This is not a sister-clade method but ...
If you are happy with a model in which there are underlying polygenic
quantitative characters, covarying ones whose evolution is modeled by
Brownian Motion model, and some two-state discrete characters arise by
imposing a developmental threshold on each quantitative character, you
might look at my 2012 paper in American Naturalist:
http://www.jstor.org/stable/10.1086/663681
The method is designed for use with a known phylogeny and infers the
evolutionary covariances of the underlying quantitative characters (the
"liabilities").
My C program Threshml analysis this model by MCMC sampling. It can, I
believe, be called by Liam Revell's R package phytools.
This threshold model, a phylogenetic version of one which originated in
1934 with Sewall Wright, is mentioned in the Maddison and FitzJohn paper
that William Gearty cited. It is just briefly mentioned by them, I gather
because the authors forgot about it until the last minute when writing the
review. Nevertheless it is getting increasing use.
Joe
----
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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