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What affects power to estimate speciation rate shifts?

The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal factors. A growing number of researchers are interested in testing whether t...

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Detalles Bibliográficos
Autores principales: Kodandaramaiah, Ullasa, Murali, Gopal
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6108317/
https://www.ncbi.nlm.nih.gov/pubmed/30155369
http://dx.doi.org/10.7717/peerj.5495
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author Kodandaramaiah, Ullasa
Murali, Gopal
author_facet Kodandaramaiah, Ullasa
Murali, Gopal
author_sort Kodandaramaiah, Ullasa
collection PubMed
description The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rate, and three modelling methods—BiSSE, MEDUSA and BAMM—have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (speciation rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide suggestions to users of these methods.
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spelling pubmed-61083172018-08-28 What affects power to estimate speciation rate shifts? Kodandaramaiah, Ullasa Murali, Gopal PeerJ Bioinformatics The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rate, and three modelling methods—BiSSE, MEDUSA and BAMM—have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (speciation rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide suggestions to users of these methods. PeerJ Inc. 2018-08-21 /pmc/articles/PMC6108317/ /pubmed/30155369 http://dx.doi.org/10.7717/peerj.5495 Text en ©2018 Kodandaramaiah and Murali 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 Bioinformatics
Kodandaramaiah, Ullasa
Murali, Gopal
What affects power to estimate speciation rate shifts?
title What affects power to estimate speciation rate shifts?
title_full What affects power to estimate speciation rate shifts?
title_fullStr What affects power to estimate speciation rate shifts?
title_full_unstemmed What affects power to estimate speciation rate shifts?
title_short What affects power to estimate speciation rate shifts?
title_sort what affects power to estimate speciation rate shifts?
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6108317/
https://www.ncbi.nlm.nih.gov/pubmed/30155369
http://dx.doi.org/10.7717/peerj.5495
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