Genome beginnings: rooting the tree of life
Open Access
- 12 August 2009
- journal article
- review article
- Published by The Royal Society in Philosophical Transactions B
- Vol. 364 (1527), 2177-2185
- https://doi.org/10.1098/rstb.2009.0035
Abstract
A rooted tree of life provides a framework to answer central questions about the evolution of life. Here we review progress on rooting the tree of life and introduce a new root of life obtained through the analysis of indels, insertions and deletions, found within paralogous gene sets. Through the analysis of indels in eight paralogous gene sets, the root is localized to the branch between the clade consisting of the Actinobacteria and the double-membrane (Gram-negative) prokaryotes and one consisting of the archaebacteria and the firmicutes. This root provides a new perspective on the habitats of early life, including the evolution of methanogenesis, membranes and hyperthermophily, and the speciation of major prokaryotic taxa. Our analyses exclude methanogenesis as a primitive metabolism, in contrast to previous findings. They parsimoniously imply that the ether archaebacterial lipids are not primitive and that the cenancestral prokaryotic population consisted of organisms enclosed by a single, ester-linked lipid membrane, covered by a peptidoglycan layer. These results explain the similarities previously noted by others between the lipid synthesis pathways in eubacteria and archaebacteria. The new root also implies that the last common ancestor was not hyperthermophilic, although moderate thermophily cannot be excluded.Keywords
This publication has 67 references indexed in Scilit:
- The eocyte hypothesis and the origin of eukaryotic cellsProceedings of the National Academy of Sciences of the United States of America, 2008
- The archaebacterial origin of eukaryotesProceedings of the National Academy of Sciences of the United States of America, 2008
- Genome-Wide Experimental Determination of Barriers to Horizontal Gene TransferScience, 2007
- Evidence Excluding the Root of the Tree of Life from the ActinobacteriaMolecular Biology and Evolution, 2007
- The origin and evolution of Archaea: a state of the artPhilosophical Transactions B, 2006
- Ancient gene duplications and the root(s) of the tree of lifeProtoplasma, 2005
- Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901PLoS Genetics, 2005
- Some Like It Hot, But Not the First BiomoleculesScience, 2002
- Antiquity of the biological sulphur cycle: evidence from sulphur and carbon isotopes in 2700 million–year–old rocks of the Belingwe Belt, ZimbabweProceedings. Biological sciences, 2001
- Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleusCurrent Biology, 1994