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
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
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
Dear Charlotte,
No, you do not want to do this.
As shown in Blomberg et al. (2003), the tests for statistical significance do
not work well when you have fewer than about 20 species.
The estimate of the K statistic (indicating the amoung of phylogentic signal)
is fine for small sample sizes,
Hi Annemarie,
I do think this makes sense - *if* (and this may be a big if,
depending on your data) we have a value for a hypothetical ancestor for
which we are very confident and which we are sure belongs at a
particularly ancestral node.
In that case, you could indeed use ace() by
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
