Cargando…

A62 A major likelihood-based approach gives problematic estimates of diversification dynamics and rates

The diversity of life is shaped by rates of speciation and extinction, and so estimating these rates correctly is crucial for understanding diversity patterns among clades, regions, and habitats. In 2011, Morlon and collaborators developed a promising likelihood-based approach to estimate speciation...

Descripción completa

Detalles Bibliográficos
Autores principales: Di, Chenlu, Meyer, Andreas L S, Wiens, John J
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735765/
http://dx.doi.org/10.1093/ve/vez002.061
_version_ 1783450407316488192
author Di, Chenlu
Meyer, Andreas L S
Wiens, John J
author_facet Di, Chenlu
Meyer, Andreas L S
Wiens, John J
author_sort Di, Chenlu
collection PubMed
description The diversity of life is shaped by rates of speciation and extinction, and so estimating these rates correctly is crucial for understanding diversity patterns among clades, regions, and habitats. In 2011, Morlon and collaborators developed a promising likelihood-based approach to estimate speciation and extinction and to infer the model describing how these rates change over time based on AICc. This approach is now implemented in an R package (RPANDA). Here, we test the accuracy of this approach under simulated conditions, to evaluate its ability to correctly estimate rates of speciation, extinction, and diversification (speciation—extinction) and to choose the correct underlying model of diversification (e.g. constant or changing rates of speciation and extinction over time). We found that this likelihood-based approach frequently picked the incorrect model. For example, with changing speciation rates over time, the correct model was chosen in only ∼10 per cent of replicates. There were significant relationships between true and estimated speciation rates using this approach, but relationships were weak when speciation rates were constant within clades. Relationships were consistently weak between true and estimated rates of extinction and of diversification. Overall, we suggest that results from this approach should be interpreted with considerable caution.
format Online
Article
Text
id pubmed-6735765
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-67357652019-09-16 A62 A major likelihood-based approach gives problematic estimates of diversification dynamics and rates Di, Chenlu Meyer, Andreas L S Wiens, John J Virus Evol Abstract Overview The diversity of life is shaped by rates of speciation and extinction, and so estimating these rates correctly is crucial for understanding diversity patterns among clades, regions, and habitats. In 2011, Morlon and collaborators developed a promising likelihood-based approach to estimate speciation and extinction and to infer the model describing how these rates change over time based on AICc. This approach is now implemented in an R package (RPANDA). Here, we test the accuracy of this approach under simulated conditions, to evaluate its ability to correctly estimate rates of speciation, extinction, and diversification (speciation—extinction) and to choose the correct underlying model of diversification (e.g. constant or changing rates of speciation and extinction over time). We found that this likelihood-based approach frequently picked the incorrect model. For example, with changing speciation rates over time, the correct model was chosen in only ∼10 per cent of replicates. There were significant relationships between true and estimated speciation rates using this approach, but relationships were weak when speciation rates were constant within clades. Relationships were consistently weak between true and estimated rates of extinction and of diversification. Overall, we suggest that results from this approach should be interpreted with considerable caution. Oxford University Press 2019-08-22 /pmc/articles/PMC6735765/ http://dx.doi.org/10.1093/ve/vez002.061 Text en © Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access publication 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 Abstract Overview
Di, Chenlu
Meyer, Andreas L S
Wiens, John J
A62 A major likelihood-based approach gives problematic estimates of diversification dynamics and rates
title A62 A major likelihood-based approach gives problematic estimates of diversification dynamics and rates
title_full A62 A major likelihood-based approach gives problematic estimates of diversification dynamics and rates
title_fullStr A62 A major likelihood-based approach gives problematic estimates of diversification dynamics and rates
title_full_unstemmed A62 A major likelihood-based approach gives problematic estimates of diversification dynamics and rates
title_short A62 A major likelihood-based approach gives problematic estimates of diversification dynamics and rates
title_sort a62 a major likelihood-based approach gives problematic estimates of diversification dynamics and rates
topic Abstract Overview
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735765/
http://dx.doi.org/10.1093/ve/vez002.061
work_keys_str_mv AT dichenlu a62amajorlikelihoodbasedapproachgivesproblematicestimatesofdiversificationdynamicsandrates
AT meyerandreasls a62amajorlikelihoodbasedapproachgivesproblematicestimatesofdiversificationdynamicsandrates
AT wiensjohnj a62amajorlikelihoodbasedapproachgivesproblematicestimatesofdiversificationdynamicsandrates