What affects power to estimate speciation rate shifts?

PeerJ
Ullasa Kodandaramaiah, Gopal Murali

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 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 estimatio...Continue Reading

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Citations

Jul 25, 2018·Evolution; International Journal of Organic Evolution·Bonnie B BlaimerSeán G Brady
Jan 11, 2019·BMC Evolutionary Biology·Joshua W LambertDaniel Pincheira-Donoso
May 1, 2021·Scientific Reports·Eva TurkMatjaž Kuntner
Jul 31, 2021·Current Biology : CB·Nathan S UphamWalter Jetz

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Software Mentioned

tess
QuaSSE
BISSE
Cladogenetic SSE
BAMM
BAMMtools
turboMEDUSA
MEDUSA
MuSSE
GeoSSE SSE

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