The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History
Open accessAbstract
It has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms, but up to now, no satisfying approach has been proposed to use efficiently these data. For instance, if the coding of presence or absence of genes in complete genomes gives interesting results, it does not take into account the phylogenetic information contained in sequences and ignores hidden paralogies by using a BLAST reciprocal best hit definition of orthology. In addition, concatenation of sequences of different genes as well as building of consensus trees only consider the few genes that are shared among all organisms. Here we present an attempt to use a supertree method to build the phylogenetic tree of 45 organisms, with special focus on bacterial phylogeny. This led us to perform a phylogenetic study of congruence of tree topologies, which allows the identification of a core of genes supporting similar species phylogeny. We then used this core of genes to infer a tree. This phylogeny presents several differences with the rRNA phylogeny, notably for the position of hyperthermophilic bacteria.
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Cites
Woese, C. R. (1987) · Microbiological Reviews · doi:10.1128/mr.51.2.221-271.1987 · Cited by 5,042 · cited 12×
“First, the monophyly of these bacteria contradicts small subunit ribosomal RNA analysis, which branch them successively at the base of the Bacteria and thus supports a thermophilic origin of Bacteria (Woese 1987; Barns et al. 1996, Bocchetta et al. 2000).”
BackgroundMethodInfluentialLateral gene transfer and the nature of bacterial innovation
Ochman, H., Lawrence, J. G., & Groisman, E. A. (2000) · Nature · doi:10.1038/35012500 · Cited by 3,816
Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies
Strimmer, K., & von Haeseler, A. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025664 · Cited by 2,531
The Hydrogen Hypothesis for the First Eukaryote
Martin, W., & Müller, M. (1998) · Nature · doi:10.1038/32096 · Cited by 1,282
Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss?
Salzberg, S. L., White, O., Peterson, J., & Eisen, J. A. (2001) · Science · doi:10.1126/science.1061036 · Cited by 326
How good are deep phylogenetic trees?
Philippe, H., & Laurent, J. (1998) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(98)80028-2 · Cited by 324 · cited 1×
“…this raises other problems such as reconstruction artifacts and hidden paralogies, and though phylogeneticists steadily warn against these problems (Philippe and Laurent 1998; Glansdorff 2000), the difficulty of obtaining congruent gene phylogenies is often seen as a result of lateral exchanges.”
BackgroundHansmann, S., & Martin, W. (2000) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/00207713-50-4-1655 · Cited by 99
Cited by
Relaxed Phylogenetics and Dating with Confidence
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040088 · Cited by 6,463
“subset of a larger dataset comprising 730 genes representing 45 species of bacteria [38].”
BackgroundEukaryotic evolution, changes and challenges
Embley, T. M., & Martin, W. (2006) · Nature · doi:10.1038/nature04546 · Cited by 867
The origin and evolution of model organisms
Hedges, S. B. (2002) · Nature Reviews Genetics · doi:10.1038/nrg929 · Cited by 806
Comparative genomics, minimal gene-sets and the last universal common ancestor
Koonin, E. V. (2003) · Nature Reviews Microbiology · doi:10.1038/nrmicro751 · Cited by 661
Boyer, F., Fichant, G., Berthod, J., Vandenbrouck, Y., & Attree, I. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-104 · Cited by 580
Metadata
- Authors
- Daubin, V., Gouy, M., & Perrière, G.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2002-07-01
- Volume
- 12
- Issue
- 7
- Pages
- 1080-1090
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2156668042
- Cited by
- 313
- References
- 7
- Type
- posted content
- Language
- en
- Open access
- bronze
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