[R-sig-phylo] ancestral state reconstruction with fixed internal node(s)

Theodore Garland Jr theodore.garland at ucr.edu
Thu Jun 30 20:10:01 CEST 2011


Hi Graham,

I, too, have done this under Brownian motion and "squared-change parsimony" reconstructions.
In my experience (which was a while ago, and memory fades ...), the confidence intervals for nodes near to the one you constrain ("near" in terms of the length of the branches connecting the nodes) should be reduced, and sometimes substantially, if the constrained node is close by.  Right? 

Cheers,
Ted

Theodore Garland, Jr.
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Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments
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________________________________________
From: r-sig-phylo-bounces at r-project.org [r-sig-phylo-bounces at r-project.org] on behalf of Graham Slater [gslater at ucla.edu]
Sent: Thursday, June 30, 2011 10:09 AM
To: r-sig-phylo at r-project.org
Subject: Re: [R-sig-phylo] ancestral state reconstruction with fixed internal node(s)

Hi AnneMarie,

The way Paolo suggests would be the best/right way to do this. We're
working on some methods for incorporating fossil info in comparative
methods and I have some code that will do this that i can send you
off-list if you would like. I should add that, at least based on what
we've found so far, doing this probably won't make much difference to
your reconstructed ancestral states, simply because under BM, your CIs
are so wide without constraining nodes that doing so has little effect.

best,

Graham

On 06/30/2011 09:40 AM, ppiras at uniroma3.it wrote:
> Hi AnneMarie,
> I dont really know if this makes sense; in fact
> ancestral state reconstruction is an ** a posteriori
> estimation ** of nodal values starting from tips
> observations.
>
> A trick could be to add a false taxon lnked to that
> node  and giving to it a 0 branch length (i.e.
> plitomized - you can then resolve this during
> computation using multi2di() ) and assigning your
> desired trait value.
>
> I'm not sure if this helps....
>
> Best
> Paolo
>
>
>
>
>
>
> Dear phylo-sig list people,
>
> I want to do ancestral state reconstruction
> (preferably with ace) with
> one (or more) of the internal nodes 'fixed' for a
> range / a distribution
> of values. For instance, I want a node leading to one
> particular clade
> that is present a subset of my trees to have a value
> from 0.2-0.5, and
> then do the ancestral state reconstruction with this
> restriction on that
> node.
>
> I have been searching the archives and the net for
> discussion of this
> (but maybe with the wrong search terms), and I cannot
> find anything
> about it - not how to do it in R or in any other
> package.
>
> Thanks for your input!
> Annemarie
>
> --
> Annemarie Verkerk, MA
> Evolutionary Processes in Language and Culture (PhD
> student)
> Max Planck Institute for Psycholinguistics
> P.O. Box 310, 6500AH Nijmegen, The Netherlands
> +31 (0)24 3521 185
> http://www.mpi.nl/research/research-projects/evolutionary-processes
>
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