Ford Doolittle

Summary

Affiliation: Dalhousie University
Country: Canada

Publications

  1. ncbi request reprint Distinguishing between "function" and "effect" in genome biology
    W Ford Doolittle
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
    Genome Biol Evol 6:1234-7. 2014
  2. pmc Is junk DNA bunk? A critique of ENCODE
    W Ford Doolittle
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 4R2
    Proc Natl Acad Sci U S A 110:5294-300. 2013
  3. doi request reprint Population genomics: how bacterial species form and why they don't exist
    W Ford Doolittle
    Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, PO Box 15000, Halifax, Nova Scotia, Canada B3H 4R2
    Curr Biol 22:R451-3. 2012
  4. pmc Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species
    Boris A Legault
    Evolutionary Genomics Group, Division de Microbiologia, Universidad Miguel Hernandez, Apartado 18, San Juan 03550, Alicante, Spain
    BMC Genomics 7:171. 2006
  5. pmc Evolution of rhodopsin ion pumps in haloarchaea
    Adrian K Sharma
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    BMC Evol Biol 7:79. 2007
  6. 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
  7. pmc Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio
    Yan Boucher
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
    BMC Evol Biol 6:3. 2006
  8. pmc ACID: annotation of cassette and integron data
    Michael J Joss
    Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02139, USA
    BMC Bioinformatics 10:118. 2009
  9. pmc Genomics and the bacterial species problem
    W Ford Doolittle
    Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, Canada B3H 1X5
    Genome Biol 7:116. 2006
  10. doi request reprint On the origin of prokaryotic species
    W Ford Doolittle
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
    Genome Res 19:744-56. 2009

Detail Information

Publications102 found, 100 shown here

  1. ncbi request reprint Distinguishing between "function" and "effect" in genome biology
    W Ford Doolittle
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
    Genome Biol Evol 6:1234-7. 2014
    ..Although it will very often be difficult or impossible to establish function (strictly defined), it should not automatically be assumed. We enjoin genomicists in particular to pay greater attention to parsing biological effects. ..
  2. pmc Is junk DNA bunk? A critique of ENCODE
    W Ford Doolittle
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 4R2
    Proc Natl Acad Sci U S A 110:5294-300. 2013
    ..A larger theoretical framework, embracing informational and structural roles for DNA, neutral as well as adaptive causes of complexity, and selection as a multilevel phenomenon, is needed...
  3. doi request reprint Population genomics: how bacterial species form and why they don't exist
    W Ford Doolittle
    Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, PO Box 15000, Halifax, Nova Scotia, Canada B3H 4R2
    Curr Biol 22:R451-3. 2012
    ..Recent work shows that data taken as evidence supporting the former may be explained by the latter, raising further problems for the idea of bacterial 'species'...
  4. pmc Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species
    Boris A Legault
    Evolutionary Genomics Group, Division de Microbiologia, Universidad Miguel Hernandez, Apartado 18, San Juan 03550, Alicante, Spain
    BMC Genomics 7:171. 2006
    ..Similar studies carried out in other extreme environments have revealed very little diversity in gene content among the cell lineages present...
  5. pmc Evolution of rhodopsin ion pumps in haloarchaea
    Adrian K Sharma
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    BMC Evol Biol 7:79. 2007
    ..In this initial study, we assess the roles of LGT and gene loss in the evolution of haloarchaeal rhodopsin ion pump genes, using phylogenetics and comparative genomics approaches...
  6. 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...
  7. pmc Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio
    Yan Boucher
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
    BMC Evol Biol 6:3. 2006
    ..We describe an approach to systematically isolate, sequence and annotate large integron gene cassette arrays from bacterial strains...
  8. pmc ACID: annotation of cassette and integron data
    Michael J Joss
    Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02139, USA
    BMC Bioinformatics 10:118. 2009
    ..These genetic elements have been overlooked in comparison to other vectors that facilitate lateral gene transfer between microorganisms...
  9. pmc Genomics and the bacterial species problem
    W Ford Doolittle
    Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, Canada B3H 1X5
    Genome Biol 7:116. 2006
    ....
