Evolutionary Biology, Canadian Institue for Advanced Research, National Research Council of Canada, Halifax, Nova Scotia, Canada
    FEMS Microbiol Lett 144:151-5. 1996
    ..The nuclear localization signal and negatively charged carboxy-terminus characteristic of eukaryotic pelota-like proteins are absent from the S. solfataricus homolog, and hence may be indicative of the acquired eukaryotic function(s)...
  21. ncbi request reprint Recurrent paralogy in the evolution of archaeal chaperonins
    J M Archibald
    Program in Evolutionary Biology Canadian Institute for Advanced Research Department of Biochemistry and Molecular Biology Dalhousie University Halifax, Nova Scotia, B3H 4H7, Canada ca
    Curr Biol 9:1053-6. 1999
    ..The persistence of paralogous genes for chaperonin subunits in multiple archaeal lineages may involve a process of co-evolution, where chaperonin subunit heterogeneity changes independently of selection on function...
  22. ncbi request reprint Evidence for the early divergence of tryptophanyl- and tyrosyl-tRNA synthetases
    J R Brown
    Department of Biochemistry, Canadian Institute for Advanced Research, Dalhousie University, Sir Charles Tupper Building, Halifax, Nova Scotia, Canada
    J Mol Evol 45:9-16. 1997
    ..Furthermore, reciprocally rooted phylogenies of TrpRS and TyrRS sequences confirm the closer evolutionary relationship of Archaea to eukaryotes by placing the root of the universal tree in the Bacteria...
  23. ncbi request reprint An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes
    A J Roger
    Department of Biochemistry Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 16:218-33. 1999
    ..It is also consistent with the nearly simultaneous diversification of major eukaryotic lineages implied by the "big-bang" hypothesis of eukaryote evolution...
  24. ncbi request reprint Gene duplication and the evolution of group II chaperonins: implications for structure and function
    J M Archibald
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    J Struct Biol 135:157-69. 2001
    ..In light of recent biochemical and electron microscopic data describing specific CCT-substrate interactions, our results have implications for the evolution of subunit-specific functions in CCT...
  25. pmc Evidence that eukaryotic triosephosphate isomerase is of alpha-proteobacterial origin
    P J Keeling
    Department of Biochemistry, Dalhousie University, Halifax, NS Canada
    Proc Natl Acad Sci U S A 94:1270-5. 1997
    ..Among these eukaryotic genes are some from deeply branching, amitochondrial eukaryotes (namely Giardia), which further suggests that this event took place quite early in eukaryotic evolution...
  26. ncbi request reprint The Sulfolobus solfataricus P2 genome project
    R L Charlebois
    Canadian Institute for Advanced Research, University of Ottawa, ON, Canada
    FEBS Lett 389:88-91. 1996
    ..An examination of completely sequenced cosmids suggests a clustering of genes by function in the S. solfataricus genome...
  27. ncbi request reprint Alpha-tubulin from early-diverging eukaryotic lineages and the evolution of the tubulin family
    P J Keeling
    Department of Biochemistry, Dalhousie University, Nova Scotia, Canada
    Mol Biol Evol 13:1297-305. 1996
    ....
  28. ncbi request reprint Evolutionary relationships of bacterial and archaeal glutamine synthetase genes
    J R Brown
    Canadian Institute for Advanced Research, Department of Biochemistry, Halifax, Nova Scotia
    J Mol Evol 38:566-76. 1994
    ..The GSI gene of Sulfolobus solfataricus, a member of the Crenarchaeota (extreme thermophiles), is exceptional and could not be definitely placed in either subdivision...
  29. ncbi request reprint Phylogenetic analyses of two "archaeal" genes in thermotoga maritima reveal multiple transfers between archaea and bacteria
    C L Nesbo
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
    Mol Biol Evol 18:362-75. 2001
    ..For hyperthermophiles, we hypothesize that LGT may be as much a consequence as the cause of adaptation to hyperthermophily...
