Hi Milton,
The drift model gives a time-dependent change in the expected, or mean value of
the trait. If we denote the drift parameter as M, then the expected value of
the trait, E(x), at time t is a+Mt where a is the root state of the trait. So
if M is positive, your trait tends to get larger over time and if it is
negative, the trait tends to get smaller. Note that this is a tendency because
the trait is actually evolving under a biased random walk, so variance still
increases with time, as in Brownian motion. For this reason, you wouldn’t do a
branch length reconstruction to infer ancestral states under drift. Because we
are modeling change in the expected value of the trait through time, the model
is unidentifiable without non-comtemporaneous (i.e. fossil, time series) tips
or a very strong prior / bound on the root state. This is a good reference for
the model in a non-phylogenetic context
http://www.psjournals.org/doi/abs/10.1666/05070.1
You can do ancestral state estimation under the drift model using
fitContinuousMCMC in geiger (this also allows you to place informative priors
on node values) and I think Liam has a function in phytools to give you the ML
estimates.
Cheers,
Graham
On May 28, 2015, at 4:07 PM, Milton Tan
mzt0...@tigermail.auburn.edumailto:mzt0...@tigermail.auburn.edu wrote:
Hello all,
I have some questions about the drift model implemented in geiger to test for a
trend in increasing or decreasing trait values over time. I'm curious how to
interpret the drift parameter, as well as whether BM is nested within BM. Is
there a citation I can read for more information? I haven't seen the parameters
of the drift model described anywhere explicitly, though perhaps I have missed
it. It seems similar to the test for a directional pressure implemented in
Pagel 1997, but I don't see any mention of the drift parameter.
Additionally, I'm curious if there's a good way to incorporate a drift model
into ancestral state reconstruction? I imagine I can transform the branch
lengths based on the drift parameter somehow and simply reconstruct ancestral
trait states under BM, but I'm unsure how to do the branch length
transformation for a drift model given that I'm not entirely sure what the
drift parameter represents.
Thanks all,
Milton Tan
Auburn University
Department of Biological Sciences
PhD Candidate
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Graham Slater
Peter Buck Post-Doctoral Fellow
Department of Paleobiology
National Museum of Natural History
The Smithsonian Institution [NHB, MRC 121]
P.O. Box 37012
(202) 633-1316
slat...@si.edumailto:slat...@si.edu
www.fourdimensionalbiology.com
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