  10. doi request reprint On the origin of prokaryotic species
    W Ford Doolittle
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
    Genome Res 19:744-56. 2009
    ..These questions can, however, be reformulated so that metagenomic methods and thinking will meaningfully address the biological patterns and processes whose understanding is our ultimate target...
  11. doi request reprint Microbial evolution: stalking the wild bacterial species
    W Ford Doolittle
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 1X5
    Curr Biol 18:R565-7. 2008
    ..But, for bacteria, 'species' remains undefined and undefinable...
  12. ncbi request reprint Evolution: reducible complexity -- the case for bacterial flagella
    W Ford Doolittle
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
    Curr Biol 17:R510-2. 2007
    ..A recent paper, which will surely figure centrally in the debate between evolutionists and Intelligent Design creationists, proposes a (perhaps too simple) scheme for the evolution of bacterial flagella...
  13. pmc Pattern pluralism and the Tree of Life hypothesis
    W Ford Doolittle
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5
    Proc Natl Acad Sci U S A 104:2043-9. 2007
    ....
  14. pmc 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
    W Ford Doolittle
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Philos Trans R Soc Lond B Biol Sci 364:2221-8. 2009
    ..I will propose a more general and relaxed evolutionary theory and point out why anti-evolutionists should take no comfort from disproof of the TOL hypothesis...
  15. 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...
  16. 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...
  17. 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...
  18. 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...
  19. 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...
  20. 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...
  21. 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
    ....
  22. 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...
  23. 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...
  24. 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...
  25. 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...
  26. 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...
  27. 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...
  28. 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...
  29. 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...
  30. pmc Weighted genome trees: refinements and applications
    Uri Gophna
    Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia
    J Bacteriol 187:1305-16. 2005
    ..Comparisons of results obtained with different methods can provide further clues to major events and processes in genome evolution...
  31. 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...
  32. 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
    ....
  33. 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...
  34. 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)...
  35. 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...
  36. 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
    ....
  37. 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...
  38. 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...
  39. 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...
  40. 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...
  41. 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...
  42. ncbi request reprint Lateral transfer of an EF-1alpha gene: origin and evolution of the large subunit of ATP sulfurylase in eubacteria
    Yuji Inagaki
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Curr Biol 12:772-6. 2002
    ..To our knowledge, this is the first unequivocal case of LGT followed by functional modification to be described; this mechanism could be a potentially important force in establishing genes with novel functions in genomes...
  43. pmc Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement
    Dave MacLeod
    GenomeAtlantic, 1721 Lower Water Street, Suite 401, Halifax, NS, B3J 1S5, Canada
    BMC Evol Biol 5:27. 2005
    ..Indeed, even when the true history is a mixture of vertical descent for some genes and lateral gene transfer (LGT) for others, such methods produce unique topologies...
  44. 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...
  45. 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...
  46. 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...
  47. 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...
  48. pmc Evidence for existence of "mesotogas," members of the order Thermotogales adapted to low-temperature environments
    Camilla L Nesbø
    Dalhousie University, Biochemistry and Molecular Biology, 5850 College Street, Halifax, Nova Scotia B3H 1X5, Canada
    Appl Environ Microbiol 72:5061-8. 2006
    ....
  49. ncbi request reprint Some thoughts on the tree of life
    W Ford Doolittle
    Canadian Institute for Advanced Research Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia
    Harvey Lect 99:111-28. 2003
  50. pmc Integron gene cassettes and degradation of compounds associated with industrial waste: the case of the Sydney tar ponds
    Jeremy E Koenig
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    PLoS ONE 4:e5276. 2009
    ..Nevertheless, our cassette library provides a snapshot of a complex evolutionary process involving integron-meditated LGT likely to be important in natural bioremediation...
  51. pmc Computing prokaryotic gene ubiquity: rescuing the core from extinction
    Robert L Charlebois
    Genome Atlantic, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 1X5, Canada
    Genome Res 14:2469-77. 2004
    ..Cores, however delimited, preferentially contain informational rather than operational genes; we present a new hypothesis for why this might be so...
  52. 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...
  53. 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...
  54. 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...
  55. 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...
  56. 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...
