In what will surely become one of the most influential papers of 2007, Maddison and colleagues propose a new model to resolve an important and often unrecognized problem in ancestral state reconstructions and studies of key innovations.
Specifically, the effect of character states on the process that generates the observed phylogeny (speciation and extinction rates differ depending on whether the lineage is in state 0 or 1, for example) frequently made it almost impossible for previous models used in reconstruction of ancestry to infer the correct ancestral states and transition rates. The opposite is also true--the inaccurate inference of ancestry made it impossible to infer correct state-associated speciation and extinction rates associated with each character state. The new model, named BiSSE (binary state speciation and extinction), is implemented in Mesquite.
Plainly stated, if one wishes to analyze the evolution of a character with two states, each of which is associated with different speciation and extinction rates, the use of the old Mk-family of models is likely inadequate. Equal net diversification rates for alternate states are unlikely, as are equal transition rates.
And who wants to study characters that do not affect net diversification rates?
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