ArticlePLoS computational biology2012
Universal pacemaker of genome evolution.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- The heterogeneous selection landscape of genome evolution in prokaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The heterogeneous selection landscape of genome evolution in prokaryotes.Research square · 2025Article
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- Privacy-preserving biological age prediction over federated human methylation data using fully homomorphic encryption.Genome research · 2024Article
- ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data.Genome biology and evolution · 2024Article
- Hibernation slows epigenetic ageing in yellow-bellied marmots.Nature ecology & evolution · 2022Article
- Log Transformation Improves Dating of Phylogenies.Molecular biology and evolution · 2021Article
- Inference of mutability landscapes of tumors from single cell sequencing data.PLoS computational biology · 2020Article
- The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework.Bioinformatics (Oxford, England) · 2020Article
- Epigenetic pacemaker: closed form algebraic solutions.BMC genomics · 2020Article
- Detecting horizontal gene transfer: a probabilistic approach.BMC genomics · 2020Article
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- Article
- The Estimated Pacemaker for Great Apes Supports the Hominoid Slowdown Hypothesis.Evolutionary bioinformatics online · 2019Article
- Reconstruction of real and simulated phylogenies based on quartet plurality inference.BMC genomics · 2018Article
- Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families.Genome biology and evolution · 2017Article
- Article
- A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging.PLoS computational biology · 2016Article
- Ordered orthology as a tool in prokaryotic evolutionary inference.Mobile genetic elements · 2016Review
- Detecting Horizontal Gene Transfer between Closely Related Taxa.PLoS computational biology · 2015Article
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3 authors.
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Abstract
A fundamental observation of comparative genomics is that the distribution of evolution rates across the complete sets of orthologous genes in pairs of related genomes remains virtually unchanged throughout the evolution of life, from bacteria to mammals. The most straightforward explanation for the conservation of this distribution appears to be that the relative evolution rates of all genes remain nearly constant, or in other words, that evolutionary rates of different genes are strongly correlated within each evolving genome. This correlation could be explained by a model that we denoted Universal PaceMaker (UPM) of genome evolution. The UPM model posits that the rate of evolution changes synchronously across genome-wide sets of genes in all evolving lineages. Alternatively, however, the correlation between the evolutionary rates of genes could be a simple consequence of molecular clock (MC). We sought to differentiate between the MC and UPM models by fitting thousands of phylogenetic trees for bacterial and archaeal genes to supertrees that reflect the dominant trend of vertical descent in the evolution of archaea and bacteria and that were constrained according to the two models. The goodness of fit for the UPM model was better than the fit for the MC model, with overwhelming statistical significance, although similarly to the MC, the UPM is strongly overdispersed. Thus, the results of this analysis reveal a universal, genome-wide pacemaker of evolution that could have been in operation throughout the history of life.
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