[R-sig-phylo] quantitative state dependent diversification of another quantitative trait

[Zach Culumber]

Hi everyone,

We are interested in examining whether shifts in one continuous trait have
preceded shifts in another continuous trait through evolutionary time for a
phylogeny of ~80 species. To do this we were thinking of calculating the
change in the value of each trait for each tip to its most recent ancestor
(i.e., node) and then for each node to its most recent ancestral node. We
have all the tip values and conducted ASR to get the node values. However,
we are unaware of any functions or packages that would automate calculation
of all these distances for teach tip and node to its most recent ancestor.
Does anyone have any suggestions of functions or packages that might
possibly do this? Alternatively, are there better existing options for
exploring this question? I.e., something similar to QuaSSE but for analysis
between two quantitative traits rather than traits and species
diversification? Something like Bayes Traits or PGLS would allow tests of
correlated evolution, but not the order of evolutionary shifts.

Thank you for any insights!

Zach

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[Brian O'Meara]

I think you want SLOUCH: Hansen et al. 2008:
https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.2008.00412.x.
One trait evolves under Brownian motion, another trait follows it.

Best,
Brian

_______________________________________________________________________
Brian O'Meara, http://www.brianomeara.info, especially Calendar
<http://brianomeara.info/calendars/omeara/>, CV
<http://brianomeara.info/cv/>, and Feedback
<http://brianomeara.info/teaching/feedback/>

Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Director for Postdoctoral Activities, National Institute for
Mathematical & Biological Synthesis <http://www.nimbios.org> (NIMBioS)


On Wed, Apr 4, 2018 at 2:43 PM, Zach Culumber <***@gmail.com> wrote:

> Hi everyone,
>
> We are interested in examining whether shifts in one continuous trait have
> preceded shifts in another continuous trait through evolutionary time for a
> phylogeny of ~80 species. To do this we were thinking of calculating the
> change in the value of each trait for each tip to its most recent ancestor
> (i.e., node) and then for each node to its most recent ancestral node. We
> have all the tip values and conducted ASR to get the node values. However,
> we are unaware of any functions or packages that would automate calculation
> of all these distances for teach tip and node to its most recent ancestor.
> Does anyone have any suggestions of functions or packages that might
> possibly do this? Alternatively, are there better existing options for
> exploring this question? I.e., something similar to QuaSSE but for analysis
> between two quantitative traits rather than traits and species
> diversification? Something like Bayes Traits or PGLS would allow tests of
> correlated evolution, but not the order of evolutionary shifts.
>
> Thank you for any insights!
>
> Zach
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-phylo mailing list - R-sig-***@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-
> sig-***@r-project.org/
>

[[alternative HTML version deleted]]

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[Julien Clavel]

Hi Zach,

In addition to SLOUCH (for a OU tracking a BM process) you can use mvMORPH for fitting a model where a trait evolving under an OU process follow another trait evolving under OU with some evolutionary lag (see p. 14-15 of the package vignette “How to use mvMORPH”).

Best wishes,

Julien

________________________________
De : R-sig-phylo <r-sig-phylo-***@r-project.org> de la part de Brian O'Meara <***@gmail.com>
Envoyé : mercredi 4 avril 2018 22:39
À : Zach Culumber
Cc : mailman, r-sig-phylo
Objet : Re: [R-sig-phylo] quantitative state dependent diversification of another quantitative trait

I think you want SLOUCH: Hansen et al. 2008:
https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.2008.00412.x.
One trait evolves under Brownian motion, another trait follows it.

Best,
Brian

_______________________________________________________________________
Brian O'Meara, http://www.brianomeara.info, especially Calendar
<http://brianomeara.info/calendars/omeara/>, CV
<http://brianomeara.info/cv/>, and Feedback
<http://brianomeara.info/teaching/feedback/>

Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Director for Postdoctoral Activities, National Institute for
Mathematical & Biological Synthesis <http://www.nimbios.org> (NIMBioS)


On Wed, Apr 4, 2018 at 2:43 PM, Zach Culumber <***@gmail.com> wrote:

