ArticleGenome biology and evolution2011
Faster than neutral evolution of constrained sequences: the complex interplay of mutational biases and weak selection.
Article in Genome biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Evolution of Epistasis: Small Populations Go Their Separate Ways.Journal of molecular evolution · 2020Article
- Article
- Selfing in Haploid Plants and Efficacy of Selection: Codon Usage Bias in the Model Moss Physcomitrella patens.Genome biology and evolution · 2017Article
- Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum.PLoS genetics · 2017Article
- SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage.Genome biology and evolution · 2016Article
- Are Synonymous Sites in Primates and Rodents Functionally Constrained?Journal of molecular evolution · 2016Article
- RNA-Seq analysis identifies genes associated with differential reproductive success under drought-stress in accessions of wild barley Hordeum spontaneum.BMC plant biology · 2015Article
- Trends in substitution models of molecular evolution.Frontiers in genetics · 2015Article
- The fundamental tradeoff in genomes and proteomes of prokaryotes established by the genetic code, codon entropy, and physics of nucleic acids and proteins.Biology direct · 2014Article
- Purifying selection, drift, and reversible mutation with arbitrarily high mutation rates.Genetics · 2014Article
- Precise estimates of mutation rate and spectrum in yeast.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Comparative population genomics: power and principles for the inference of functionality.Trends in genetics : TIG · 2014Review
- Strong purifying selection at synonymous sites in D. melanogaster.PLoS genetics · 2013Article
- Purifying selection modulates the estimates of population differentiation and confounds genome-wide comparisons across single-nucleotide polymorphisms.Molecular biology and evolution · 2012Article
- The allele-frequency spectrum in a decoupled Moran model with mutation, drift, and directional selection, assuming small mutation rates.Theoretical population biology · 2012Article
- The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome.Molecular biology and evolution · 2012Article
- Molecular evolution in nonrecombining regions of the Drosophila melanogaster genome.Genome biology and evolution · 2012Article
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3 authors.
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Abstract
Comparative genomics has become widely accepted as the major framework for the ascertainment of functionally important regions in genomes. The underlying paradigm of this approach is that most of the functional regions are assumed to be under selective constraint, which in turn reduces the rate of evolution relative to neutrality. This assumption allows detection of functional regions through sequence conservation. However, constraint does not always lead to sequence conservation. When purifying selection is weak and mutation is biased, constrained regions can even evolve faster than neutral sequences and thus can appear to be under positive selection. Moreover, conservation estimates depend also on the orientation of selection relative to mutational biases and can vary over time. In the light of recent data of the ubiquity of mutational biases and weak selective forces, these effects should reduce the power of conservation analyses to define functional regions using comparative genomics data. We argue that the estimation of true mutational biases and the use of explicit evolutionary models are essential to improve methods inferring the action of natural selection and functionality in genome sequences.
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