Hi all,
I am
working with different populations of a single species (sheep). I now want to
visualize the (dis)similarities between my populations using plotGMPhyloMorphoSpace.
Being a newbie with phylogeny and trees and the like, I feel a bit uncertain, if I am getting this right. I thought
of getting the tree from the nj function (ape package) with the
LS means distance matrix from my advanced.procD.lm as input. Is this the right
way to do this?
Best and many thanks for the great work you're doing,
Nadja
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At present, there is no correct way of doing non-BM ancestral state estimation for multivariate data.
For multivariate data, all presently proposed methods for evaluating non-Brownian motion evolutionary models (e.g., OU, EB, etc.) display very high rates of misspecification (type I error). That is, they find strong support for more complex models than were used to generate the data (e.g., generate multivariate data under BM, and the methods find strong support for OU). This is undesirable to say the least, and some methods are even worse than this! A recent review of the problems is found in Adams and Collyer, 2018: Systematic Biology.
By extension of these results, working ‘backwards’ to estimate ancestral states using anything except BM will not work as intended.
At the present time, if one wishes to make correct inferences with multivariate data, one is restricted to Brownian motion.
Dean
Dr. Dean C. Adams
Director of Graduate Education, EEB Program
Professor
Department of Ecology, Evolution, and Organismal Biology
Department of Statistics
Iowa State University
www.public.iastate.edu/~dcadams/
phone: 515-294-3834
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Nadja,
There are multiple ways to do this, depending on your analytical pipeline.
For instance, if you have multiple specimens per group, one could perform a linear model using ‘procD.lm’, followed by ‘pairwise’. In the output from pairwise, the first component of the LS.means contains these (e.g., PW.output$LS.means[[1]] ).
If you look at the help file for procD.lm there is an example of both the anova and the pairwise tests.
This is one of many ways to obtain them.
Dean
Dr. Dean C. Adams
Director of Graduate Education, EEB Program
Professor
Department of Ecology, Evolution, and Organismal Biology
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