ArticleGenome research2004
Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
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- Why Do Some Vertebrates Have Microchromosomes?Cells · 2021Review
- Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes.Molecular ecology resources · 2016Article
- Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana.Molecular ecology · 2015Article
- The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force?BMC systems biology · 2012Article
- Variation in the mutation rate across mammalian genomes.Nature reviews. Genetics · 2011Review
- Significant selective constraint at 4-fold degenerate sites in the avian genome and its consequence for detection of positive selection.Genome biology and evolution · 2011Article
- Genome-wide heterogeneity of nucleotide substitution model fit.Genome biology and evolution · 2011Article
- Evidence that replication-associated mutation alone does not explain between-chromosome differences in substitution rates.Genome biology and evolution · 2009Article
- Spontaneous mutational and standing genetic (co)variation at dinucleotide microsatellites in Caenorhabditis briggsae and Caenorhabditis elegans.Molecular biology and evolution · 2009Article
- Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.Genome biology · 2008Article
- Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome.BMC evolutionary biology · 2008Article
- Similarity of synonymous substitution rates across mammalian genomes.Journal of molecular evolution · 2007Article
- Widespread positive selection in synonymous sites of mammalian genes.Molecular biology and evolution · 2007Article
- Chromatin structure and evolution in the human genome.BMC evolutionary biology · 2007Article
- Splicing and the evolution of proteins in mammals.PLoS biology · 2007Article
- A gradient in the distribution of introns in eukaryotic genes.Journal of molecular evolution · 2006Article
- Multiple mechanisms promote the retained expression of gene duplicates in the tetraploid frog Xenopus laevis.PLoS genetics · 2006Article
- Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics.BMC evolutionary biology · 2006Article
- Evolutionary constraints in conserved nongenic sequences of mammals.Genome research · 2005Article
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3 authors.
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Abstract
In mammalian genomes, linked genes show similar rates of evolution, both at fourfold degenerate synonymous sites (K4) and at nonsynonymous sites (KA). Although it has been suggested that the local similarity in the synonymous substitution rate is an artifact caused by the inclusion of disparately evolving gene pairs, we demonstrate here that this is not the case: after removal of disparately evolving genes, both (1) linked genes and (2) introns from the same gene have more similar silent substitution rates than expected by chance. What causes the local similarity in both synonymous and nonsynonymous substitution rates? One class of hypotheses argues that both may be related to the observed clustering of genes of comparable expression profile. We investigate these hypotheses using substitution rates from both human-mouse and mouse-rat comparisons, and employing three different methods to assay expression parameters. Although we confirm a negative correlation of expression breadth with both K4 and KA, we find no evidence that clustering of similarly expressed genes explains the clustering of genes of comparable substitution rates. If gene expression is not responsible, what about other causes? At least in the human-mouse comparison, the local similarity in KA can be explained by the covariation of KA and K4. As regards K4, our results appear consistent with the notion that local similarity is due to processes associated with meiotic recombination.
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