Hi Glenn & Ted,
An overview of phylogeny data simulation can be found in the chapter
included in Garamszegi's book "Modern Phylogenetic Comparative Methods".
There is an accompanying page on the book's web site:
http://www.mpcm-evolution.org/practice/online-practical-material-chapter-13
This includes several case studies.
Best,
Emmanuel
Le 10/07/2015 19:06, Theodore Garland Jr a écrit :
Hi Glenn,
I am not up on the latest simulation options in R, but for some relevant
general discussions you might check these old papers (PDFs are on my website):
Garland, T., Jr., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993.
Phylogenetic analysis of
covariance by computer simulation. Systematic Biology 42:265-292.
Díaz-Uriarte, R., and T. Garland, Jr. 1996. Testing hypotheses of correlated
evolution using
phylogenetically independent contrasts: sensitivity to deviations from
Brownian motion.
Systematic Biology 45:27-47. Abstract [PDF file]
Díaz-Uriarte, R., and T. Garland, Jr. 1998. Effects of branch length errors on
the performance of
phylogenetically independent contrasts. Systematic Biology 47:654-672.
Garland, T., Jr., and R. Díaz-Uriarte. 1999. Polytomies and phylogenetically
independent contrasts:
an examination of the bounded degrees of freedom approach. Systematic
Biology 48:547-558.
Cheers,
Ted
Theodore Garland, Jr., Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone: (951) 827-3524
Facsimile: (951) 827-4286 (not confidential)
Email: tgarl...@ucr.edu
http://www.biology.ucr.edu/people/faculty/Garland.html
http://scholar.google.com/citations?hl=en&user=iSSbrhwAAAAJ
Director, UCR Institute for the Development of Educational Applications
Editor in Chief, Physiological and Biochemical Zoology
Fail Lab: Episode One
http://testtube.com/faillab/zoochosis-episode-one-evolution
http://www.youtube.com/watch?v=c0msBWyTzU0
________________________________________
From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Glenn
Seeholzer [seeholzer.gl...@gmail.com]
Sent: Friday, July 10, 2015 9:56 AM
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] simulating a labile trait
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
--
Glenn F. Seeholzer
Museum of Natural Science
Foster Hall 119
LSU, Baton Rouge, LA 70803
215-872-3017
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