  57. ncbi request reprint Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability
    Christophe J Douady
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 20:248-54. 2003
    ..Both posterior probabilities and bootstrap supports are of great interest to phylogeny as potential upper and lower bounds of node reliability, but they are surely not interchangeable and cannot be directly compared...
  58. pmc Evidence for Golgi bodies in proposed 'Golgi-lacking' lineages
    Joel B Dacks
    Canadian Institute for Advanced Research Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia
    Proc Biol Sci 270:S168-71. 2003
    ..This substantiates the suggestion that there are no extant primitively 'Golgi-lacking' lineages, and that this apparatus was present in the last common eukaryotic ancestor, but has been altered beyond recognition several times...
  59. ncbi request reprint A hyperconserved protein in Prochlorococcus and marine Synechococcus
    Olga Zhaxybayeva
    Department of Biochemistry and Molecular Biology, Dalhousie University, NS, Canada
    FEMS Microbiol Lett 274:30-4. 2007
    ..Comparative analyses indicate that the hyperconserved protein, which may be involved in interactions with nucleic acids, is under stabilizing selection and has resided in these genomes since the last common ancestor of the group...
  60. ncbi request reprint Novel syntaxin gene sequences from Giardia, Trypanosoma and algae: implications for the ancient evolution of the eukaryotic endomembrane system
    Joel B Dacks
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, N S, B3H 4H7, Canada
    J Cell Sci 115:1635-42. 2002
    ..These speak to ancient events in the evolution of the syntaxin system and emphasize the universal role of the syntaxins in the eukaryotic intracellular compartment system...
  61. pmc Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events
    Olga Zhaxybayeva
    Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
    Genome Res 16:1099-108. 2006
    ..However, in interphylum as compared to intraphylum transfers, the proportion of metabolic (operational) gene transfers increases, while the proportion of informational gene transfers decreases...
  62. doi request reprint Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environments
    Adrian K Sharma
    Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St, Halifax, Nova Scotia, Canada, B3H 1X5
    Environ Microbiol 10:1039-56. 2008
    ....
  63. pmc The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea
    Camilla L Nesbø
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    J Bacteriol 191:1974-8. 2009
    ..Firmicutes emerge as the principal LGT partner. Twenty-six percent of phylogenetic trees suggest LGT with this group, while 13% of the open reading frames indicate LGT with Archaea...
  64. doi request reprint Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria
    Adrian K Sharma
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    ISME J 3:726-37. 2009
    ..The co-occurrence of an acI organism with a specific ActR variant in a mixed culture supports our hypothesis...
  65. pmc On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales
    Olga Zhaxybayeva
    Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, Canada B3H 1X5
    Proc Natl Acad Sci U S A 106:5865-70. 2009
    ....
  66. ncbi request reprint Microbial rhodopsins: functional versatility and genetic mobility
    Adrian K Sharma
    Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St, Halifax, Nova Scotia B3H 1X5, Canada
    Trends Microbiol 14:463-9. 2006
    ....
  67. pmc Recombination in Thermotoga: implications for species concepts and biogeography
    Camilla L Nesbø
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
    Genetics 172:759-69. 2006
    ..We can, however, recast biogeographical questions in terms of the distribution of genes and their alleles...
  68. ncbi request reprint Lateral gene transfer and phylogenetic assignment of environmental fosmid clones
    Camilla L Nesbø
    Department of Biochemistry and Molecular Biology, Dalhousie University and Genome Atlantic, 5850 College Street, Halifax, Nova Scotia, Canada, B3H1X5
    Environ Microbiol 7:2011-26. 2005
    ..In several cases, we can infer co-transfer of functionally related genes, and generate hypotheses about mechanism and ecological significance of transfer...
  69. ncbi request reprint Complex histories of genes encoding 3-hydroxy-3-methylglutaryl-CoenzymeA reductase
    Uri Gophna
    Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 23:168-78. 2006
    ..We demonstrate that even in Vibrio species, where HMGR is not clustered with other genes to form an operon or a metabolic cluster, it is under strong purifying selection...
  70. ncbi request reprint Have archaeal genes contributed to bacterial virulence?
