ArticleJournal of molecular evolution2004
The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise.
Article in Journal of molecular evolution, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Bifidobacterium castoris strains isolated from wild mice show evidence of frequent host switching and diverse carbohydrate metabolism potential.ISME communications · 2022Article
- Open pangenome ofFrontiers in microbiology · 2022Article
- Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome.Genome biology · 2020Article
- Bacterial diversity in aqueous/sludge phases within diesel fuel storage tanks.World journal of microbiology & biotechnology · 2020Article
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- Linking pangenomes and metagenomes: thePeerJ · 2018Article
- Metagenomics of Coral Reefs Under Phase Shift and High Hydrodynamics.Frontiers in microbiology · 2018Article
- The post-vaccine microevolution of invasive Streptococcus pneumoniae.Scientific reports · 2015Article
- Phylogenomic network and comparative genomics reveal a diverged member of the ΦKZ-related group, marine vibrio phage ΦJM-2012.Journal of virology · 2013Article
- Phylogenomics and molecular signatures for species from the plant pathogen-containing order xanthomonadales.PloS one · 2013Article
- Reference-independent comparative metagenomics using cross-assembly: crAss.Bioinformatics (Oxford, England) · 2012Article
- New weighting methods for phylogenetic tree reconstruction using multiple loci.Journal of molecular evolution · 2012Article
- Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis.PloS one · 2012Article
- Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling.Evolutionary bioinformatics online · 2012Article
- Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution.Frontiers in cellular and infection microbiology · 2012Review
- Article
- AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses.BMC bioinformatics · 2009Article
- GO4genome: a prokaryotic phylogeny based on genome organization.Journal of molecular evolution · 2009Article
- Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs.Gene · 2009Article
- The convergence of carbohydrate active gene repertoires in human gut microbes.Proceedings of the National Academy of Sciences of the United States of America · 2008 · on this mapArticle
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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