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A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes

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...

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Detalles Bibliográficos
Autores principales: Sabath, Niv, Landan, Giddy, Graur, Dan
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2601044/
https://www.ncbi.nlm.nih.gov/pubmed/19098983
http://dx.doi.org/10.1371/journal.pone.0003996
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author Sabath, Niv
Landan, Giddy
Graur, Dan
author_facet Sabath, Niv
Landan, Giddy
Graur, Dan
author_sort Sabath, Niv
collection PubMed
description 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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spelling pubmed-26010442008-12-22 A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes Sabath, Niv Landan, Giddy Graur, Dan PLoS One Research Article 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. Public Library of Science 2008-12-22 /pmc/articles/PMC2601044/ /pubmed/19098983 http://dx.doi.org/10.1371/journal.pone.0003996 Text en Sabath et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Sabath, Niv
Landan, Giddy
Graur, Dan
A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes
title A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes
title_full A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes
title_fullStr A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes
title_full_unstemmed A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes
title_short A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes
title_sort method for the simultaneous estimation of selection intensities in overlapping genes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2601044/
https://www.ncbi.nlm.nih.gov/pubmed/19098983
http://dx.doi.org/10.1371/journal.pone.0003996
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