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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

Is Cited by the Following 25 Articles in this Archive:

Lateral gene transfer as a support for the tree of life
Sophie S. Abby, Eric Tannier, Manolo Gouy, Vincent Daubin
Proc Natl Acad Sci U S A. 2012 March 27; 109(13): 4962–4967. Published online 2012 March 13. doi: 10.1073/pnas.1116871109
PMCID:
PMC3323970
Free in PMC on 2012/09/27
An Evolutionary Network of Genes Present in the Eukaryote Common Ancestor Polls Genomes on Eukaryotic and Mitochondrial Origin
Thorsten Thiergart, Giddy Landan, Marc Schenk, Tal Dagan, William F. Martin
Genome Biol Evol. 2012; 4(4): 466–485. Published online 2012 February 21. doi: 10.1093/gbe/evs018
PMCID:
PMC3342870
Abstract Full Text PDF–2.4M
Random Addition Concatenation Analysis: A Novel Approach to the Exploration of Phylogenomic Signal Reveals Strong Agreement between Core and Shell Genomic Partitions in the Cyanobacteria
Apurva Narechania, Richard H. Baker, Ryan Sit, Sergios-Orestis Kolokotronis, Rob DeSalle, Paul J. Planet
Genome Biol Evol. 2012; 4(1): 30–43. Published online 2011 November 16. doi: 10.1093/gbe/evr121
PMCID:
PMC3267395
Abstract Full Text PDF–562K
Origin and evolution of gene families in Bacteria and Archaea
R Eric Collins, Hugh Merz, Paul G Higgs
BMC Bioinformatics. 2011; 12(Suppl 9): S14. Published online 2011 October 5. doi: 10.1186/1471-2105-12-S9-S14
PMCID:
PMC3283305
Abstract Full Text PDF–716K
Biased gene transfer and its implications for the concept of lineage
Cheryl P Andam, J Peter Gogarten
Biol Direct. 2011; 6: 47. Published online 2011 September 23. doi: 10.1186/1745-6150-6-47
PMCID:
PMC3191353
Abstract Full Text PDF–2.3M
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
Lateral Transfer of Genes and Gene Fragments in Staphylococcus Extends beyond Mobile Elements
Cheong Xin Chan, Robert G. Beiko, Mark A. Ragan
J Bacteriol. 2011 August; 193(15): 3964–3977. doi: 10.1128/JB.01524-10
PMCID:
PMC3147504
Abstract Full Text PDF–1.4M Supplementary Material
Physiological Differentiation within a Single-Species Biofilm Fueled by Serpentinization
William J. Brazelton, Mausmi P. Mehta, Deborah S. Kelley, John A. Baross
mBio. 2011 Jul-Aug; 2(4): e00127-11. Published online 2011 July 26. doi: 10.1128/mBio.00127-11
PMCID:
PMC3143844
Abstract Full Text PDF–1.2M Supplementary Material
The Vein Patterning 1 (VEP1) Gene Family Laterally Spread through an Ecological Network
Rosa Tarrío, Francisco J. Ayala, Francisco Rodríguez-Trelles
PLoS One. 2011; 6(7): e22279. Published online 2011 July 26. doi: 10.1371/journal.pone.0022279
PMCID:
PMC3144213
Abstract Full Text PDF–1.9M
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
Split-based computation of majority-rule supertrees
Anne Kupczok
BMC Evol Biol. 2011; 11: 205. Published online 2011 July 13. doi: 10.1186/1471-2148-11-205
PMCID:
PMC3169514
Abstract Full Text PDF–574K
Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits
John Larsson, Johan AA Nylander, Birgitta Bergman
BMC Evol Biol. 2011; 11: 187. Published online 2011 June 30. doi: 10.1186/1471-2148-11-187
PMCID:
PMC3141437
Abstract Full Text PDF–1.2M 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
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
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
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
Computational methods for Gene Orthology inference
David M. Kristensen, Yuri I. Wolf, Arcady R. Mushegian, Eugene V. Koonin
Brief Bioinform. 2011 September; 12(5): 379–391. Published online 2011 June 17. doi: 10.1093/bib/bbr030
PMCID:
PMC3178053
Free in PMC on 2012/09/01
Defining Pathogenic Bacterial Species in the Genomic Era
Kalliopi Georgiades, Didier Raoult
Front Microbiol. 2010; 1: 151. Published online 2011 January 17. doi: 10.3389/fmicb.2010.00151
PMCID:
PMC3109419
Abstract Full Text PDF–2.3M
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
The Tree and Net Components of Prokaryote Evolution
Pere Puigbò, Yuri I. Wolf, Eugene V. Koonin
Genome Biol Evol. 2010; 2: 745–756. Published online 2010 October 1. doi: 10.1093/gbe/evq062
PMCID:
PMC2997564
Abstract Full Text PDF–1.7M
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
Genome Networks Root the Tree of Life between Prokaryotic Domains
Tal Dagan, Mayo Roettger, David Bryant, William Martin
Genome Biol Evol. 2010; 2: 379–392. Published online 2010 May 18. doi: 10.1093/gbe/evq025
PMCID:
PMC2997548
Abstract Full Text PDF–1017K
The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum
Eugene V Koonin, Yuri I Wolf
Biol Direct. 2009; 4: 33. Published online 2009 September 29. doi: 10.1186/1745-6150-4-33
PMCID:
PMC2761301
Abstract Full Text PDF–647K
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