Uncertainty in divergence time estimation
Understanding and representing uncertainty is crucial in academic research, because it enables studies to build on the conclusions of previous studies, leading to robust advances in a particular field. Here, we evaluate the nature of uncertainty and the manner by which it is represented in divergenc...
| Main Authors: | , |
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| Format: | Journal article |
| Language: | English |
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Oxford University Press
2020
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| _version_ | 1797052560666787840 |
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| author | Carruthers, T Scotland, RW |
| author_facet | Carruthers, T Scotland, RW |
| author_sort | Carruthers, T |
| collection | OXFORD |
| description | Understanding and representing uncertainty is crucial in academic research, because it enables studies to build on the conclusions of previous studies, leading to robust advances in a particular field. Here, we evaluate the nature of uncertainty and the manner by which it is represented in divergence time estimation, a field that is fundamental to many aspects of macroevolutionary research, and where there is evidence that uncertainty has been seriously underestimated. We address this issue in the context of methods used in divergence time estimation, and with respect to the manner by which time-calibrated phylogenies are interpreted. With respect to methods, we discuss how the assumptions underlying different methods may not adequately reflect uncertainty about molecular evolution, the fossil record, or diversification rates. Therefore, divergence time estimates may not adequately reflect uncertainty, and may be directly contradicted by subsequent findings. For the interpretation of time-calibrated phylogenies, we discuss how the use of time-calibrated phylogenies for reconstructing general evolutionary timescales leads to inferences about macroevolution that are highly sensitive to methodological limitations in how uncertainty is accounted for. By contrast, we discuss how the use of time-calibrated phylogenies to test specific hypotheses leads to inferences about macroevolution that are less sensitive to methodological limitations. Given that many biologists wish to use time-calibrated phylogenies to reconstruct general evolutionary timescales, we conclude that the development of methods of divergence time estimation that adequately account for uncertainty is necessary. |
| first_indexed | 2024-03-06T18:33:15Z |
| format | Journal article |
| id | oxford-uuid:0a62dc7d-b925-4879-9bb7-78a185d6b409 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T18:33:15Z |
| publishDate | 2020 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:0a62dc7d-b925-4879-9bb7-78a185d6b4092022-03-26T09:23:33ZUncertainty in divergence time estimationJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:0a62dc7d-b925-4879-9bb7-78a185d6b409EnglishSymplectic ElementsOxford University Press2020Carruthers, TScotland, RWUnderstanding and representing uncertainty is crucial in academic research, because it enables studies to build on the conclusions of previous studies, leading to robust advances in a particular field. Here, we evaluate the nature of uncertainty and the manner by which it is represented in divergence time estimation, a field that is fundamental to many aspects of macroevolutionary research, and where there is evidence that uncertainty has been seriously underestimated. We address this issue in the context of methods used in divergence time estimation, and with respect to the manner by which time-calibrated phylogenies are interpreted. With respect to methods, we discuss how the assumptions underlying different methods may not adequately reflect uncertainty about molecular evolution, the fossil record, or diversification rates. Therefore, divergence time estimates may not adequately reflect uncertainty, and may be directly contradicted by subsequent findings. For the interpretation of time-calibrated phylogenies, we discuss how the use of time-calibrated phylogenies for reconstructing general evolutionary timescales leads to inferences about macroevolution that are highly sensitive to methodological limitations in how uncertainty is accounted for. By contrast, we discuss how the use of time-calibrated phylogenies to test specific hypotheses leads to inferences about macroevolution that are less sensitive to methodological limitations. Given that many biologists wish to use time-calibrated phylogenies to reconstruct general evolutionary timescales, we conclude that the development of methods of divergence time estimation that adequately account for uncertainty is necessary. |
| spellingShingle | Carruthers, T Scotland, RW Uncertainty in divergence time estimation |
| title | Uncertainty in divergence time estimation |
| title_full | Uncertainty in divergence time estimation |
| title_fullStr | Uncertainty in divergence time estimation |
| title_full_unstemmed | Uncertainty in divergence time estimation |
| title_short | Uncertainty in divergence time estimation |
| title_sort | uncertainty in divergence time estimation |
| work_keys_str_mv | AT carrutherst uncertaintyindivergencetimeestimation AT scotlandrw uncertaintyindivergencetimeestimation |