The Rooting of the Universal Tree of Life Is Not Reliable (original) (raw)
Abstract.
Several composite universal trees connected by an ancestral gene duplication have been used to root the universal tree of life. In all cases, this root turned out to be in the eubacterial branch. However, the validity of results obtained from comparative sequence analysis has recently been questioned, in particular, in the case of ancient phylogenies. For example, it has been shown that several eukaryotic groups are misplaced in ribosomal RNA or elongation factor trees because of unequal rates of evolution and mutational saturation. Furthermore, the addition of new sequences to data sets has often turned apparently reasonable phylogenies into confused ones. We have thus revisited all composite protein trees that have been used to root the universal tree of life up to now (elongation factors, ATPases, tRNA synthetases, carbamoyl phosphate synthetases, signal recognition particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant groupings at different levels of the tree. Furthermore, the respective phylogenies contradicted each others, so that various ad hoc scenarios (paralogy or lateral gene transfer) must be proposed in order to obtain the traditional Archaebacteria–Eukaryota sisterhood. More importantly, all of the markers are heavily saturated with respect to amino acid substitutions. As phylogenies inferred from saturated data sets are extremely sensitive to differences in evolutionary rates, present phylogenies used to root the universal tree of life could be biased by the phenomenon of long branch attraction. Since the eubacterial branch was always the longest one, the eubacterial rooting could be explained by an attraction between this branch and the long branch of the outgroup. Finally, we suggested that an eukaryotic rooting could be a more fruitful working hypothesis, as it provides, for example, a simple explanation to the high genetic similarity of Archaebacteria and Eubacteria inferred from complete genome analysis.
Access this article
Subscribe and save
- Get 10 units per month
- Download Article/Chapter or eBook
- 1 Unit = 1 Article or 1 Chapter
- Cancel anytime Subscribe now
Buy Now
Price excludes VAT (USA)
Tax calculation will be finalised during checkout.
Instant access to the full article PDF.
Similar content being viewed by others
Author information
Authors and Affiliations
- Phylogénie et Evolution Moléculaires (UPRESA 8080 CNRS), Bâtiment 444, Université Paris-Sud, 91405 Orsay-Cedex, France, , , , , , FR
Hervé Philippe - Institut de Génétique et Microbiologie (UMR 8621 CNRS), Bâtiment 409, Université Paris-Sud, 91405 Orsay-Cedex, France, , , , , , FR
Patrick Forterre
Authors
- Hervé Philippe
You can also search for this author inPubMed Google Scholar - Patrick Forterre
You can also search for this author inPubMed Google Scholar
Rights and permissions
About this article
Cite this article
Philippe, H., Forterre, P. The Rooting of the Universal Tree of Life Is Not Reliable.J Mol Evol 49, 509–523 (1999). https://doi.org/10.1007/PL00006573
- Issue Date: October 1999
- DOI: https://doi.org/10.1007/PL00006573