[R-sig-Geo] [R-sig-phylo] BiSSE/MacroCAIC on Non-Ultrametric Tree with Polytomies?

[Nick Matzke]

Hi again...brief thought -- I am so used to thinking about diversification
in terms of speciation and extinction rates in units of time, it's hard to
think about how a study of correlation between a trait and
diversification/species richness would work without a time-scaled tree.
However, there are some methods that use tree-balance statistics, and thus
only require topology -- see work by Brian Moore. I think they require
pretty dramatic differences between sister groups to infer rate shifts
though.  Cheers!
Nick



On Fri, Apr 15, 2016 at 6:59 AM, Brian A. Gill <gillbriana at gmail.com> wrote:

> Hi David and Joe.
>
> Thanks for your input/questions.
>
> David: My tree is non-ultrametric because it is undated tree of extant
> taxa. It does not include taxa from the fossil record. Making a dated tree
> seems like a good option, but what about the option of using NonParametric
> Rate Smoothing (NPRS) or some other conversion to make my existing tree
> ultrametric? I see this approach in some studies.
>
> Alternatively, sister-clade comparisons could be an option, but it seems
> like they are old and not powerful. Based on my tree topology and the
> number of taxa, I'm not sure I have enough contrasts for a robust test.
>
> Joe: For BiSSE, the discrete binary predictor is assumed to evolve
> according to a Markov model along the tree. The model is then used to
> estimate speciation, extinction, and character transition rates. For
> MacroCAIC, I assume the a discrete binary trait would be modeled in a
> similar way to determine the states of internal nodes on the tree.
>
> So, thinking about evolution of a discrete trait by a Markov process on a
> non-ultrametric tree, it seems for BiSSE having non-contemporaneous
> lineages would inappropriately inflate the extinction parameter. For
> MacroCAIC, I can't think of a reason why a non-ultrametric tree would be
> problematic other than how differences in lengths of branches based on
> relative divergence vs. absolute time might affect estimates of states at
> internal nodes. If this is the case, does that mean that other procedures
> using Markov transition matrices cannot be used on trees with relative
> divergence for branch lengths (e.g. stochastic character mapping)?
>
> Thanks for all the help.
>
>
> Brian
>
>
>
>
>
>
>
> On Thu, Apr 14, 2016 at 8:26 AM, David Bapst <dwbapst at gmail.com> wrote:
>
> > Brian-
> >
> > Is your tree non-ultrametric because it contains extinct taxa from the
> > fossil record, or is it simply an undated tree of extant taxa?
> >
> > To my knowledge, there isn't yet a satisfactory solution to the first
> > (no BISSE for paleo-phylogenies) but if the second then, it seems the
> > best route would be to date it and use the methods developed for
> > ultrametric trees.
> >
> > Cheers,
> > -Dave
> >
> > On Wed, Apr 13, 2016 at 3:09 PM, Brian A. Gill <gillbriana at gmail.com>
> > wrote:
> > > Hi Everyone.
> > >
> > > I'm trying to look at the association between a discrete binary
> predictor
> > > (Latitude: Colorado/Ecuador) and a continuous response (species
> > richness).
> > >
> > > My phylogeny is a 50% majority rule consensus tree made in MrBayes. The
> > > tree has polytomies and is not ultrametric.
> > >
> > > I've found the methods below for looking at the influence of a discrete
> > > binary trait on richness, but I'm not sure if my tree is suitable or if
> > > there is a better approach.
> > >
> > > 1) Diversitree package BiSSE
> > > 2) Caper package using MacroCAIC
> > >
> > > Any suggestions would be greatly appreciated.
> > >
> > > Thank You.
> > >
> > >
> > > Brian
> > >
> > > --
> > > Brian A. Gill
> > >
> > > VISIT MY WEBSITE:
> > > http://gillbriana.wix.com/brian-gill
> > >
> > > FOLLOW ME ON TWITTER:
> > > @CSUBrianGill
> > >
> > > Colorado State University Biology
> > > 1878 Campus Delivery
> > > Fort Collins, CO 80523
> > > United States of America
> > >
> > > 970-215-7037
> > >
> > >         [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
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> > > Searchable archive at
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> >
> >
> >
> > --
> > David W. Bapst, PhD
> > Adjunct Asst. Professor, Geology and Geol. Eng.
> > South Dakota School of Mines and Technology
> > 501 E. St. Joseph
> > Rapid City, SD 57701
> >
> > http://webpages.sdsmt.edu/~dbapst/
> > http://cran.r-project.org/web/packages/paleotree/index.html
> >
>
>
>
> --
> Brian A. Gill
>
> VISIT MY WEBSITE:
> http://gillbriana.wix.com/brian-gill
>
> FOLLOW ME ON TWITTER:
> @CSUBrianGill
>
> Colorado State University Biology
> 1878 Campus Delivery
> Fort Collins, CO 80523
> United States of America
>
> 970-215-7037
>
>         [[alternative HTML version deleted]]
>
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