Hi Belinda, I agree with Brian�s comment. I�d also add the more general point that OU models don�t really have a clearly interpretable rate parameter in the same way that BM models do. In BM models, the sigma parameter controls the pace of trait evolution: the expected change over a given time interval depends strightforwardly on sigma (and only on sigma).
OU models also have a sigma parameter that has the same meaning � it is the variance of the diffusion process. But, it is perilous to interpret it in the OU context as a rate parameter as one would for BM. This is because the expected change over a given interval depends on sigma, but also on alpha and the distance to the optimum. This complexity means that OU models don�t have any single number you can point to as a generic rate of change for the process. So, if your scientific question hinges on saying something about rates on branches, I think this is all the more reason to follow Brian�s suggestion of looking into one of the BM rate heterogeneity methods. Best, Gene -- Gene Hunt Curator, Department of Paleobiology National Museum of Natural History Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 Washington DC 20013-7012 Phone: 202-633-1331 Fax: 202-786-2832 http://paleobiology.si.edu/staff/individuals/hunt.cfm From: Brian O'Meara <omeara.br...@gmail.com<mailto:omeara.br...@gmail.com>> Reply-To: "omeara.br...@gmail.com<mailto:omeara.br...@gmail.com>" <omeara.br...@gmail.com<mailto:omeara.br...@gmail.com>> Date: Friday, April 15, 2016 at 11:00 AM To: Belinda Kahnt <belind...@gmx.de<mailto:belind...@gmx.de>>, "mailman, r-sig-phylo" <r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org>> Subject: Re: [R-sig-phylo] estimating the evolutionary rate of a continous trait Hi, Belinda. One thing to watch is over-intepretation: BM is consistent with drift, OU is consistent with selection, but various kinds of selection can also lead to BM. [1]. A lot of the people involved in these methods (including me) are guilty of sloppiness in language in this area, leading to confusion. Also, another issue could be branch lengths: are they proportional to time (or, arguably, something like number of generations)? All these methods are basically stretching the tree in various ways (and, for OU, adjusting expected means), so if branch lengths are arbitrary, so are the results. I ask due to the lambda fit. Other things that can cause this are unincorporated measurement error (b/c it looks like a lot of evolution right at the tips, meaning little evolution along the branches). I'd suggest incorporating this (you can give known estimates of measurement error; some programs allow this to be estimated as well (I forget whether we have the estimation bit exposed in OUwie, but known error should be there at least)). Surface can estimate different regimes on the tree, but IIRC it does not estimate different rates, just OU means. I believe auteur (in geiger) and BAMM can model different BM rates on different branches, which sounds like your question. We have some code to try different OU models (including perhaps ones with different rates) on different branches buried somewhere in OUwie (we call it OUwie-dredge so people know to be cautious) but it hasn't been tested or published yet. One other caution: if you have a BM model, and are just modeling different rates, it can be done well. Trying to estimate different rates with OU models is harder to do well: there's interaction between alpha and sigma that can make them difficult to distinguish (not formally nonidentifiable [unlike OU means sometimes], just difficult). For me, I'd probably lean towards one of the BM rate heterogeneity methods for your question. Hope this helps, Brian [1] Hansen, T. F. and E. P. Martins. 1996. Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data. Evolution 50:1404-1417. _______________________________________ Brian O'Meara Associate Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info On Fri, Apr 15, 2016 at 10:20 AM, Belinda Kahnt <belind...@gmx.de<mailto:belind...@gmx.de>> wrote: Dear all, I am a newbie to this mailing list and phylogenetic analyses in R and hope you can comment on a question I have. I would like to estimate the rate of evolution of a continous trait and check if the trait evolves faster along some branches of the topology. I already checked with Pagels lambda if the trait evolves according to a Brownian motion model,(i.e. pure drift), which it did not (lambda ~ 0). Modelling the trait evolution under the Ornstein-Uhlenbeck (OU) model provided a significant better fit (p<- 0.01) with a very high alpha parameter of 8.7 (indicating a role of selection in trait evolution). In order to infer now the rate of trait evolution I am searching for a R package that is able to do this inference based on the OU model. However, so far I either just found methods based on the Brownian motion model (e.g. brownie.lite function in phytools, Motmot) or methods that also rely on the reconstruction of ancestral selective regimes beforehand (like mvMORPH or OUwie). I want to keep the model as simple as possible and therefore don't know if it is necessary to also model ancestral selective regimes if I just want to know if the evolutionary rate of the trait varies along branches and which branches show an accelerated rate?! Which programm would you recommend? I would be very thankful for your help and recommendations. Best wishes, Belinda _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org<mailto:R-sig-phylo@r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org<mailto:R-sig-phylo@r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]]
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