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PMID: 15170256 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise.

Journal of molecular evolution ·Vol. 58 ·No. 5 ·2004-05-00 ·Pages 527-39

Dutilh BE, Huynen MA, Bruno WJ, Snel B

Abstract

Phylogenetic trees based on gene repertoires are remarkably similar to the current consensus of life history. Yet it has been argued that shared gene content is unreliable for phylogenetic reconstruction because of convergence in gene content due to horizontal gene transfer and parallel gene loss. Here we test this argument, by filtering out as noise those orthologous groups that have an inconsistent phylogenetic distribution, using two independent methods. The resulting phylogenies do indeed contain small but significant improvements. More importantly, we find that the majority of orthologous groups contain some phylogenetic signal and that the resulting phylogeny is the only detectable signal present in the gene distribution across genomes. Horizontal gene transfer or parallel gene loss does not cause systematic biases in the gene content tree.

MeSH Terms
Computational Biology/methods Evolution, Molecular Gene Transfer, Horizontal/genetics Genome Genomics/methods Phylogeny
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Dutilh Bas E
Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, University of Nijmegen, Nijmegen, The Netherlands. [email protected]
Huynen Martijn A
Bruno William J
Snel Berend
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Article Info
Journal
Journal of molecular evolution
Abbr.
J Mol Evol
ISSN
0022-2844
DOI
10.1007/s00239-003-2575-6
Email
[email protected]
Published
2004-05-00
Pages
527-39
Language
English
Region
Germany
NLM ID
0360051
Subset
IM
External Links
PubMed source DOI: 10.1007/s00239-003-2575-6 View journal details
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