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The tree of one percent
Tal Dagan, William Martin
Genome Biol. 2006; 7(10): 118. Published online 2006 November 1. doi: 10.1186/gb-2006-7-10-118
PMCID:
PMC1794558
Abstract Full Text PDF–435K Supplementary Material
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 Is Cited by the Following 38 Articles in this Archive:
Molecular musings in microbial ecology and evolution
Rebecca J Case, Yan Boucher
Biol Direct. 2011; 6: 58. Published online 2011 November 10. doi: 10.1186/1745-6150-6-58
PMCID:
PMC3254073
Abstract Full Text PDF–314K
The public goods hypothesis for the evolution of life on Earth
James O McInerney, Davide Pisani, Eric Bapteste, Mary J O'Connell
Biol Direct. 2011; 6: 41. Published online 2011 August 23. doi: 10.1186/1745-6150-6-41
PMCID:
PMC3179745
Abstract Full Text PDF–796K
Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer
Christopher J. Creevey, Tobias Doerks, David A. Fitzpatrick, Jeroen Raes, Peer Bork
PLoS One. 2011; 6(8): e22099. Published online 2011 August 5. doi: 10.1371/journal.pone.0022099
PMCID:
PMC3151239
Abstract Full Text PDF–947K Supplementary Material
Phylogenomics-Based Reconstruction of Protozoan Species Tree
Kary A.C.S. Ocaña, Alberto M.R. Dávila
Evol Bioinform Online. 2011; 7: 107–121. Published online 2011 July 31. doi: 10.4137/EBO.S6861
PMCID:
PMC3153122
Abstract Full Text PDF–1.0M Supplementary Material
Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli
Julie Beauregard-Racine, Cédric Bicep, Klaus Schliep, Philippe Lopez, François-Joseph Lapointe, Eric Bapteste
Biol Direct. 2011; 6: 39. Published online 2011 July 20. doi: 10.1186/1745-6150-6-39
PMCID:
PMC3160433
Abstract Full Text PDF–977K Supplementary Material
How stands the Tree of Life a century and a half after The Origin?
Maureen A O'Malley, Eugene V Koonin
Biol Direct. 2011; 6: 32. Published online 2011 June 30. doi: 10.1186/1745-6150-6-32
PMCID:
PMC3158114
Abstract Full Text PDF–521K
Telling the whole story in a 10,000-genome world
Robert G Beiko
Biol Direct. 2011; 6: 34. Published online 2011 June 30. doi: 10.1186/1745-6150-6-34
PMCID:
PMC3158115
Abstract Full Text PDF–3.8M
Early evolution without a tree of life
William F Martin
Biol Direct. 2011; 6: 36. Published online 2011 June 30. doi: 10.1186/1745-6150-6-36
PMCID:
PMC3158116
Abstract Full Text PDF–2.2M
Evaluating Phylogenetic Congruence in the Post-Genomic Era
Jessica W. Leigh, François-Joseph Lapointe, Philippe Lopez, Eric Bapteste
Genome Biol Evol. 2011; 3: 571–587. Published online 2011 June 28. doi: 10.1093/gbe/evr050
PMCID:
PMC3156567
Abstract Full Text PDF–1000K
Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses
Tom A. Williams, T. Martin Embley, Eva Heinz
PLoS One. 2011; 6(6): e21080. Published online 2011 June 16. doi: 10.1371/journal.pone.0021080
PMCID:
PMC3116878
Abstract Full Text PDF–1.2M Supplementary Material
A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes
Diana Chernikova, Sam Motamedi, Miklós Csürös, Eugene V Koonin, Igor B Rogozin
Biol Direct. 2011; 6: 26. Published online 2011 May 19. doi: 10.1186/1745-6150-6-26
PMCID:
PMC3125394
Abstract Full Text PDF–1.2M Supplementary Material
The Giant Cafeteria roenbergensis Virus That Infects a Widespread Marine Phagocytic Protist Is a New Member of the Fourth Domain of Life
Philippe Colson, Gregory Gimenez, Mickaël Boyer, Ghislain Fournous, Didier Raoult
PLoS One. 2011; 6(4): e18935. Published online 2011 April 29. doi: 10.1371/journal.pone.0018935
PMCID:
PMC3084725
Abstract Full Text PDF–779K Supplementary Material
The advantages and disadvantages of horizontal gene transfer and the emergence of the first species
Aaron A Vogan, Paul G Higgs
Biol Direct. 2011; 6: 1. Published online 2011 January 3. doi: 10.1186/1745-6150-6-1
PMCID:
PMC3043529
Abstract Full Text PDF–381K
Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths
Thorsten Kloesges, Ovidiu Popa, William Martin, Tal Dagan
Mol Biol Evol. 2011 February; 28(2): 1057–1074. Published online 2010 November 8. doi: 10.1093/molbev/msq297
PMCID:
PMC3021791
Abstract Full Text PDF–1.8M Supplementary Material
Save the tree of life or get lost in the woods
Ruben E Valas, Philip E Bourne
Biol Direct. 2010; 5: 44. Published online 2010 July 1. doi: 10.1186/1745-6150-5-44
PMCID:
PMC2910001
