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Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications

Genomic data have provided evidence of previously unknown ancient whole genome duplications (WGDs) and highlighted the role of WGDs in the evolution of many eukaryotic lineages. Ancient WGDs often are detected by examining distributions of synonymous substitutions per site (Ks) within a genome, or “...

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Autores principales: Tiley, George P, Barker, Michael S, Burleigh, J Gordon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6225891/
https://www.ncbi.nlm.nih.gov/pubmed/30239709
http://dx.doi.org/10.1093/gbe/evy200
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author Tiley, George P
Barker, Michael S
Burleigh, J Gordon
author_facet Tiley, George P
Barker, Michael S
Burleigh, J Gordon
author_sort Tiley, George P
collection PubMed
description Genomic data have provided evidence of previously unknown ancient whole genome duplications (WGDs) and highlighted the role of WGDs in the evolution of many eukaryotic lineages. Ancient WGDs often are detected by examining distributions of synonymous substitutions per site (Ks) within a genome, or “Ks plots.” For example, WGDs can be detected from Ks plots by using univariate mixture models to identify peaks in Ks distributions. We performed gene family simulation experiments to evaluate the effects of different Ks estimation methods and mixture models on our ability to detect ancient WGDs from Ks plots. The simulation experiments, which accounted for variation in substitution rates and gene duplication and loss rates across gene families, tested the effects of WGD age and gene retention rates following WGD on inferring WGDs from Ks plots. Our simulations reveal limitations of Ks plot analyses. Strict interpretations of mixture model analyses often overestimate the number of WGD events, and Ks plot analyses typically fail to detect WGDs when ≤10% of the duplicated genes are retained following the WGD. However, WGDs can accurately be characterized over an intermediate range of Ks. The simulation results are supported by empirical analyses of transcriptomic data, which also suggest that biases in gene retention likely affect our ability to detect ancient WGDs. Although our results indicate mixture model results should be interpreted with great caution, using node-averaged Ks estimates and applying more appropriate mixture models can improve the accuracy of detecting WGDs.
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spelling pubmed-62258912018-11-14 Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications Tiley, George P Barker, Michael S Burleigh, J Gordon Genome Biol Evol Research Article Genomic data have provided evidence of previously unknown ancient whole genome duplications (WGDs) and highlighted the role of WGDs in the evolution of many eukaryotic lineages. Ancient WGDs often are detected by examining distributions of synonymous substitutions per site (Ks) within a genome, or “Ks plots.” For example, WGDs can be detected from Ks plots by using univariate mixture models to identify peaks in Ks distributions. We performed gene family simulation experiments to evaluate the effects of different Ks estimation methods and mixture models on our ability to detect ancient WGDs from Ks plots. The simulation experiments, which accounted for variation in substitution rates and gene duplication and loss rates across gene families, tested the effects of WGD age and gene retention rates following WGD on inferring WGDs from Ks plots. Our simulations reveal limitations of Ks plot analyses. Strict interpretations of mixture model analyses often overestimate the number of WGD events, and Ks plot analyses typically fail to detect WGDs when ≤10% of the duplicated genes are retained following the WGD. However, WGDs can accurately be characterized over an intermediate range of Ks. The simulation results are supported by empirical analyses of transcriptomic data, which also suggest that biases in gene retention likely affect our ability to detect ancient WGDs. Although our results indicate mixture model results should be interpreted with great caution, using node-averaged Ks estimates and applying more appropriate mixture models can improve the accuracy of detecting WGDs. Oxford University Press 2018-09-18 /pmc/articles/PMC6225891/ /pubmed/30239709 http://dx.doi.org/10.1093/gbe/evy200 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 Research Article
Tiley, George P
Barker, Michael S
Burleigh, J Gordon
Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications
title Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications
title_full Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications
title_fullStr Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications
title_full_unstemmed Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications
title_short Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications
title_sort assessing the performance of ks plots for detecting ancient whole genome duplications
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6225891/
https://www.ncbi.nlm.nih.gov/pubmed/30239709
http://dx.doi.org/10.1093/gbe/evy200
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