Gavin Leighton asked:
> >
> > > I have 500 trees of 80 species downloaded from birdtree.org and am
> > primarily interested in two traits. I have used PGLS to determine the
> > traits are related but would ideally like to test if there is an order to
> > trait evolution. To complicate matters one trait (Trait A) is continuous
> > while the second (Trait B) is presence/absence. I was hoping someone
> could
> > direct me to methods (assuming they exist) that would allow me to
> determine
> > the estimated value of Trait A before a gain of Trait B evolves in a
> > lineage.
> > >
>
A superior model (if I do say so myself) is the threshold model of Sewall
Wright (1934). I have described in a paper in American Naturalist in 2012
how to use it to model discrete traits on a phylogeny. It allows the case
of one trait continuous and another discrete.
It is implemented in my program Threshml, which should be callable from
Liam Revell's "phytools" R package.
However it does not precisely answer the question you posed, but just asks
whether the two traits evolve in a correlated fashion.
J.F.
----
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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