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Influence of Effective Population Size on Genes under Varying Levels of Selection Pressure

The ratio of diversities at amino acid changing (nonsynonymous) and neutral (synonymous) sites (ω = π(N)/π(S)) is routinely used to measure the intensity of selection pressure. It is well known that this ratio is influenced by the effective population size (N(e)) and selection coefficient (s). Here,...

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Autor principal: Subramanian, Sankar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5841380/
https://www.ncbi.nlm.nih.gov/pubmed/29608718
http://dx.doi.org/10.1093/gbe/evy047
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author Subramanian, Sankar
author_facet Subramanian, Sankar
author_sort Subramanian, Sankar
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description The ratio of diversities at amino acid changing (nonsynonymous) and neutral (synonymous) sites (ω = π(N)/π(S)) is routinely used to measure the intensity of selection pressure. It is well known that this ratio is influenced by the effective population size (N(e)) and selection coefficient (s). Here, we examined the effects of effective population size on ω by comparing protein-coding genes from Mus musculus castaneus and Mus musculus musculus—two mouse subspecies with different N(e). Our results revealed a positive relationship between the magnitude of selection intensity and the ω estimated for genes. For genes under high selective constraints, the ω estimated for the subspecies with small N(e) (M. m. musculus) was three times higher than that observed for that with large N(e) (M. m. castaneus). However, this difference was only 18% for genes under relaxed selective constraints. We showed that the observed relationship is qualitatively similar to the theoretical predictions. We also showed that, for highly expressed genes, the ω of M. m. musculus was 2.1 times higher than that of M.m. castaneus and this difference was only 27% for genes with low expression levels. These results suggest that the effect of effective population size is more pronounced in genes under high purifying selection. Hence the choice of genes is important when ω is used to infer the effective size of a population.
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spelling pubmed-58413802018-03-28 Influence of Effective Population Size on Genes under Varying Levels of Selection Pressure Subramanian, Sankar Genome Biol Evol Letter The ratio of diversities at amino acid changing (nonsynonymous) and neutral (synonymous) sites (ω = π(N)/π(S)) is routinely used to measure the intensity of selection pressure. It is well known that this ratio is influenced by the effective population size (N(e)) and selection coefficient (s). Here, we examined the effects of effective population size on ω by comparing protein-coding genes from Mus musculus castaneus and Mus musculus musculus—two mouse subspecies with different N(e). Our results revealed a positive relationship between the magnitude of selection intensity and the ω estimated for genes. For genes under high selective constraints, the ω estimated for the subspecies with small N(e) (M. m. musculus) was three times higher than that observed for that with large N(e) (M. m. castaneus). However, this difference was only 18% for genes under relaxed selective constraints. We showed that the observed relationship is qualitatively similar to the theoretical predictions. We also showed that, for highly expressed genes, the ω of M. m. musculus was 2.1 times higher than that of M.m. castaneus and this difference was only 27% for genes with low expression levels. These results suggest that the effect of effective population size is more pronounced in genes under high purifying selection. Hence the choice of genes is important when ω is used to infer the effective size of a population. Oxford University Press 2018-02-21 /pmc/articles/PMC5841380/ /pubmed/29608718 http://dx.doi.org/10.1093/gbe/evy047 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Letter
Subramanian, Sankar
Influence of Effective Population Size on Genes under Varying Levels of Selection Pressure
title Influence of Effective Population Size on Genes under Varying Levels of Selection Pressure
title_full Influence of Effective Population Size on Genes under Varying Levels of Selection Pressure
title_fullStr Influence of Effective Population Size on Genes under Varying Levels of Selection Pressure
title_full_unstemmed Influence of Effective Population Size on Genes under Varying Levels of Selection Pressure
title_short Influence of Effective Population Size on Genes under Varying Levels of Selection Pressure
title_sort influence of effective population size on genes under varying levels of selection pressure
topic Letter
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5841380/
https://www.ncbi.nlm.nih.gov/pubmed/29608718
http://dx.doi.org/10.1093/gbe/evy047
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