Ah, I didn't realize you only had character data for the 64 taxa. Then
yes, you
should just map with those taxa. Option (2), pruning out the missing
taxa from
the set of MrBayes trees in the .t file, can be done in R. Search the list
archives for pruning trees.
Stacey
Quoting Marion Chartier <[email protected]>:
Hi Stacey,
thank you for your help!
Yes, SIMMAP deals with short branches: I used this tree to map characters
in Mesquite, and then I kept it as the topology was ok, but finally this was
not because of SIMMAP ! :)
For the sampling, if I only have character data for 64 taxa, I thought I
could : (1) keep the total 116 species tree for the mapping even if 52
species are no documented, (2) run the total tree, remove the 52 species,
and do the mapping on the remaining 64 species (but is it possible to do
that easily on 10000 trees??), (3) run the 64 taxa tree and use it for the
mapping.
i think it is not good for the mapping to have a tree with taxa without
information on character states in it. So a reduced tree might be better...
the 64 species tree is quite well resolved and the topology is the same than
in the total tree, but I am interested in knowing if solution (2) is
feasible! What do you think?
Cheers,
m
2011/3/30 <[email protected]>
Hi Marion,
About your questions, method (1) would still take into account phylogenetic
uncertainty, just among the 64 taxa instead of 116. It seems a shame,
though,
to lose those extra taxa. I'm surprised SIMMAP can't deal with the short
branches.
Second, about the sample from MrBayes, you will want to use the trees from
the
.t file, not the trees from the .trprobs. The ones in the .t file do have
branch lengths. Also you do not want to take the most probable trees but
instead a random sample (a sample from the .t file) for mapping. This is
how
to account for phylogenetic uncertainty appropriately.
Cheers,
Stacey
Quoting Marion Chartier <[email protected]>:
Hi everybody,
I am a PhD student new on the list! I am working for my thesis on the
evolution of pollination in the Araceae family, and so beginning to
perform
phylogenetic analyses!
I am using SIMMAP to map floral traits on a phylogeny of the family, and
to
identify correlations between the evolution of pollination type and some
floral traits.
I have some questions about the parameters to set in the analysis of
correlation!
Method (1)
So far, I have contructed a phylogeny (64 genera), and taken the best ML
tree topology to map 20 characters in SIMMAP. This was more simple for me,
as I had to remove taxons from a big 116 genera tree before running the
SIMMAP analysis. I also did this because the big tree was well supported,
I
needed to get branch lenghts different from zero, and the topology was the
same than in my Bayesian tree.
Thus, I was thinking of largely improving the number of samples
(mutationnal
maps simulations) in the SIMMAP parameters of the correlation analysis...
(like from 10 (default) to 100,000).
Method (2)
A better (I guess) way to do it is to take the 10000 most probable trees
from a Bayesian analysis of my 64 genera alone (less supported than the
big
tree), as it is suggested in the manual, and keep a small number of
samples.
So here come my questions:
1- I know that the method (1) doesn't take acount to the phylogenetic
uncertainty, is it anyway statistically correct?
2- When running MrBayes, I get an output file containing the most probable
trees, but with no branch lengths... (the .trprobs file). I guess this are
the trees I should import in SIMMAP for method (2), but is it ok without
the
branch lengths??
Thank you very much for helping me!
Merci beaucoup de votre aide !
Marion
--
*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*
Marion Chartier
PhD director: Marc Gibernau
UMR Ecofog
Campus Agronomique - BP 709 {|}
97 387 Kourou Cedex |
FRENCH GUIANA |()
mail : [email protected] ||
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--
*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*
Marion Chartier
PhD director: Marc Gibernau
UMR Ecofog
Campus Agronomique - BP 709 {|}
97 387 Kourou Cedex |
FRENCH GUIANA |()
mail : [email protected] ||
*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*¤*
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