Does a tree–like phylogeny only exist at the tips in the prokaryotes?
Open accessAbstract
The extent to which prokaryotic evolution has been influenced by horizontal gene transfer (HGT) and therefore might be more of a network than a tree is unclear. Here we use supertree methods to ask whether a definitive prokaryotic phylogenetic tree exists and whether it can be confidently inferred using orthologous genes. We analysed an 11-taxon dataset spanning the deepest divisions of prokaryotic relationships, a 10-taxon dataset spanning the relatively recent gamma-proteobacteria and a 61-taxon dataset spanning both, using species for which complete genomes are available. Congruence among gene trees spanning deep relationships is not better than random. By contrast, a strong, almost perfect phylogenetic signal exists in gamma-proteobacterial genes. Deep-level prokaryotic relationships are difficult to infer because of signal erosion, systematic bias, hidden paralogy and/or HGT. Our results do not preclude levels of HGT that would be inconsistent with the notion of a prokaryotic phylogeny. This approach will help decide the extent to which we can say that there is a prokaryotic phylogeny and where in the phylogeny a cohesive genomic signal exists.
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By viewing the tree in terms of how often different genes find the same branch for the concatenated tree they purport to uphold, what we see is not a tree of life, but a tree of tips.
“But by viewing the tree in terms of how often different genes find the same branch for the concatenated tree they purport to uphold, what we see is not a tree of life, but a tree of tips [228].”
From Early bioenergetic evolution (2013) · cites this paper as [228]
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Gene and genome trees conflict at many levels
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- Authors
- Creevey, C. J., Fitzpatrick, D. A., Philip, G. K., Kinsella, R. J., O'Connell, M. J., Pentony, M. M., Travers, S. A., Wilkinson, M., & McInerney, J. O.
- Affiliations
- National University of Ireland, Maynooth (IE)
- Bioinformatics and Pharmacogenomics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
- Natural History Museum (GB)
- Corresponding author
- McInerney, James O.
- ORCID
- Venue
- Proceedings of the Royal Society of London. Series B: Biological Sciences
- Publisher
- The Royal Society
- Published
- 2004-12-22
- Volume
- 271
- Issue
- 1557
- Pages
- 2551-2558
- ISSN
- 0080-4649 (ISSN-L)
- 0962-8452
- 1471-2954
- PMC
- PMC1691901
- OpenAlex
- W2060665252
- Cited by
- 126
- References
- 30
- Citations by year
- 2026: 2 · 2025: 1 · 2023: 3 · 2022: 2 · 2021: 2 · 2020: 5 · 2019: 1 · 2018: 1 · 2017: 3 · 2016: 3 · 2015: 6 · 2014: 5 · 2013: 7 · 2012: 3
- FWCI
- 4.75
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Proceedings of the Royal Society B Biological Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Maynooth University ePrints and eTheses Archive (Maynooth University) (acceptedVersion)
- Research Explorer (The University of Manchester) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- prokaryotic phylogeny, horizontal gene transfer, supertree methods, orthologs, gene tree discordance, Gammaproteobacteria, phylogenetic signal
- MeSH terms
- Bacteria, Classification, Models, Genetic, Phylogeny, Likelihood Functions, Genome, Bacterial, Gene Transfer, Horizontal
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