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Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses
With the emergence of analytical software for the inference of viral evolution, a number of studies have focused on estimating important parameters such as the substitution rate and the time to the most recent common ancestor (t (MRCA)) for rapidly evolving viruses. Coupled with an increasing abunda...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667911/ https://www.ncbi.nlm.nih.gov/pubmed/26630483 http://dx.doi.org/10.1371/journal.pone.0143605 |
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author | Pedersen, Casper-Emil T. Frandsen, Peter Wekesa, Sabenzia N. Heller, Rasmus Sangula, Abraham K. Wadsworth, Jemma Knowles, Nick J. Muwanika, Vincent B. Siegismund, Hans R. |
author_facet | Pedersen, Casper-Emil T. Frandsen, Peter Wekesa, Sabenzia N. Heller, Rasmus Sangula, Abraham K. Wadsworth, Jemma Knowles, Nick J. Muwanika, Vincent B. Siegismund, Hans R. |
author_sort | Pedersen, Casper-Emil T. |
collection | PubMed |
description | With the emergence of analytical software for the inference of viral evolution, a number of studies have focused on estimating important parameters such as the substitution rate and the time to the most recent common ancestor (t (MRCA)) for rapidly evolving viruses. Coupled with an increasing abundance of sequence data sampled under widely different schemes, an effort to keep results consistent and comparable is needed. This study emphasizes commonly disregarded problems in the inference of evolutionary rates in viral sequence data when sampling is unevenly distributed on a temporal scale through a study of the foot-and-mouth (FMD) disease virus serotypes SAT 1 and SAT 2. Our study shows that clustered temporal sampling in phylogenetic analyses of FMD viruses will strongly bias the inferences of substitution rates and t (MRCA) because the inferred rates in such data sets reflect a rate closer to the mutation rate rather than the substitution rate. Estimating evolutionary parameters from viral sequences should be performed with due consideration of the differences in short-term and longer-term evolutionary processes occurring within sets of temporally sampled viruses, and studies should carefully consider how samples are combined. |
format | Online Article Text |
id | pubmed-4667911 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-46679112015-12-10 Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses Pedersen, Casper-Emil T. Frandsen, Peter Wekesa, Sabenzia N. Heller, Rasmus Sangula, Abraham K. Wadsworth, Jemma Knowles, Nick J. Muwanika, Vincent B. Siegismund, Hans R. PLoS One Research Article With the emergence of analytical software for the inference of viral evolution, a number of studies have focused on estimating important parameters such as the substitution rate and the time to the most recent common ancestor (t (MRCA)) for rapidly evolving viruses. Coupled with an increasing abundance of sequence data sampled under widely different schemes, an effort to keep results consistent and comparable is needed. This study emphasizes commonly disregarded problems in the inference of evolutionary rates in viral sequence data when sampling is unevenly distributed on a temporal scale through a study of the foot-and-mouth (FMD) disease virus serotypes SAT 1 and SAT 2. Our study shows that clustered temporal sampling in phylogenetic analyses of FMD viruses will strongly bias the inferences of substitution rates and t (MRCA) because the inferred rates in such data sets reflect a rate closer to the mutation rate rather than the substitution rate. Estimating evolutionary parameters from viral sequences should be performed with due consideration of the differences in short-term and longer-term evolutionary processes occurring within sets of temporally sampled viruses, and studies should carefully consider how samples are combined. Public Library of Science 2015-12-02 /pmc/articles/PMC4667911/ /pubmed/26630483 http://dx.doi.org/10.1371/journal.pone.0143605 Text en © 2015 Pedersen 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 Pedersen, Casper-Emil T. Frandsen, Peter Wekesa, Sabenzia N. Heller, Rasmus Sangula, Abraham K. Wadsworth, Jemma Knowles, Nick J. Muwanika, Vincent B. Siegismund, Hans R. Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses |
title | Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses |
title_full | Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses |
title_fullStr | Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses |
title_full_unstemmed | Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses |
title_short | Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses |
title_sort | time clustered sampling can inflate the inferred substitution rate in foot-and-mouth disease virus analyses |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667911/ https://www.ncbi.nlm.nih.gov/pubmed/26630483 http://dx.doi.org/10.1371/journal.pone.0143605 |
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