What affects power to estimate speciation rate shifts?
- Published
- Accepted
- Subject Areas
- Bioinformatics, Computational Biology, Evolutionary Studies
- Keywords
- diversification, BiSSE, BAMM, MEDUSA, rate shift, phylogenetics, key innovation, macroevolution, simulation, speciation rates
- Copyright
- © 2018 Kodandaramaiah et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, 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 Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. What affects power to estimate speciation rate shifts? PeerJ Preprints 6:e3206v2 https://doi.org/10.7287/peerj.preprints.3206v2
Abstract
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 ecological factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rates, 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 (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 some suggestions to users of these methods.
Author Comment
This is a major revision of the previous version with a new experimental design that rectified some serious flaws in the previous version. We are now able to distinguish between the effects of tree size and rate asymmetry (which were tightly correlaed in the previous version). We also test the relative effects of basetree size, subtree size, overall tree size and tip-ratio.
Supplemental Information
Variation in basetree:subtree size ratio in trees from Simulation Set 1
Variation in ratio of the number of basetree:subtree tips for trees from Simulation Set 1 across the three Sages (A: 20%, B: 40% and C: 60%) and speciation rate asymmetry values (Y axis) and tree size classes (X axis; 50±10, 100±10, 200±10, 400±10 and 800±1). The ratios are colour coded according to the legends
