Hi Glenn.
The phytools function fastBM does Brownian motion simulation with
bounds. It is pretty straightforward to figure out, but let me know if
you have difficult with the details.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 7/10/2015 12:56 PM, Glenn Seeholzer wrote:
Hi all,
I'm looking for a way to simulate a labile trait given a phylogenetic tree
of say 200-300 tips. The ultimate goal is to examine the behavior of BAMM
when a trait violates the underlying assumption of Brownian motion trait
evolution.
I'd like the simulated trait to mimic the evolution of a trait like the
climatic-niche, in which there is a bounded trait space and distantly
related lineages may converge on the same distribution of trait values
(think two clades independently diversifying into the same set of diverse
environments).
In my empirical data, when I divide a tree into independent subclades,
climatic-niche evolution within these subclades is best fit by a BM model
relative to OU. Let's assume for the moment that BM is a good model for
climatic-niche evolution within subclades, yet not across an entire tree.
One thought I had was to divide a simulated tree into subclades, then
simulate a BM trait for each subclade. This would result in simulated trait
values for all tips in the tree and with the desired pattern of convergence
among distantly related lineages. However, I'm unsure if the trait values
overall would be that different from a BM trait simulated on the entire
tree, or if there a more appropriate approach.
Thanks in advance for your help.
Cheers,
Glenn
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