The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods

BMC Evolutionary Biology

Volumn 8, Issue 1, 2008, Pages

  McCann, Angela ^a   Cotton, James A ^a   McInerney, James O ^a  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA; RNA 16S;

ALGORITHM; ARTICLE; CORRELATION ANALYSIS; GENE; GENE DUPLICATION; GENE LOSS; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOME; HORIZONTAL GENE TRANSFER; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; ARCHAEAL GENOME; BIOLOGICAL MODEL; BIOLOGY; DNA SEQUENCE; GENETIC DATABASE; GENETICS; GENOMICS; METHODOLOGY; MOLECULAR EVOLUTION; RNA GENE; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENES, RRNA; GENOME, ARCHAEAL; GENOMICS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 57049148533     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-8-312     Document Type: Article

References (51)

1. COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. P Janssen AJ Enright B Audit I Cases L Goldovsky N Harte V Kunin CA Ouzounis, Bioinformatics (Oxford, England) 2003 19 11 1451 1452 12874064
2. Analytical methods for detecting paralogy in molecular datasets. JA Cotton, Methods in enzymology 2005 395 700 724 15865991
3. Discordance of species trees with their most likely gene trees. JH Degnan NA Rosenberg, PLoS genetics 2006 2 5 e68 16733550
4. Genes and homology. C Webber CP Ponting, Curr Biol 2004 14 9 R332 333 15120081
5. Phylogenetic classification and the universal tree. WF Doolittle, Science 1999 284 5423 2124 2129 10381871
6. Universal trees based on large combined protein sequence data sets. JR Brown CJ Douady MJ Italia WE Marshall MJ Stanhope, Nature genetics 2001 28 3 281 285 11431701
7. Toward automatic reconstruction of a highly resolved tree of life. FD Ciccarelli T Doerks C von Mering CJ Creevey B Snel P Bork, Science 2006 311 5765 1283 1287 16513982
8. Genome-scale approaches to resolving incongruence in molecular phylogenies. A Rokas BL Williams N King SB Carroll, Nature 2003 425 6960 798 804 14574403
9. Genome-scale phylogeny and the detection of systematic biases. MJ Phillips F Delsuc D Penny, Mol Biol Evol 2004 21 7 1455 1458 15084674
10. Whole genome-based phylogenetic analysis of free-living microorganisms. ST Fitz-Gibbon CH House, Nucleic acids research 1999 27 21 4218 4222 10518613
11. Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. JA Lake MC Rivera, Mol Biol Evol 2004 21 4 681 690 14739244
12. Genome phylogeny based on gene content. B Snel P Bork MA Huynen, Nature genetics 1999 21 1 108 110 9916801
13. Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences. AF Auch SR Henz BR Holland M Goker, BMC bioinformatics 2006 7 350 16854218
14. Geobiological analysis using whole genome-based tree building applied to the Bacteria, Archaea, and Eukarya. CH House B Runnegar S Fitz-Gibbon, Geobiology 2003 1 15 26
15. Does a tree-like phylogeny only exist at the tips in the prokaryotes? CJ Creevey DA Fitzpatrick GK Philip RJ Kinsella MJ O'Connell MM Pentony SA Travers M Wilkinson JO McInerney, Proceedings 2004 271 1557 2551 2558 15615680
16. Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales. DA Fitzpatrick CJ Creevey JO McInerney, Mol Biol Evol 2006 23 1 74 85 16151187
17. How much can evolved characters tell us about the tree that generated them? E Mossel M Steel, Mathematics of evolution and phylogeny New York: Oxford University Press, Gascuel O, 2005 384 412
18. On the desirability of models for inferring genome phylogenies. JO McInerney, Trends in microbiology 2006 14 1 1 2 16271477
19. The ring of life provides evidence for a genome fusion origin of eukaryotes. MC Rivera JA Lake, Nature 2004 431 7005 152 155 15356622
20. SHOT: a web server for the construction of genome phylogenies. JO Korbel B Snel MA Huynen P Bork, Trends Genet 2002 18 3 158 162 11858840
21. Clann: investigating phylogenetic information through supertree analyses. CJ Creevey JO McInerney, Bioinformatics (Oxford, England) 2005 21 3 390 392 15374874
22. On conditioned reconstruction, gene content data, and the recovery of fusion genomes. CD Bailey MG Fain P Houde, Mol Phylogenet Evol 2006 39 1 263 270 16414287
23. MultiPhyl: a high-throughput phylogenomics webserver using distributed computing. TM Keane TJ Naughton JO McInerney, Nucleic acids research 2007 35 Web Server W33 37 17553837