    Uri Gophna
    Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia B3H 1X5, Canada
    Trends Microbiol 12:213-9. 2004
  71. ncbi request reprint Diversity of bacteriorhodopsins in different hypersaline waters from a single Spanish saltern
    R Thane Papke
    Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Building, Halifax, NS B3H 4H7, Canada
    Environ Microbiol 5:1039-45. 2003
    ..In some instances, identical genes were discovered in seemingly different habitats suggesting that some haloarchaea are present over widely varying concentrations of salt...
  72. ncbi request reprint Targeting clusters of transferred genes in Thermotoga maritima
    Camilla L Nesbø
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
    Environ Microbiol 5:1144-54. 2003
    ....
  73. ncbi request reprint Frequent recombination in a saltern population of Halorubrum
    R Thane Papke
    Department of Biochemistry and Molecular Biology, Dalhousie University, 5859 University Avenue, Halifax, Nova Scotia B3H 4H7, Canada
    Science 306:1928-9. 2004
    ..We used multi-locus sequence typing to demonstrate that haloarchaea exchange genetic information promiscuously, exhibiting a degree of linkage equilibrium approaching that of a sexual population...
  74. ncbi request reprint Origins and evolution of isoprenoid lipid biosynthesis in archaea
    Yan Boucher
    Canadian Institute for Advanced Research, Dalhousie University, Halifax, Nova Scotia, 5859 University Avenue, B3H 4H7 Canada
    Mol Microbiol 52:515-27. 2004
    ....
  75. ncbi request reprint Evolution of the RNA polymerase B' subunit gene (rpoB') in Halobacteriales: a complementary molecular marker to the SSU rRNA gene
    David A Walsh
    Canadian Institute for Advanced Research Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 21:2340-51. 2004
    ..In addition, we present a valuable phylogenetic framework encompassing a broad diversity of Halobacteriales, in which novel sequences can be inserted for evolutionary, ecological, or taxonomic investigations...
  76. ncbi request reprint Phylogenetic reconstruction and lateral gene transfer
    Eric Bapteste
    Canadian Institute for Advanced Research and Genome Atlantic, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Trends Microbiol 12:406-11. 2004
    ..We suggest instead a more complex but more natural framework for classification, which we call the Synthesis of Life...
  77. pmc Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes
    Yan Boucher
    Dalhousie University, Department of Biochemistry, Sir Charles Tupper Building, 5859 University Avenue, Room 8C, Halifax, Nova Scotia, B3H 4H7 Canada
    J Bacteriol 186:3980-90. 2004
    ..We suggest that intragenomic heterogeneity of rRNA operons is an ancient and stable trait in several lineages of the Halobacteriales. The impact of this phenomenon on the taxonomy of extremely halophilic archaea is discussed...
  78. ncbi request reprint The real 'domains' of life
    David A Walsh
    Genome Atlantic, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Curr Biol 15:R237-40. 2005
  79. ncbi request reprint Archaeal diversity along a soil salinity gradient prone to disturbance
    David A Walsh
    Canadian Institute for Advanced Research Program in Evolutionary Biology and Genome Atlantic, Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia B3H1X5, Canada
    Environ Microbiol 7:1655-66. 2005
    ..We speculate that ecosystem disturbance -- in the form of salinity fluctuations -- is one mechanism for maintaining a diverse community of haloarchaea at Salt Spring...
  80. ncbi request reprint Lateral gene transfer and the origins of prokaryotic groups
    Yan Boucher
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry, Sir Charles Tupper Medical Building, 5859 University Avenue, Halifax, Nova Scotia, Canada, B3H 4H7
    Annu Rev Genet 37:283-328. 2003
    ..Sometimes transfer of complex gene clusters may have been involved, whereas other times separate exchanges of many genes must be invoked...
  81. ncbi request reprint Evolutionary plasticity of methionine biosynthesis
    Uri Gophna
    Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5
    Gene 355:48-57. 2005
    ..This study illustrates how diverse molecular solutions can fulfill a conserved function in living beings...
  82. 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...
  83. 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...
