Hello all,

The package mvMORPH can also do ancestral state reconstruction of
continuous characters for some OU-related models, including OUM, but I
don't believe it has all the models Bruno is after. There's an example
given in one of the vignettes of using mvMORPH for reconstructing a
continuous character.

John


John Soghigian, Ph.D.
Postdoctoral Associate
Deparment of Ecology and Evolutionary Biology
Yale University
21 Sachem Street
New Haven, CT
06511


On Mon, Jun 11, 2018 at 11:55 PM, Brian O'Meara <omeara.br...@gmail.com>
wrote:

> Prompted by Bruno's email, and similar requests by some students at the
> Arnold & Felsenstein Evolutionary Quantitative Genetics course, we've
> started adding ancestral state reconstruction to OUwie. It still needs
> debugging and testing, but should be ready fairly soon. I do believe bayou
> does ancestral state estimation, too, but I don't think all the models you
> want will be in the set. Could be adequate to answering the biological
> question, though.
>
> Best,
> Brian
>
> _______________________________________________________________________
> Brian O'Meara, http://www.brianomeara.info, especially Calendar
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> Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville
> Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville
> Associate Director for Postdoctoral Activities, National Institute for
> Mathematical & Biological Synthesis <http://www.nimbios.org> (NIMBioS)
>
>
>
> On Mon, Jun 11, 2018 at 6:01 PM David Bapst <dwba...@tamu.edu> wrote:
>
> > Just to follow off what Lucas said, but please note you cannot rescale
> > branches of a phylogeny using an OU model when the tree is
> > non-ultrametric (such as when it contains extinct, fossil taxa as
> > tips). Slater (2014, MEE) discusses this more in a brief correction to
> > Slater (2013).
> >
> > I don't know if anyone in this conversation has a non-ultrametric
> > tree, but I wanted to make that clear for anyone who stumbles on this
> > thread n the future using a google search.
> > -Dave
> >
> >
> >
> > On Sun, Jun 10, 2018 at 12:25 PM, Lucas Jardim <lucas.ljard...@gmail.com
> >
> > wrote:
> > > Hi Bruno,
> > >
> > > You can transform the branches of your phylogeny using the estimated
> > > parameters of OU models. Then, if those models describe the observed
> data
> > > adequatly, the transformed tree should model the observed data as a
> > > Brownian motion model. So you can use an ancestral state reconstruction
> > > based on Brownian motion model. However, I do not know if that is the
> > best
> > > approach as optimum values would not be included into the
> reconstruction
> > > process.
> > >
> > > Best,
> > > --
> > > Lucas Jardim
> > > Doutor em Ecologia e Evolução
> > > Bolsista do INCT-EECBio (Ecologia, Evolução e Conservação da
> > > Biodiversidade)
> > > Instituto de Ciências Biológicas
> > > Laboratório de Ecologia Teórica e Síntese
> > > Universidade Federal de Goiás
> > > http://dinizfilho.wix.com/dinizfilholab
> > >
> > >         [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > R-sig-phylo mailing list - R-sig-phylo@r-project.org
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> > > Searchable archive at
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> >
> >
> >
> > --
> > David W. Bapst, PhD
> > Asst Research Professor, Geology & Geophysics, Texas A & M University
> > https://github.com/dwbapst/paleotree
> > Google Calendar: https://goo.gl/EpiM4J
> >
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