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 <[email protected]<mailto:[email protected]>> 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 [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected]<mailto:[email protected]> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/ ------------------------------------------------------------ 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 [email protected]<mailto:[email protected]> www.fourdimensionalbiology.com [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
