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Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability

The birth–death model is commonly used to infer speciation and extinction rates by fitting the model to phylogenetic trees with exclusively extant taxa. Recently, it was demonstrated that speciation and extinction rates are not identifiable if the rates are allowed to vary freely over time. The grou...

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Autores principales: Kopperud, Bjørn T., Magee, Andrew F., Höhna, Sebastian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9963352/
https://www.ncbi.nlm.nih.gov/pubmed/36757894
http://dx.doi.org/10.1073/pnas.2208851120
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author Kopperud, Bjørn T.
Magee, Andrew F.
Höhna, Sebastian
author_facet Kopperud, Bjørn T.
Magee, Andrew F.
Höhna, Sebastian
author_sort Kopperud, Bjørn T.
collection PubMed
description The birth–death model is commonly used to infer speciation and extinction rates by fitting the model to phylogenetic trees with exclusively extant taxa. Recently, it was demonstrated that speciation and extinction rates are not identifiable if the rates are allowed to vary freely over time. The group of birth–death models that have the same likelihood is called a congruence class, and there is no statistical evidence to favor one model over the other. This issue has led researchers to question if and what patterns can reliably be inferred from phylogenies of only extant taxa and whether time-variable birth–death models should be fitted at all. We explore the congruence class in the context of several empirical phylogenies as well as hypothetical scenarios. For these empirical phylogenies, we assume that we inferred the true congruence class. Thus, our conclusions apply to any empirical phylogeny for which we robustly inferred the true congruence class. When we summarize shared patterns in the congruence class, we show that strong directional trends in speciation and extinction rates are shared among most models. Therefore, we conclude that the inference of strong directional trends is robust. Conversely, estimates of constant rates or gentle slopes are not robust and must be treated with caution. Interestingly, the space of valid speciation rates is narrower and more limited in contrast to extinction rates, which are less constrained. These results provide further evidence and insights that speciation rates can be estimated more reliably than extinction rates.
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spelling pubmed-99633522023-08-09 Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability Kopperud, Bjørn T. Magee, Andrew F. Höhna, Sebastian Proc Natl Acad Sci U S A Biological Sciences The birth–death model is commonly used to infer speciation and extinction rates by fitting the model to phylogenetic trees with exclusively extant taxa. Recently, it was demonstrated that speciation and extinction rates are not identifiable if the rates are allowed to vary freely over time. The group of birth–death models that have the same likelihood is called a congruence class, and there is no statistical evidence to favor one model over the other. This issue has led researchers to question if and what patterns can reliably be inferred from phylogenies of only extant taxa and whether time-variable birth–death models should be fitted at all. We explore the congruence class in the context of several empirical phylogenies as well as hypothetical scenarios. For these empirical phylogenies, we assume that we inferred the true congruence class. Thus, our conclusions apply to any empirical phylogeny for which we robustly inferred the true congruence class. When we summarize shared patterns in the congruence class, we show that strong directional trends in speciation and extinction rates are shared among most models. Therefore, we conclude that the inference of strong directional trends is robust. Conversely, estimates of constant rates or gentle slopes are not robust and must be treated with caution. Interestingly, the space of valid speciation rates is narrower and more limited in contrast to extinction rates, which are less constrained. These results provide further evidence and insights that speciation rates can be estimated more reliably than extinction rates. National Academy of Sciences 2023-02-09 2023-02-14 /pmc/articles/PMC9963352/ /pubmed/36757894 http://dx.doi.org/10.1073/pnas.2208851120 Text en Copyright © 2023 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by-nc-nd/4.0/This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) .
spellingShingle Biological Sciences
Kopperud, Bjørn T.
Magee, Andrew F.
Höhna, Sebastian
Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability
title Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability
title_full Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability
title_fullStr Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability
title_full_unstemmed Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability
title_short Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability
title_sort rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability
topic Biological Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9963352/
https://www.ncbi.nlm.nih.gov/pubmed/36757894
http://dx.doi.org/10.1073/pnas.2208851120
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