Hi Dan, Fitting models with two distinct modes of trait evolution is possible with the mvSHIFT function in mvMORPH. You just need to map on the tree the two clades (or selective regimes, groups... otherwise) of interest rather than two times periods. The mapping can easily be done using the make.simmap or the paintSupTree functions in phytools. The package handle both univariate and multivariate data. Best, Julien
Date: Fri, 29 May 2015 08:27:31 -0700 From: [email protected] To: [email protected] CC: [email protected]; [email protected]; [email protected] Subject: Re: [R-sig-phylo] clade-specific release and radiate model? Hi Brian, Thanks for your thoughtful response! Those are very good points about identifiability and penalization of the OU mean for the "released" clade. The censored model is an appealing approach, especially since the timing of the release along the (stem) branch leading to the released clade is unknown, and somewhat beside the point. In the case in question several novel morphological-mechanical structures had to evolve to enable the release, and whether those evolved gradually or not along the stem branch is an open question -- perhaps unknowable from analyzing extant taxa. In thinking about this a bit more, though, I think methods for an epoch release may be able to accommodate a clade-specific scenario, at least if the timing of the mode shift is specified using SIMMAP trees and not a shift-time parameter. Slater 2013 has R code associated with it that implements release models, and there's a multivariate implementation of release (and other mode shift) models in the new mvMORPH package (which is on CRAN, but not yet published as a manuscript as far as I can tell). In skimming Slater's code it doesn't seem to use SIMMAP trees. However, mvMORPH's shift specification can be done with SIMMAP trees, and I see no reason why its mvSHIFT function would care whether the shift is clade-specific or not. I'm cc'ing Graham and Julien to see if they have something to add. Regarding the use of mvSHIFT, I don't have multivariate data; hopefully that won't be a problem. Cheers, Dan. Brian O'Meara wrote: Hi, Daniel. It's a bit arguable whether as alpha -> 0, OU -> BM: I think it should, but IIRC in OUCH this doesn't happen, and that's a deliberate choice. That said, I think that an OU with alpha near zero would be ok for your question, though you might want to think about how to penalize parameters (that is, for that clade there'd be an OU mean parameter that is unidentifiable (alpha of zero, so no pull, so no evidence for it): should you count this as a parameter when doing model comparison? I'd argue no: you're doing OU with alpha of zero as a kludgy hack to treat it as BM). Another approach would be to resuscitate the "censored" model of O'Meara et al. 2006. Slice your tree on the edge leading to the released clade (I guess this truly releases the clade to roam free of its relatives) so you have the paraphyletic non-released set and the released clade as separate trees. Then you can try fitting the same or different models to the two trees. The downside of this is that you must use an additional ancestral state (at the MRCA of the released clade); the upside is that any weird changes happening on the edge leading to the released clade aren't in the model and so don't affect the fit (you could imagine that whatever led the clade to be ecologically released happened somewhere on the stem edge, but you don't know where, and it could be associated with a major single shift in your continuous trait, too). You could try an OU on the non-released tree (let's call this A) and an OU on the released clade (B), OU on A and BM on B, etc. The only practical difficulty with this is constraining the cases where A and B are supposed to have the same model: by default, optimization will happen separately in different trees, but you can create a wrapper function that calls OUwie.fixed() separately on A and B but with the same parameters and adds the likelihood and then optimize the parameters in this wrapper function. Hope this helps,Brian On Fri, May 29, 2015 at 2:02 AM, Daniel Fulop <[email protected]> wrote: Hi All, Do you know if there are any methods out there for fitting ecological release and release and radiate models that are clade-specific? That is, in which the change in mode (OU to BM) happens at the root of a clade instead of at specific time for the whole phylogeny (as in Slater 2013). As far as I know the closest out there are models in OUwie, say with a clade-specific second OU process with a very low alpha. However, I don't think that biologically OU is a good model for the trait and clade in question (though it is for the rest of the tree). I know that at the limit as alpha -> 0 OU converts to BM, but I would ideally still like compare standard models' fits (including OUwie models) to the fits of clade-specific release models. Any leads or suggestions would be much appreciated, especially about how to implement these clade-specific models with current tools or about how to "roll my own". Thanks! Dan. -- Daniel Fulop, Ph.D. Postdoctoral Scholar Dept. Plant Biology, UC Davis Maloof Lab, Rm. 2220 Life Sciences Addition, One Shields Ave. Davis, CA 95616 _______________________________________________ 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]/ -- Daniel Fulop, Ph.D. Postdoctoral Scholar Dept. Plant Biology, UC Davis Maloof Lab, Rm. 2220 Life Sciences Addition, One Shields Ave. Davis, CA 95616 510-253-7462 [email protected] [[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]/
