Do orthologous gene phylogenies really support tree-thinking?
-
* Corresponding author: E Bapteste eric.bapteste@dal.ca
BMC Evolutionary Biology 2005, 5:33 doi:10.1186/1471-2148-5-33
Evaulated on
Faculty of 1000
Accesses
- Last 30 days: 96 accesses
- Last 365 days: 1335 accesses
- All time: 9334 accesses
Cited by
BioMed Central: 11 citations
|
Opinion
The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum Eugene V Koonin, Yuri I Wolf Biology Direct 2009, 4:33 (29 September 2009) This article is part of a collection on Evolutionary Biology 150... A tree is a natural representation of evolution owing to the inherent tree-like character of the replication process but the fundamental units of evolution amenable to tree analysis seem to be individual genetic elements rather than complete genomes.
|
|
Research article
Search for a 'Tree of Life' in the thicket of the phylogenetic forest Pere Puigbò, Yuri I Wolf, Eugene V Koonin Journal of Biology 2009, 8:59 (13 July 2009) Koonin and colleagues, comparing a forest of 7000 phylogenetic trees, discern vertical inheritance even at the earliest stages of prokaryotic evolution, despite horizontal gene transfer, but the branching order of the earliest radiations may never be resolved.
|
|
Research
Co-evolutionary networks of genes and cellular processes across fungal species Tamir Tuller, Martin Kupiec, Eytan Ruppin Genome Biology 2009, 10:R48 (5 May 2009) Two new measures of evolution are used to study co-evolutionary networks of fungal genes and cellular processes; links between co-evolution and co-functionality are revealed. |
|
Research article
Factors affecting the concordance between orthologous gene trees and species tree in bacteria Santiago Castillo-Ramírez, Víctor González BMC Evolutionary Biology 2008, 8:300 (30 October 2008) |
|
Research
Evolutionary rate and gene expression across different brain regions Tamir Tuller, Martin Kupiec, Eytan Ruppin Genome Biology 2008, 9:R142 (23 September 2008) Cortically expressed genes are more conserved than sub-cortical ones and gene expression levels exert stronger constraints on sequence evolution in cortical than in sub-cortical regions. |
|
Research article
Uncovering rate variation of lateral gene transfer during bacterial genome evolution Weilong Hao, G Brian Golding BMC Genomics 2008, 9:235 (20 May 2008) |
|
Method
DarkHorse: a method for genome-wide prediction of horizontal gene transfer Sheila Podell, Terry Gaasterland Genome Biology 2007, 8:R16 (2 February 2007) DarkHorse is a new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins. |
|
Research
Refuting phylogenetic relationships James Bucknam, Yan Boucher, Eric Bapteste Biology Direct 2006, 1:26 (6 September 2006) |
|
Research
Kira S Makarova, Nick V Grishin, Svetlana A Shabalina, Yuri I Wolf, Eugene V Koonin Biology Direct 2006, 1:7 (16 March 2006) Computational analysis shows that CRISPR repeats and associated Cas proteins in prokaryotes might act in conjunction as a RNA-silencing mechanism against plasmids and viruses, similar to the eukaryotic RNA-interference system.
|
|
Software
Taxonomic colouring of phylogenetic trees of protein sequences Gareth Palidwor, Emmanuel G Reynaud, Miguel A Andrade-Navarro BMC Bioinformatics 2006, 7:79 (17 February 2006) |
|
Research article
John W Stiller, Leslie Harrell BMC Evolutionary Biology 2005, 5:71 (9 December 2005) |