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Systematic Biology 2007 56(5):701-710; doi:10.1080/10635150701607033
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© 2007 Society of Systematic Biologists

Estimating a Binary Character's Effect on Speciation and Extinction

Wayne P. Maddison1,2,3,4, Peter E. Midford1 and Sarah P. Otto1,2

1 Department of Zoology, University of British Columbia Vancouver, BC V6T 1Z4, Canada E-mail: wmaddisn{at}interchange.ubc.ca
2 Biodiversity Research Centre, University of British Columbia Vancouver, BC V6T 1Z4, Canada
3 Department of Botany, University of British Columbia Vancouver, BC, V6T 1Z4, Canada
4 Wissenschaftskolleg zu Berlin Wallotstraße 19, Berlin, 14193, Germany

Edited by Todd Oakley


  Abstract

Determining whether speciation and extinction rates depend on the state of a particular character has been of long-standing interest to evolutionary biologists. To assess the effect of a character on diversification rates using likelihood methods requires that we be able to calculate the probability that a group of extant species would have evolved as observed, given a particular model of the character's effect. Here we describe how to calculate this probability for a phylogenetic tree and a two-state (binary) character under a simple model of evolution (the "BiSSE" model, binary-state speciation and extinction). The model involves six parameters, specifying two speciation rates (rate when the lineage is in state 0; rate when in state 1), two extinction rates (when in state 0; when in state 1), and two rates of character state change (from 0 to 1, and from 1 to 0). Using these probability calculations, we can do maximum likelihood inference to estimate the model's parameters and perform hypothesis tests (e.g., is the rate of speciation elevated for one character state over the other?). We demonstrate the application of the method using simulated data with known parameter values.

Keywords: Birth-death process; branching process; cladogenesis; extinction; key innovation; macroevolution; phylogeny; speciation; speciose; statistical inference

Received December 22, 2006; Revised May 23, 2007; Accepted May 29, 2007
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