My question is probably more theoretical than practical. I have completed a
small phylogenetic study (ingroup = 5 congenerics, outgroup = 2
confamilials) that indicates that the ingroup species arose from a rapid
radiation event. Individual trees for 30 genes yield 24 distinct
topologies. My idea was to represent the topological uncertainty of the
phylogeny in an ordination plot such that each species would have 30 points
associated, and the overlap would show the lack of resolution among ingroup
species. I have maximum composite likelihood distance matrices for each
gene, and have plotted a few individually using cmscale, but I am very new
to R and have been unable to find any reference to combining matrices in
PCoA. I realize that, if this is even possible, my data would need to be
normalized since the genes (nuclear and mitochondrial) have very different
evolutionary rates (min. dist. range = 0.011- 0.238, max. dist. range =
0.238- 6.258). Perhaps there is another way to do this? Thank you.
essayl
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