  30. pmc Archaea and the prokaryote-to-eukaryote transition
    J R Brown
    Canadian Institute for Advanced Research, Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
    Microbiol Mol Biol Rev 61:456-502. 1997
    ..One horizontal gene exchange might have involved the gram-positive Bacteria and the Archaea, while the other might have occurred between proteobacteria and eukaryotes and might have been mediated by endosymbiosis...
  31. ncbi request reprint Evidence for the Heterolobosea from phylogenetic analysis of genes encoding glyceraldehyde-3-phosphate dehydrogenase
    A J Roger
    Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
    J Eukaryot Microbiol 43:475-85. 1996
    ..We propose that several of the incongruencies observed between GAPDH and other molecular phylogenies are artifacts resulting from substitutional saturation of this enzyme...
  32. pmc Class I release factors in ciliates with variant genetic codes
    Y Inagaki
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Nucleic Acids Res 29:921-7. 2001
    ..This observation suggests that domain 1 contains the codon recognition site, but that the mechanism of eRF1 codon recognition may be more complex than proposed by Nakamura et al. or Knight and Landweber...
  33. ncbi request reprint Cytoskeletal proteins: the evolution of cell division
    D M Faguy
    Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
    Curr Biol 8:R338-41. 1998
    ..The evolutionary transition from FtsZ to tubulin could provide a window into the transition from prokaryotic cells to eukaryotic cells...
  34. ncbi request reprint The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways
    Y Boucher
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Microbiol 37:703-16. 2000
    ..The phylogenetic diversity of the organisms involved and the range of possible causes and effects of these transfer events make the IPP biosynthetic pathways an ideal system for studying the evolutionary role of LGT...
  35. ncbi request reprint Microbial genomes: dealing with diversity
    Y Boucher
    Canadian Institute for Advanced Research Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia BSH 4H7, Canada
    Curr Opin Microbiol 4:285-9. 2001
    ..Surprisingly, even strains of the same species can differ by as much as 20% in gene content. Conceptual and methodological approaches for dealing with such diversity are now being developed, and should transform microbial genomics...
  36. pmc Genes for tryptophan biosynthesis in the halophilic archaebacterium Haloferax volcanii: the trpDFEG cluster
    W L Lam
    Canadian Institute for Advanced Research, Dalhousie University, Halifax, Nova Scotia
    J Bacteriol 174:1694-7. 1992
    ..Residues involved in feedback inhibition of eubacterial anthranilate synthetases are conserved...
  37. pmc Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications
    J R Brown
    Canadian Institute for Advanced Research, Department of Biochemistry, Dalhousie University, Halifax, NS
    Proc Natl Acad Sci U S A 92:2441-5. 1995
    ..vaginalis clustered with other eukaryotic ValRS genes, which may have been transferred from the mitochondrial genome to the nuclear genome, suggesting that this amitochondrial trichomonad once harbored an endosymbiotic bacterium...
  38. doi request reprint Eradicating typological thinking in prokaryotic systematics and evolution
    W F Doolittle
    Biochemistry and Molecular Biology, Dalhousie University, Nova Scotia, Canada B3H 1X5
    Cold Spring Harb Symp Quant Biol 74:197-204. 2009
    ..With examples from phylogenomics, I argue that "species," "domains," and the "TOL" are reifications that we can do without, especially as genomics dissolves into metagenomics...
  39. pmc U2 and U6 snRNA genes in the microsporidian Nosema locustae: evidence for a functional spliceosome
    N M Fast
    Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Nucleic Acids Res 26:3202-7. 1998
    ..These results indicate that the N.locustae U6 and U2 snRNAs may be functional components of an active spliceosome, even though introns have not yet been found in microsporidian genes...
  40. pmc Intron "sliding" and the diversity of intron positions
    A Stoltzfus
    Canadian Institute for Advanced Research Program in Evolutionary Biology, and Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4H7
    Proc Natl Acad Sci U S A 94:10739-44. 1997
    ..The results suggest that sliding, if it occurs at all, has contributed little to the diversity of intron positions...
