ArticleGenome biology and evolution2013
Stability along with extreme variability in core genome evolution.
Article in Genome biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 31 citations in OpenAlex.
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- Epigenetic pacemaker: closed form algebraic solutions.BMC genomics · 2020Article
- Detecting horizontal gene transfer: a probabilistic approach.BMC genomics · 2020Article
- Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence.Nature communications · 2019Article
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- The Estimated Pacemaker for Great Apes Supports the Hominoid Slowdown Hypothesis.Evolutionary bioinformatics online · 2019Article
- Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families.Genome biology and evolution · 2017Article
- ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation.Nucleic acids research · 2017Article
- Phylogeny ofFrontiers in microbiology · 2017Article
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- 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
- Universal pacemaker of genome evolution in animals and fungi and variation of evolutionary rates in diverse organisms.Genome biology and evolution · 2014Article
- Evolution and classification of myosins, a paneukaryotic whole-genome approach.Genome biology and evolution · 2014Article
- On the number of genomic pacemakers: a geometric approach.Algorithms for molecular biology : AMB · 2014Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
The shape of the distribution of evolutionary distances between orthologous genes in pairs of closely related genomes is universal throughout the entire range of cellular life forms. The near invariance of this distribution across billions of years of evolution can be accounted for by the Universal Pace Maker (UPM) model of genome evolution that yields a significantly better fit to the phylogenetic data than the Molecular Clock (MC) model. Unlike the MC, the UPM model does not assume constant gene-specific evolutionary rates but rather postulates that, in each evolving lineage, the evolutionary rates of all genes change (approximately) in unison although the pacemakers of different lineages are not necessarily synchronized. Here, we dissect the nearly constant evolutionary rate distribution by comparing the genome-wide relative rates of evolution of individual genes in pairs or triplets of closely related genomes from diverse bacterial and archaeal taxa. We show that, although the gene-specific relative rate is an important feature of genome evolution that explains more than half of the variance of the evolutionary distances, the ranges of relative rate variability are extremely broad even for universal genes. Because of this high variance, the gene-specific rate is a poor predictor of the conservation rank for any gene in any particular lineage.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.