> Hi everyone,
>
> We are interested in examining whether shifts in one continuous trait have
> preceded shifts in another continuous trait through evolutionary time for a
> phylogeny of ~80 species. To do this we were thinking of calculating the
> change in the value of each trait for each tip to its most recent ancestor
> (i.e., node) and then for each node to its most recent ancestral node. We
> have all the tip values and conducted ASR to get the node values. However,
> we are unaware of any functions or packages that would automate calculation
> of all these distances for teach tip and node to its most recent ancestor.
> Does anyone have any suggestions of functions or packages that might
> possibly do this? Alternatively, are there better existing options for
> exploring this question? I.e., something similar to QuaSSE but for analysis
> between two quantitative traits rather than traits and species
> diversification? Something like Bayes Traits or PGLS would allow tests of
> correlated evolution, but not the order of evolutionary shifts.
>
[[elided Hotmail spam]]
>
> Zach
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-phylo mailing list - R-sig-***@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-
> sig-***@r-project.org/
>

[[alternative HTML version deleted]]

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[Zach Culumber]

Thank you Brian and Julien! Those packages do indeed make it easier to get
at our question!

Cheers,
Zach

On Wed, Apr 4, 2018 at 5:57 PM, Julien Clavel <***@hotmail.fr>
wrote:

> Hi Zach,
>
>
>
> In addition to SLOUCH (for a OU tracking a BM process) you can use mvMORPH
> for fitting a model where a trait evolving under an OU process follow
> another trait evolving under OU with some evolutionary lag (see p. 14-15 of
> the package vignette “How to use mvMORPH”).
>
>
>
> Best wishes,
>
>
>
> Julien
>
> ------------------------------
> *De :* R-sig-phylo <r-sig-phylo-***@r-project.org> de la part de
> Brian O'Meara <***@gmail.com>
> *Envoyé :* mercredi 4 avril 2018 22:39
> *À :* Zach Culumber
> *Cc :* mailman, r-sig-phylo
> *Objet :* Re: [R-sig-phylo] quantitative state dependent diversification
> of another quantitative trait
>
> I think you want SLOUCH: Hansen et al. 2008:
> https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.2008.00412.x.
> One trait evolves under Brownian motion, another trait follows it.
>
> Best,
> Brian
>
> _______________________________________________________________________
> Brian O'Meara, http://www.brianomeara.info, especially Calendar
> <http://brianomeara.info/calendars/omeara/>, CV
> <http://brianomeara.info/cv/>, and Feedback
> <http://brianomeara.info/teaching/feedback/>
>
> Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville
> Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville
> Associate Director for Postdoctoral Activities, National Institute for
> Mathematical & Biological Synthesis <http://www.nimbios.org> (NIMBioS)
>
>
>
> On Wed, Apr 4, 2018 at 2:43 PM, Zach Culumber <***@gmail.com> wrote:
>
> > Hi everyone,
> >
> > We are interested in examining whether shifts in one continuous trait
> have
> > preceded shifts in another continuous trait through evolutionary time
> for a
> > phylogeny of ~80 species. To do this we were thinking of calculating the
> > change in the value of each trait for each tip to its most recent
> ancestor
> > (i.e., node) and then for each node to its most recent ancestral node.
> We
> > have all the tip values and conducted ASR to get the node values.
> However,
> > we are unaware of any functions or packages that would automate
> calculation
> > of all these distances for teach tip and node to its most recent
> ancestor.
> > Does anyone have any suggestions of functions or packages that might
> > possibly do this? Alternatively, are there better existing options for
> > exploring this question? I.e., something similar to QuaSSE but for
> analysis
> > between two quantitative traits rather than traits and species
> > diversification? Something like Bayes Traits or PGLS would allow tests
> of
> > correlated evolution, but not the order of evolutionary shifts.
> >
> > Thank you for any insights!
> >
> > Zach
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-phylo mailing list - R-sig-***@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> > Searchable archive at http://www.mail-archive.com/r-
> > sig-***@r-project.org/
> >
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-phylo mailing list - R-sig-***@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-
> sig-***@r-project.org/
>



--
Zachary W. Culumber
Postdoctoral Research Associate
Florida State University
Department of Biological Science
http://www.zwcresearch.com

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