Abstract Full Text PDF–1000K Supplementary Material
Prokaryotic evolution and the tree of life are two different things
Eric Bapteste, Maureen A O'Malley, Robert G Beiko, Marc Ereshefsky, J Peter Gogarten, Laura Franklin-Hall, François-Joseph Lapointe, John Dupré, Tal Dagan, Yan Boucher, William Martin
Biol Direct. 2009; 4: 34. Published online 2009 September 29. doi: 10.1186/1745-6150-4-34
PMCID:
PMC2761302
Abstract Full Text PDF–403K
On the need for widespread horizontal gene transfers under genome size constraint
Hervé Isambert, Richard R Stein
Biol Direct. 2009; 4: 28. Published online 2009 August 25. doi: 10.1186/1745-6150-4-28
PMCID:
PMC2740843
Abstract Full Text PDF–528K
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
Philos Trans R Soc Lond B Biol Sci. 2009 August 12; 364(1527): 2221–2228. doi: 10.1098/rstb.2009.0032
PMCID:
PMC2873000
Abstract Full Text PDF–184K
Genome beginnings: rooting the tree of life
James A. Lake, Ryan G. Skophammer, Craig W. Herbold, Jacqueline A. Servin
Philos Trans R Soc Lond B Biol Sci. 2009 August 12; 364(1527): 2177–2185. doi: 10.1098/rstb.2009.0035
PMCID:
PMC2873003
Abstract Full Text PDF–400K
Gene and genome trees conflict at many levels
Leanne S. Haggerty, Fergal J. Martin, David A. Fitzpatrick, James O. McInerney
Philos Trans R Soc Lond B Biol Sci. 2009 August 12; 364(1527): 2209–2219. doi: 10.1098/rstb.2009.0042
PMCID:
PMC2873008
Abstract Full Text PDF–1.1M
Search for a 'Tree of Life' in the thicket of the phylogenetic forest
Pere Puigbò, Yuri I Wolf, Eugene V Koonin
J Biol. 2009; 8(6): 59. Published online 2009 July 13. doi: 10.1186/jbiol159
PMCID:
PMC2737373
Abstract Full Text PDF–3.3M Supplementary Material
Trees in the Web of Life
Kristen S Swithers, J Peter Gogarten, Gregory P Fournier
J Biol. 2009; 8(6): 54. Published online 2009 July 13. doi: 10.1186/jbiol160
PMCID:
PMC2737374
Abstract Full Text PDF–602K
Molecular Data are Transforming Hypotheses on the Origin and Diversification of Eukaryotes
Yonas I. Tekle, Laura Wegener Parfrey, Laura A. Katz
Bioscience. Author manuscript; available in PMC 2010 September 13.
Published in final edited form as: Bioscience. 2009 June; 59(6): 471–481. doi: 10.1525/bio.2009.59.6.5
PMCID:
PMC2938078
Abstract Full Text PDF–639K
Analysis of Rare Genomic Changes Does Not Support the Unikont–Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes
Igor B. Rogozin, Malay Kumar Basu, Miklós Csürös, Eugene V. Koonin
Genome Biol Evol. 2009; 1: 99–113. Published online 2009 May 25. doi: 10.1093/gbe/evp011
PMCID:
PMC2817406
Abstract Full Text PDF–674K Supplementary Material
On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales
Olga Zhaxybayeva, Kristen S. Swithers, Pascal Lapierre, Gregory P. Fournier, Derek M. Bickhart, Robert T. DeBoy, Karen E. Nelson, Camilla L. Nesbø, W. Ford Doolittle, J. Peter Gogarten, Kenneth M. Noll
Proc Natl Acad Sci U S A. 2009 April 7; 106(14): 5865–5870. Published online 2009 March 23. doi: 10.1073/pnas.0901260106
PMCID:
PMC2667022
Abstract Full Text PDF–702K Supplementary Material
Darwinian evolution in the light of genomics
Eugene V. Koonin
Nucleic Acids Res. 2009 March; 37(4): 1011–1034. Published online 2009 March. doi: 10.1093/nar/gkp089
PMCID:
PMC2651812
Abstract Full Text PDF–3.8M
The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome
Marina Marcet-Houben, Toni Gabaldón
PLoS ONE. 2009; 4(2): e4357. Published online 2009 February 3. doi: 10.1371/journal.pone.0004357
PMCID:
PMC2629814
Abstract Full Text PDF–280K Supplementary Material
The eocyte hypothesis and the origin of eukaryotic cells
John M. Archibald
Proc Natl Acad Sci U S A. 2008 December 23; 105(51): 20049–20050. Published online 2008 December 17. doi: 10.1073/pnas.0811118106
PMCID:
PMC2629348
Full Text PDF–102K
The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods
Angela McCann, James A Cotton, James O McInerney
BMC Evol Biol. 2008; 8: 312. Published online 2008 November 12. doi: 10.1186/1471-2148-8-312
PMCID:
PMC2592249
Abstract Full Text PDF–556K Supplementary Material
Dealing with incongruence in phylogenomic analyses
Nicolas Galtier, Vincent Daubin
Philos Trans R Soc Lond B Biol Sci. 2008 December 27; 363(1512): 4023–4029. Published online 2008 October 7. doi: 10.1098/rstb.2008.0144
PMCID:
PMC2607408
Abstract Full Text PDF–159K
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