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Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary

BACKGROUND: An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates th...

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Autores principales: Ritchie, Andrew M., Hua, Xia, Bromham, Lindell
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9088092/
https://www.ncbi.nlm.nih.gov/pubmed/35538412
http://dx.doi.org/10.1186/s12862-022-02015-8
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author Ritchie, Andrew M.
Hua, Xia
Bromham, Lindell
author_facet Ritchie, Andrew M.
Hua, Xia
Bromham, Lindell
author_sort Ritchie, Andrew M.
collection PubMed
description BACKGROUND: An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used methods rely on idealised models of rate variation, such as the uncorrelated and autocorrelated clocks, and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as current evidence suggests, they may have a significant influence on molecular dates. RESULTS: We simulate phylogenies and molecular sequences under three different realistic rate variation models—one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test three commonly used “relaxed clock” molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior using BEAST 2, to up to 91% when sequences evolved under the punctuated model are reconstructed under an autocorrelated prior using PAML. CONCLUSIONS: We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-022-02015-8.
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spelling pubmed-90880922022-05-11 Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary Ritchie, Andrew M. Hua, Xia Bromham, Lindell BMC Ecol Evol Research BACKGROUND: An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used methods rely on idealised models of rate variation, such as the uncorrelated and autocorrelated clocks, and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as current evidence suggests, they may have a significant influence on molecular dates. RESULTS: We simulate phylogenies and molecular sequences under three different realistic rate variation models—one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test three commonly used “relaxed clock” molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior using BEAST 2, to up to 91% when sequences evolved under the punctuated model are reconstructed under an autocorrelated prior using PAML. CONCLUSIONS: We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-022-02015-8. BioMed Central 2022-05-10 /pmc/articles/PMC9088092/ /pubmed/35538412 http://dx.doi.org/10.1186/s12862-022-02015-8 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Ritchie, Andrew M.
Hua, Xia
Bromham, Lindell
Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary
title Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary
title_full Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary
title_fullStr Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary
title_full_unstemmed Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary
title_short Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary
title_sort investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9088092/
https://www.ncbi.nlm.nih.gov/pubmed/35538412
http://dx.doi.org/10.1186/s12862-022-02015-8
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