  84. ncbi request reprint Molecular and phylogenetic characterization of syntaxin genes from parasitic protozoa
    Joel B Dacks
    Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS, Canada B3H 1X5
    Mol Biochem Parasitol 136:123-36. 2004
    ..Because of their integral role in membrane trafficking, the syntaxin genes represent a valuable potential molecular marker for the experimental study of the endomembrane system of disease-causing protists...
  85. pmc Active self-splicing group I introns in 23S rRNA genes of hyperthermophilic bacteria, derived from introns in eukaryotic organelles
    Camilla L Nesbø
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5
    Proc Natl Acad Sci U S A 100:10806-11. 2003
    ..In vivo, their introns must be spliced at temperatures approaching 90 degrees C, making them the most thermostable natural ribozymes so far described. We demonstrate that at least some of these introns can also self-splice in vitro...
  86. pmc Suppressive subtractive hybridization detects extensive genomic diversity in Thermotoga maritima
    Camilla L Nesbø
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    J Bacteriol 184:4475-88. 2002
    ....
  87. pmc Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity
    Yuji 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 30:532-44. 2002
    ..We assess the feasibility of this alternative binding orientation with a triplet stop codon and the eRF1 domain 1 structures using molecular modeling techniques...
  88. 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...
  89. 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...
  90. 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...
  91. 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...
  92. ncbi request reprint Phage evolution: new worlds of genomic diversity
    R Thane Papke
    Department of Biochemistry, Canadian Institute for Advanced Research, Dalhousie University, B3H 4H7, Halifax, Nova Scotia, Canada
    Curr Biol 13:R606-7. 2003
    ..A recent comparative survey of genomes of phages infecting mycobacteria reveals a vast combinatorial network of gene rearrangements and may provide general models for pattern and process in genome evolution...
  93. ncbi request reprint Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus
    Uri Gophna
    Department of Molecular Microbiology and Biotechnology, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Trends Microbiol 14:64-9. 2006
    ..Although there might be little evidence for the extensive recent transfer of genes, we demonstrate that ancient lateral gene acquisition has shaped the B. bacteriovorus genome to a great extent...
  94. pmc Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies
    Rebecca J Case
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Biofouling and Bio Innovation, University of New South Wales, Randwick, Sydney NSW 2052, Australia
    Appl Environ Microbiol 73:278-88. 2007
    ..This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoB could complement the information provided by the 16S rRNA gene...
  95. ncbi request reprint Molecular phylogeny of three oxymonad genera: Pyrsonympha, Dinenympha and Oxymonas
    Shigeharu Moriya
    Bioscience Technology Center, RIKEN Institute, 2 1, Hirosawa, Wako, Saitama 351 0198, Japan
    J Eukaryot Microbiol 50:190-7. 2003
    ..Our biogeographical analysis with Japanese and Canadian Pyrsonympha and Dinenympha suggests that these genera diverged before the separation of termites that inhabit Eastern Asia and Western North America...
  96. ncbi request reprint Something new under the sea
    Yan Boucher
    Nature 417:27-8. 2002
  97. ncbi request reprint Prokaryotic evolution in light of gene transfer
    J Peter Gogarten
    Department of Molecular and Cell Biology, University of Connecticut, CT, USA
    Mol Biol Evol 19:2226-38. 2002
    ....
  98. ncbi request reprint The chaperonin genes of jakobid and jakobid-like flagellates: implications for eukaryotic evolution
    John M Archibald
    Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
    Mol Biol Evol 19:422-31. 2002
    ..In phylogenetic trees constructed from CCTalpha protein sequences, R. americana (but not M. jakobiformis) shows a weak but consistent affinity for the Heterolobosea and Euglenozoa...
  99. pmc Systematic overestimation of gene gain through false diagnosis of gene absence
    Olga Zhaxybayeva
    Genome Biol 8:402. 2007
    ..The usual BLAST-based methods for assessing gene presence and absence lead to systematic overestimation of within-species gene gain by lateral transfer...
  100. pmc Searching for species in haloarchaea
    R Thane Papke
    Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269 3125, USA
    Proc Natl Acad Sci U S A 104:14092-7. 2007
    ..Arbitrary criteria might have limited practical use, but still must be agreed upon by the community...