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The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates
Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in add...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421065/ https://www.ncbi.nlm.nih.gov/pubmed/30886768 http://dx.doi.org/10.7717/peerj.6334 |
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author | Sarver, Brice A.J. Pennell, Matthew W. Brown, Joseph W. Keeble, Sara Hardwick, Kayla M. Sullivan, Jack Harmon, Luke J. |
author_facet | Sarver, Brice A.J. Pennell, Matthew W. Brown, Joseph W. Keeble, Sara Hardwick, Kayla M. Sullivan, Jack Harmon, Luke J. |
author_sort | Sarver, Brice A.J. |
collection | PubMed |
description | Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. Accordingly, characterizing the effect of prior selection on phylogenies is an active area of research. The choice of priors may systematically bias phylogenetic reconstruction and, subsequently, affect conclusions drawn from the resulting phylogeny. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation and extinction rates) from these trees. When substitution rate heterogeneity is large, diversification rate estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate. |
format | Online Article Text |
id | pubmed-6421065 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-64210652019-03-18 The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates Sarver, Brice A.J. Pennell, Matthew W. Brown, Joseph W. Keeble, Sara Hardwick, Kayla M. Sullivan, Jack Harmon, Luke J. PeerJ Computational Biology Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. Accordingly, characterizing the effect of prior selection on phylogenies is an active area of research. The choice of priors may systematically bias phylogenetic reconstruction and, subsequently, affect conclusions drawn from the resulting phylogeny. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation and extinction rates) from these trees. When substitution rate heterogeneity is large, diversification rate estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate. PeerJ Inc. 2019-03-13 /pmc/articles/PMC6421065/ /pubmed/30886768 http://dx.doi.org/10.7717/peerj.6334 Text en © 2019 Sarver 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 (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Computational Biology Sarver, Brice A.J. Pennell, Matthew W. Brown, Joseph W. Keeble, Sara Hardwick, Kayla M. Sullivan, Jack Harmon, Luke J. The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates |
title | The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates |
title_full | The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates |
title_fullStr | The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates |
title_full_unstemmed | The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates |
title_short | The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates |
title_sort | choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates |
topic | Computational Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421065/ https://www.ncbi.nlm.nih.gov/pubmed/30886768 http://dx.doi.org/10.7717/peerj.6334 |
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