Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement

BMC Evolutionary Biology

Volumn 5, Issue , 2005, Pages

  MacLeod, Dave ^a,b   Charlebois, Robert L ^a,b   Doolittle, Ford ^a,b   Bapteste, Eric ^a,b  

^a Genome Atlantic Canada   (Canada)

^b DALHOUSIE UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

LANGAT VIRUS;

GENETIC MARKER;

ANIMAL; BIOLOGICAL MODEL; BIOLOGY; COMPUTER LANGUAGE; COMPUTER PROGRAM; DNA SEQUENCE; GENE REARRANGEMENT; GENETIC MARKER; HORIZONTAL GENE TRANSFER; MOLECULAR EVOLUTION; PHYLOGENY; PROCEDURES; STATISTICAL MODEL;

ANIMALS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE REARRANGEMENT; GENE TRANSFER, HORIZONTAL; GENETIC MARKERS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; PROGRAMMING LANGUAGES; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 18944369385     PISSN: 14712148     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2148-5-27     Document Type: Article

References (44)

1. Gribaldo S, Philippe H: Ancient phylogenetic relationships. Theor Popul Biol 2002, 61:391-408.
2. Huson DH: SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 1998, 14:68-73.
3. Makarenkov V: T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks. Bioinformatics 2001, 17:664-668.
4. Filee J, Forterre P, Laurent J: The role played by viruses in the evolution of their hosts: a view based on informational protein phylogenies. Res Microbiol 2003, 154:237-243.
5. Lawrence JG, Ochman H: Reconciling the many faces of lateral gene transfer. Trends Microbiol 2002, 10:1-4.
6. Doolittle WF: Phylogenetic classification and the universal tree. Science 1999, 284:2124-2129.
7. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM: Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 1999, 399:323-329.
8. Huang J, Mullapudi N, Sicheritz-Ponten T, Kissinger JC: A first glimpse into the pattern and scale of gene transfer in Apicomplexa. Int J Parasitol 2004, 34:265-274.
9. Andersson JO, Sarchfield SW, Roger AJ: Gene transfers from Nanoarchaeota to an ancestor of Diplomonads and Parabasalids. Mol Biol Evol in press.
10. Andersson JO, Roger AJ: Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes. BMC Evol Biol 2003, 3:14.
11. Daubin V, Gouy M, Perrière G: Bacterial molecular phylogeny using supertree approach. Genome Inform Ser Workshop Genome Inform 2001, 12:155-164.
12. Eulenstein O, Chen D, Burleigh JG, Fernandez-Baca D, Sanderson MJ: Performance of flip supertree construction with a heuristic algorithm. Syst Biol 2004, 53:299-308.
13. Semple C, Daniel P, Hordijk W, Page RD, Steel M: Supertree algorithms for ancestral divergence dates and nested taxa. Bioinformatics 2004, 20:2355-2360.
14. Creevey CJ, McInerney JO: Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 2005, 21(3):390-2.
15. Thorley JL, Page RD: RadCon: phylogenetic tree comparison and consensus. Bioinformatics 2000, 16:486-7.
16. Lapointe FJ, Cucumel G: The average consensus procedure: combination of weighted trees containing identical or overlapping sets of taxa. Syst Biol 1997, 46:306-312.
17. Steel M, Dress AWM, Bocker S: Simple but fundamental limitations on supertree and consensus tree methods. Syst Biol 2000, 49:363-368.
18. Thomas GH, Wills MA, Szekely T: A supertree approach to shorebird phylogeny. BMC Evol Biol 2004, 4:28.
19. Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF: A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 2000, 290:972-977.
20. Gophna U, Doolittle WF, Charlebois RL: Weighted genome trees: refinements and applications. J Bacteriol in press.
21. Bapteste E, Boucher Y, Leigh J, Doolittle WF: Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol 2004, 12:406-411.
22. Zhaxybayeva O, Gogarten JP: An improved probability mapping approach to assess genome mosaicism. BMC Genomics 2003, 4:37.
23. Koski LB, Golding GB: The closest BLAST hit is often not the nearest neighbor. J Mol Evol 2001, 52:540-542.
24. Daubin V, Lerat E, Perrière G: The source of laterally transferred genes in bacterial genomes. Genome Biol 2003, 4:R57.
25. Zhaxybayeva O, Lapierre P, Gogarten JP: Genome mosaicism and organismal lineages. Trends Genet 2004, 20:254-260.
26. Levasseur C, Lapointe FJ: War and peace in phylogenetics: a rejoinder on total evidence and consensus. Syst Biol 2001, 50:881-891.
27. Page RD: GeneTree: comparing gene and species phylogenies using reconciled trees. Bioinformatics 1998, 14:819-20.
28. Shimodaira H: An approximately unbiased test of phylogenetic tree selection. Syst Biol 2002, 51:492-508.
29. Lecointre G, Rachdi L, Darlu P, Denamur E: Escherichia coli molecular phylogeny using the incongruence length difference test. Mol Biol Evol 1998, 15:1685-1695.
30. Walsh DA, Bapteste E, Kamekura M, Doolittle WF: Evolution of the RNA polymerase B' subunit Gene (rpoB') in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. Mol Biol Evol 2004, 21:2340-2351.
31. Zelwer M, Daubin V: Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD test. Mol Phylogenet Evol 2004, 33:687-93.
32. Felsenstein J: Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 40:783-791.
33. Addario-Berry L, Hallett M, Lagergren J: Towards identifying lateral gene transfer events. Pac Symp Biocomput 2003, 8:279-290.
34. Lerat E, Daubin V, Moran NA: From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the gamma-Proteobacteria. PLoS Biol 2003, 1:E19.
35. Moreira D, Philippe H: Molecular phylogeny: pitfalls and progress. Int Microbiol 2000, 3:9-16.
36. Teichmann SA, Mitchison G: Is there a phylogenetic signal in prokaryote proteins? J Mol Evol 1999, 49:98-107.
37. Philippe H, Snell EA, Bapteste E, Lopez P, Holland PW, Casane D: Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol Biol Evol 2004, 21:1740-1752.
38. Ribeiro S, Golding GB: The mosaic nature of the eukaryotic nucleus. Mol Biol Evol 1998, 15:779-788.
39. González V, Bustos P, Ramírez-Romero MA, Medrano-Soto A, Salgado H, Hernández-González I, Hernández-Celis JC, Quintero V, Moreno-Hagelsieb G, Girard L, Rodríguez O, Flores M, Cevallos MA, Collado-Vides J, Romero D, Dávila G: The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments. Genome Biol 2003, 4:R36.
40. Rivera MC, Lake JA: The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 2004, 431:152-155.
41. Lawrence JG: Catalyzing bacterial speciation: correlating lateral transfer with genetic headroom. Syst Biol 2001, 50:479-496.
42. Lawrence JG: Gene transfer in Bacteria: speciation without species? Theoret Pop Biol 2002, 61:449-460.
43. Gogarten JP, Doolittle WF, Lawrence JG: Prokaryotic evolution in light of gene transfer. Mol Biol Evol 2002, 19:2226-2238.
44. Koonin EV, Makarova KS, Aravind L: Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 2001, 55:709-742.