ArticlePloS one2008
A method for the simultaneous estimation of selection intensities in overlapping genes.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it, 44 citations in OpenAlex.
- Pooled it
- Parvovirus B19 and Human Parvovirus 4 Encode Similar Proteins in a Reading Frame Overlapping the VP1 Capsid Gene.Viruses · 2024Article
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- OLGenie: Estimating Natural Selection to Predict Functional Overlapping Genes.Molecular biology and evolution · 2020Article
- Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation.Virology · 2019Article
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- Genotype-Specific Evolution of Hepatitis E Virus.Journal of virology · 2017Article
- Article
- New tools to analyze overlapping coding regions.BMC bioinformatics · 2016Article
- Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Positive Selection Analysis of Overlapping Reading Frames Is Invalid.AIDS research and human retroviruses · 2015Article
- Interspecific adaptation by binary choice at de novo polyomavirus T antigen site through accelerated codon-constrained Val-Ala toggling within an intrinsically disordered region.Nucleic acids research · 2015Article
- A simple method for estimating the strength of natural selection on overlapping genes.Genome biology and evolution · 2014Article
- Selection pressure in alternative reading frames.PloS one · 2014Article
- Identification of an overprinting gene in Merkel cell polyomavirus provides evolutionary insight into the birth of viral genes.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Evolution of viral proteins originated de novo by overprinting.Molecular biology and evolution · 2012Article
- Evolutionary conservation of the PA-X open reading frame in segment 3 of influenza A virus.Journal of virology · 2012Article
- Molecular evolution of the genomic RNA of Apple stem grooving capillovirus.Journal of molecular evolution · 2012Article
- Is life unique?Life (Basel, Switzerland) · 2011Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Inferring the intensity of positive selection in protein-coding genes is important since it is used to shed light on the process of adaptation. Recently, it has been reported that overlapping genes, which are ubiquitous in all domains of life, seem to exhibit inordinate degrees of positive selection. Here, we present a new method for the simultaneous estimation of selection intensities in overlapping genes. We show that the appearance of positive selection is caused by assuming that selection operates independently on each gene in an overlapping pair, thereby ignoring the unique evolutionary constraints on overlapping coding regions. Our method uses an exact evolutionary model, thereby voiding the need for approximation or intensive computation. We test the method by simulating the evolution of overlapping genes of different types as well as under diverse evolutionary scenarios. Our results indicate that the independent estimation approach leads to the false appearance of positive selection even though the gene is in reality subject to negative selection. Finally, we use our method to estimate selection in two influenza A genes for which positive selection was previously inferred. We find no evidence for positive selection in both cases.
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