  41. ncbi request reprint Evolutionary relationship between dinoflagellates bearing obligate diatom endosymbionts: insight into tertiary endosymbiosis
    Y Inagaki
    JT Biohistory Research Hall, Takatsuki, Osaka, Japan
    Int J Syst Evol Microbiol 50:2075-81. 2000
    ....
  42. ncbi request reprint Lessons from the Aeropyrum pernix genome
    D M Faguy
    Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Canadian Institute for Advanced Research, Dalhousie University, Halifax, B3H 4H7, Canada
    Curr Biol 9:R883-6. 1999
    ..The sequence confirms the distinct nature of crenarchaeotes and provides new insight into the relationships between the three domains: Bacteria, Archaea and Eukaryotes...
  43. pmc Transformation of members of the genus Haloarcula with shuttle vectors based on Halobacterium halobium and Haloferax volcanii plasmid replicons
    S W Cline
    Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
    J Bacteriol 174:1076-80. 1992
    ..Both Haloarcula vallismortis and Haloarcula hispanica exhibit previously unreported complex life cycles and are therefore significant as genetically approachable models of cellular differentiation within the Archaea...
  44. ncbi request reprint Complete nucleotide sequence of the Sulfolobus islandicus multicopy plasmid pRN1
    P J Keeling
    Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
    Plasmid 35:141-4. 1996
    ..The location of a cop homologue upstream of a primase-like gene in pRN1 suggests that it controls DNA replication in a manner similar to these eubacterial plasmids, but does so using a mixture of components from plasmids and viruses...
  45. pmc The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea
    E F Mongodin
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 102:18147-52. 2005
    ..The impact of these modular adaptive elements on the cell biology and ecology of S. ruber is substantial, affecting salt adaptation, bioenergetics, and photobiology...
  46. ncbi request reprint Molecular evolution: recent cases of spliceosomal intron gain?
    J M Logsdon
    Program in Evolutionary Biology Canadian Institute for Advanced Research Department of Biochemistry Dalhousie University Halifax, Nova Scotia, Canada B3H 4H7
    Curr Biol 8:R560-3. 1998
    ..Few clear examples of recent intron gains have been well documented, but two such cases have now been reported, one with possible identification of the source of the intron...
  47. doi request reprint Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments
    J E Koenig
    Dalhousie University Department of Biochemistry and Molecular Biology, 5850 College Street Halifax, Nova Scotia, Canada B3H 1X5
    Environ Microbiol 10:1024-38. 2008
    ..Finally, the two most environmentally similar sample sites considered in this study display the greatest overlap of cassette types, consistent with the hypothesis that cassette genes encode adaptive proteins...
  48. pmc 3-hydroxy-3-methylglutaryl coenzyme A reductase of Sulfolobus solfataricus: DNA sequence, phylogeny, expression in Escherichia coli of the hmgA gene, and purification and kinetic characterization of the gene product
    D A Bochar
    Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
    J Bacteriol 179:3632-8. 1997
    ..Unlike other HMG-CoA reductases, the enzyme was stable at 90 degrees C and was optimally active at pH 5.5 and 85 degrees C...
  49. pmc Evolutionary analysis of the hisCGABdFDEHI gene cluster from the archaeon Sulfolobus solfataricus P2
    R L Charlebois
    Department of Biology, University of Ottawa, Ontario, Canada
    J Bacteriol 179:4429-32. 1997
    ..Results of phylogenetic analysis of the coding regions in the putative operon give conflicting evolutionary histories for individual his genes...
  50. ncbi request reprint Sulfolobus islandicus plasmids pRN1 and pRN2 share distant but common evolutionary ancestry
    P J Keeling
    Department of Biology, Indiana University, Bloomington 47405, USA
    Extremophiles 2:391-3. 1998
    ..Two of these reading frames are likely related to replication, one encoding a large protein with a helicase domain similar to viral helicases, and the other a copy number control protein, CopG...