ArticleGenome research2000
From complete genomes to measures of substitution rate variability within and between proteins.
Article in Genome research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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46 citing papers in PubMed.
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- The Estimated Pacemaker for Great Apes Supports the Hominoid Slowdown Hypothesis.Evolutionary bioinformatics online · 2019Article
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- Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum.Nature communications · 2017Article
- Universal distribution of mutational effects on protein stability, uncoupling of protein robustness from sequence evolution and distinct evolutionary modes of prokaryotic and eukaryotic proteins.Physical biology · 2015Article
- Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics.Applied and environmental microbiology · 2014Article
- Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Universal pacemaker of genome evolution in animals and fungi and variation of evolutionary rates in diverse organisms.Genome biology and evolution · 2014Article
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- On the number of genomic pacemakers: a geometric approach.Algorithms for molecular biology : AMB · 2014Article
- Seeing the Tree of Life behind the phylogenetic forest.BMC biology · 2013Article
- Population size dependence of fitness effect distribution and substitution rate probed by biophysical model of protein thermostability.Genome biology and evolution · 2013Article
- Stability along with extreme variability in core genome evolution.Genome biology and evolution · 2013Article
- Exploring metazoan evolution through dynamic and holistic changes in protein families and domains.BMC evolutionary biology · 2012Article
- Universal pacemaker of genome evolution.PLoS computational biology · 2012Article
- Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling.Evolutionary bioinformatics online · 2012Article
- Are there laws of genome evolution?PLoS computational biology · 2011Article
- Article
- Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes.Genome biology and evolution · 2010Article
- Constraints and plasticity in genome and molecular-phenome evolution.Nature reviews. Genetics · 2010Review
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3 authors.
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Abstract
Accumulation of complete genome sequences of diverse organisms creates new possibilities for evolutionary inferences from whole-genome comparisons. In the present study, we analyze the distributions of substitution rates among proteins encoded in 19 complete genomes (the interprotein rate distribution). To estimate these rates, it is necessary to employ another fundamental distribution, that of the substitution rates among sites in proteins (the intraprotein distribution). Using two independent approaches, we show that intraprotein substitution rate variability appears to be significantly greater than generally accepted. This yields more realistic estimates of evolutionary distances from amino-acid sequences, which is critical for evolutionary-tree construction. We demonstrate that the interprotein rate distributions inferred from the genome-to-genome comparisons are similar to each other and can be approximated by a single distribution with a long exponential shoulder. This suggests that a generalized version of the molecular clock hypothesis may be valid on genome scale. We also use the scaling parameter of the obtained interprotein rate distribution to construct a rooted whole-genome phylogeny. The topology of the resulting tree is largely compatible with those of global rRNA-based trees and trees produced by other approaches to genome-wide comparison.
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