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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doaj-3922505f3dfd451994d05e8cfa5412772020-11-24T21:09:26ZengPeerJ Inc.PeerJ2167-83592018-08-016e549510.7717/peerj.5495What affects power to estimate speciation rate shifts?Ullasa Kodandaramaiah0Gopal Murali1IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE), School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, IndiaIISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE), School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, IndiaThe 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.https://peerj.com/articles/5495.pdfDiversificationBiSSEBAMMMEDUSARate shiftPhylogenetics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ullasa Kodandaramaiah Gopal Murali |
spellingShingle |
Ullasa Kodandaramaiah Gopal Murali What affects power to estimate speciation rate shifts? PeerJ Diversification BiSSE BAMM MEDUSA Rate shift Phylogenetics |
author_facet |
Ullasa Kodandaramaiah Gopal Murali |
author_sort |
Ullasa Kodandaramaiah |
title |
What affects power to estimate speciation rate shifts? |
title_short |
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_sort |
what affects power to estimate speciation rate shifts? |
publisher |
PeerJ Inc. |
series |
PeerJ |
issn |
2167-8359 |
publishDate |
2018-08-01 |
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. |
topic |
Diversification BiSSE BAMM MEDUSA Rate shift Phylogenetics |
url |
https://peerj.com/articles/5495.pdf |
work_keys_str_mv |
AT ullasakodandaramaiah whataffectspowertoestimatespeciationrateshifts AT gopalmurali whataffectspowertoestimatespeciationrateshifts |
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