On a related note- does anyone know of a function or package that can parse and store all of the metadata associated with nodes and branches from a BEAST output file? read.beast from phyloch will parse all of the data associated with internal nodes, but not with terminal branches (for example, substitution rate information). I emailed the developer of that tool and he indicated this was by design (though he may be able to offer a solution).
Jake > On Oct 18, 2015, at 12:04 PM, Jacob Berv <jakeberv.r.sig.ph...@gmail.com> > wrote: > > Yes, this has come up in my reading…but there do seem to be situations where > ’nearly neutral’ substitutions can be negatively or positively associated > with population size: > > From Lanfear 2014 Population size and the rate of evolution: > > "Putting aside variation in the mutation rate, we largely expect the total > rate of evolution to be negatively correlated with Ne if slightly deleterious > mutations dominate evolution, and to be positively correlated with Ne if > advantageous mutations dominate evolution.” > "On the other hand, any process that leads to an association between Ne and > mutation rates will cause a similar association between Ne and neutral and > effectively neutral substitution rates. These processes could include effects > such as the evolution of mutation rates, and the co-variation of Ne with > life-history traits such as generation time” > > I think I need to read more about how to simulate these different kinds of > demographic scenarios. > > I suppose the question is, what is the more likely null hypothesis? That > mutation rates can change extremely rapidly? Or that demographic fluctuations > (pop size, generation time) can induce changes in the detectable substitution > rate among lineages. > > Jake > > > >> On Oct 17, 2015, at 11:21 PM, Liam J. Revell <liam.rev...@umb.edu> wrote: >> >> Hi Jacob. >> >> Can I add the somewhat boring & probably obvious comment that under the >> neutral theory of molecular evolution the substitution rate is independent >> of the effective population size? >> >> All the best, Liam >> >> Liam J. Revell, Associate Professor of Biology >> University of Massachusetts Boston >> web: http://faculty.umb.edu/liam.revell/ >> email: liam.rev...@umb.edu >> blog: http://blog.phytools.org >> >> On 10/17/2015 11:01 PM, Jacob Berv wrote: >>> Hmmm that seems somewhat indirect but might work… I’ll look into that. >>> >>> To give you more information - I’m actually trying to come up with a way to >>> test the idea that substitution rate shifts detected with a relaxed >>> molecular clock (BEAST) may be driven by changes in effective population >>> size. Simulating data for particular scenarios, and then running that >>> simulated data through BEAST could be a useful way to test some explicit >>> hypotheses I’m interested in. But I have to simulate the data first. >>> >>> Jake >>> >>> >>>> On Oct 17, 2015, at 10:40 PM, Brian O'Meara <omeara.br...@gmail.com> wrote: >>>> >>>> Dick Hudson's ms software can simulate gene trees along a species tree or >>>> network with migration, changing population size, etc. The package >>>> phyclust can call ms. You could then just simulate nucleotides on these >>>> gene trees. >>>> >>>> Best, >>>> Brian >>>> >>>> _______________________________________ >>>> Brian O'Meara >>>> Associate Professor >>>> Dept. of Ecology & Evolutionary Biology >>>> U. of Tennessee, Knoxville >>>> http://www.brianomeara.info <http://www.brianomeara.info/> >>>> >>>> Postdoc collaborators wanted: http://nimbios.org/postdocs/ >>>> <http://nimbios.org/postdocs/> >>>> Calendar: http://www.brianomeara.info/calendars/omeara >>>> <http://www.brianomeara.info/calendars/omeara> >>>> On Sat, Oct 17, 2015 at 10:12 PM, Jacob Berv >>>> <jakeberv.r.sig.ph...@gmail.com <mailto:jakeberv.r.sig.ph...@gmail.com>> >>>> wrote: >>>> Dear R-sig-phylo, >>>> >>>> I have a somewhat general simulation question and I was hoping someone on >>>> here might have some insight. >>>> >>>> I’m trying to figure out if it’s possible to simulate nucleotide sequence >>>> data (an arbitrary number of neutral loci under a multi species coalescent >>>> model), on an ultrametric input topology (where tips represent species), >>>> with user defined changes in effective population size at the start and >>>> end of a particular internal branch. In my searching I’ve come across some >>>> software by Deren Eaton (https://github.com/dereneaton/simLoci >>>> <https://github.com/dereneaton/simLoci> >>>> <https://github.com/dereneaton/simLoci >>>> <https://github.com/dereneaton/simLoci>>) that looks like it might do what >>>> I want - but I’m not sure. It looks like I can specify migration events >>>> between taxa, but perhaps not population size changes on internal >>>> branches. There are many other applications for simulating sequence data >>>> but I am not familiar with any of them. Any thoughts would be appreciated! >>>> >>>> Thanks, >>>> >>>> Jacob Berv >>>> >>>> Ph.D. Student >>>> Lovette Lab >>>> Cornell Laboratory of Ornithology >>>> >>>> >>>> [[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 >>>> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >>>> Searchable archive at >>>> http://www.mail-archive.com/r-sig-phylo@r-project.org/ >>>> <http://www.mail-archive.com/r-sig-phylo@r-project.org/> >>> >>> Jacob Berv >>> >>> Ph.D. Student >>> Lovette Lab >>> Cornell Laboratory of Ornithology >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> R-sig-phylo mailing list - 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/ >>> > > Jacob Berv > > Ph.D. Student > Lovette Lab > Cornell Laboratory of Ornithology > _______________________________________________ R-sig-phylo mailing list - 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/