24. MODELTEST: testing the model of DNA substitution. D Posada KA Crandall, Bioinformatics (Oxford, England) 1998 14 9 817 818 9918953
25. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Felsenstein, Journal of molecular evolution 1981 17 6 368 376 7288891
26. Are combined analyses better than single gene phylogenies? A case study using SSU rDNA and rbcL sequence comparisons in the Zygnematophyceae (Streptophyta). AA Gontcharov B Marin M Melkonian, Mol Biol Evol 2004 21 3 612 624 14739253
27. Nuclear and nucleomorph SSU rDNA phylogeny in the Cryptophyta and the evolution of cryptophyte diversity. K Hoef-Emden B Marin M Melkonian, Journal of molecular evolution 2002 55 2 161 179 12107593
28. The shape of supertrees to come: tree shape related properties of fourteen supertree methods. M Wilkinson JA Cotton C Creevey O Eulenstein SR Harris FJ Lapointe C Levasseur JO McInerney D Pisani JL Thorley, Systematic biology 2005 54 3 419 431 16012108
29. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic acids research 1997 25 17 3389 3402 9254694
30. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucleic acids research 1994 22 22 4673 4680 7984417
31. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. J Castresana, Mol Biol Evol 2000 17 4 540 552 10742046
32. A randomization test for phylogenetic information in systematic data. Archie, Systematic Zoology 1989 38 251 278
33. Could a cladogram this short have arisen by chance alone? On permutation tests for cladistic structure. DP Faith PS Cranston, Cladistics 1991 7 1 28
34. Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. JA Lake, Proceedings of the National Academy of Sciences of the United States of America 1994 91 4 1455 1459 8108430
35. Recovering evolutionary trees under a more realistic model of sequence evolution. PJ Lockhart MA Steel MD Hendy D Penny, Molecular biology and evolution 1994 11 4 605 612
36. Conditioned genome reconstruction: how to avoid choosing the conditioning genome. M Spencer D Bryant E Susko, Systematic biology 2007 56 1 25 43 17366135
37. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. O Gascuel, Mol Biol Evol 1997 14 7 685 695 9254330
38. PHYLIP v3.6. J Felsenstein, Available from Author 2003
39. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. I Letunic P Bork, Bioinformatics (Oxford, England) 2007 23 1 127 128 17050570
40. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. JR Cole B Chai TL Marsh RJ Farris Q Wang SA Kulam S Chandra DM McGarrell TM Schmidt GM Garrity, Nucleic acids research 2003 31 1 442 443 12520046
41. PAUP *: Phylogenetic analysis using parsimony (* and other methods), version 4.0b 10. DL Swofford, Sinauer Associates Sunderland, Massachusetts 2003 18428704
42. Comparison of phylogenetic trees. DR Robinson LR Foulds, Mathematical Bioisciences 1981 53 131 147
43. TreeView: an application to display phylogenetic trees on personal computers. RD Page, Comput Appl Biosci 1996 12 4 357 358 8902363
44. Treemap: A Macintosh Program for the analysis of how dependent phylogenies are related, by cophylogeny mapping. MAPR Charleston, 2002
45. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. HP Klenk RA Clayton JF Tomb O White KE Nelson KA Ketchum RJ Dodson M Gwinn EK Hickey JD Peterson, Nature 1997 390 6658 364 370 9389475
46. Genome evolution at the genus level: comparison of three complete genomes of hyperthermophilic archaea. O Lecompte R Ripp V Puzos-Barbe S Duprat R Heilig J Dietrich JC Thierry O Poch, Genome research 2001 11 6 981 993 11381026
47. The neighbor-joining method: a new method for reconstructing phylogenetic trees. N Saitou M Nei, Mol Biol Evol 1987 4 4 406 425 3447015
48. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. AI Slesarev KV Mezhevaya KS Makarova NN Polushin OV Shcherbinina VV Shakhova GI Belova L Aravind DA Natale IB Rogozin, Proceedings of the National Academy of Sciences of the United States of America 2002 99 7 4644 4649 11930014
49. Global extent of horizontal gene transfer. IG Choi SH Kim, Proceedings of the National Academy of Sciences of the United States of America 2007 104 11 4489 4494 17360551
50. The prokaryotic tree of life: past, present. and future? JO McInerney JA Cotton D Pisani, Trends in ecology & evolution (Personal edition) 2008 23 5 276 281 18367290
51. The tree of one percent. T Dagan W Martin, Genome biology 2006 7 10 118 17081279