Re: [R-sig-phylo] Testing for phylogenetic signal in proportions
Hello,
pPCA will find combination of traits (chemicals) which are phylogenetically
structured, but won't provide a formal test for the structures. You could try
Abouheif's test for this; see ?abouheif.moran in adephylo. The vignette may
also be useful:
vignette("adephylo")
Cheers
Thibaut.
From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on
behalf of Emmanuel Paradis [emmanuel.para...@ird.fr]
Sent: 15 March 2012 05:09
To: Rob Lanfear; r-sig-phylo-boun...@r-project.org; Theodore Garland Jr
Cc: r-sig-phylo
Subject: Re: [R-sig-phylo] Testing for phylogenetic signal in proportions
Hi Rob,
You may try ppca() in adephylo. A "test" of phylogenetic signal is given by the
sign of the eigenvalues.
Cheers,
Emmanuel
-Original Message-
From: Rob Lanfear
Sender: r-sig-phylo-boun...@r-project.org
Date: Thu, 15 Mar 2012 15:54:29
To: Theodore Garland Jr
Cc: r-sig-phylo
Subject: Re: [R-sig-phylo] Testing for phylogenetic signal in proportions
Hi Ted,
Thanks for the pointer - I wasn't aware of that paper.
Phylogenetic signal might be out, but do you (or others) think it would be
possible to compare rates of change in the proportions. For instance, a
striking pattern in the data is that one of the proportions remains almost
constant across species, while others vary a great deal.
I had in mind that one way to statistically compare these would be to
estimate rates of change (with an appropriate model) for each trait, and
then to test for differences in rates of change by fixing rates for a given
trait to the ML rate for each of the other traits, and comparing
likelihoods with a likelihood ratio test.
That might be overkill on the data, given that the sample size is small and
the pattern is pretty obvious visually, but it would be nice to know under
some reasonable null model whether the differences we see could have arisen
by chance.
Does something like that sound plausible?
Rob
On 15 March 2012 14:23, Theodore Garland Jr wrote:
> It is really too few species to have a sufficiently powerful test for
> phylogenetic signal. See Blomberg et al. (2003), available on my website.
>
> Cheers,
> Ted
>
> Theodore Garland, Jr.
> Professor
> Department of Biology
> University of California, Riverside
> Riverside, CA 92521
> Office Phone: (951) 827-3524
> Wet Lab Phone: (951) 827-5724
> Dry Lab Phone: (951) 827-4026
> Home Phone: (951) 328-0820
> Facsimile: (951) 827-4286 = Dept. office (not confidential)
> Email: tgarl...@ucr.edu
> http://www.biology.ucr.edu/people/faculty/Garland.html
>
> Experimental Evolution: Concepts, Methods, and Applications of Selection
> Experiments. 2009.
> Edited by Theodore Garland, Jr. and Michael R. Rose
> http://www.ucpress.edu/book.php?isbn=9780520261808
> (PDFs of chapters are available from me or from the individual authors)
>
>
> From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org]
> on behalf of Rob Lanfear [rob.lanf...@gmail.com]
> Sent: Wednesday, March 14, 2012 8:18 PM
> To: r-sig-phylo
> Subject: [R-sig-phylo] Testing for phylogenetic signal in proportions
>
> Hi All,
>
> I've tried searching the literature for this but the search terms tend to
> give irrelevant papers, so I thought I'd ask for some guidance here.
>
> I have a set of 11 species, an ultrametric tree for the species, and for
> each species I have a set of proportional data for 5 chemical traits. E.g.
> for spp1 my data might be: chemicalA=10%, chemicalB=50%, chemicalC=1%,
> chemicalD=19%, chemicalE=20%. The set of traits for each species always
> sums to 100%, but I don't know, and can't measure, the absolute values of
> the traits. Biologically speaking, this is OK, because it's the proportions
> that I'm interested in.
>
> I want to test for phylogenetic signal in these traits, and estimate the
> rate of change of each proportion along the phylogeny. Can anyone point me
> to any appropriate references for the methods and pitfalls of attempting to
> do this with proportion data? I can see that proportional data will have
> some odd properties (non-independence of traits, bounded (i.e.
> non-Brownian) evolution, etc.), but the best way of accounting for these is
> not immediately apparent to me.
>
> Thanks,
>
> Rob
>
> --
> Rob Lanfear
> Research Fellow,
> Ecology, Evolution, and Genetics,
> Research School of Biology,
> Australian National University
>
> Tel: +61 2 6125 4321
> www.robertlanfear.com
>
> [[alternative HTML version deleted]]
>
> ___
> R-sig-phylo mailing list
> R-sig-phylo@r-
Re: [R-sig-phylo] Testing for phylogenetic signal in proportions
Hi Rob, You may try ppca() in adephylo. A "test" of phylogenetic signal is given by the sign of the eigenvalues. Cheers, Emmanuel -Original Message- From: Rob Lanfear Sender: r-sig-phylo-boun...@r-project.org Date: Thu, 15 Mar 2012 15:54:29 To: Theodore Garland Jr Cc: r-sig-phylo Subject: Re: [R-sig-phylo] Testing for phylogenetic signal in proportions Hi Ted, Thanks for the pointer - I wasn't aware of that paper. Phylogenetic signal might be out, but do you (or others) think it would be possible to compare rates of change in the proportions. For instance, a striking pattern in the data is that one of the proportions remains almost constant across species, while others vary a great deal. I had in mind that one way to statistically compare these would be to estimate rates of change (with an appropriate model) for each trait, and then to test for differences in rates of change by fixing rates for a given trait to the ML rate for each of the other traits, and comparing likelihoods with a likelihood ratio test. That might be overkill on the data, given that the sample size is small and the pattern is pretty obvious visually, but it would be nice to know under some reasonable null model whether the differences we see could have arisen by chance. Does something like that sound plausible? Rob On 15 March 2012 14:23, Theodore Garland Jr wrote: > It is really too few species to have a sufficiently powerful test for > phylogenetic signal. See Blomberg et al. (2003), available on my website. > > Cheers, > Ted > > Theodore Garland, Jr. > Professor > Department of Biology > University of California, Riverside > Riverside, CA 92521 > Office Phone: (951) 827-3524 > Wet Lab Phone: (951) 827-5724 > Dry Lab Phone: (951) 827-4026 > Home Phone: (951) 328-0820 > Facsimile: (951) 827-4286 = Dept. office (not confidential) > Email: tgarl...@ucr.edu > http://www.biology.ucr.edu/people/faculty/Garland.html > > Experimental Evolution: Concepts, Methods, and Applications of Selection > Experiments. 2009. > Edited by Theodore Garland, Jr. and Michael R. Rose > http://www.ucpress.edu/book.php?isbn=9780520261808 > (PDFs of chapters are available from me or from the individual authors) > > > From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] > on behalf of Rob Lanfear [rob.lanf...@gmail.com] > Sent: Wednesday, March 14, 2012 8:18 PM > To: r-sig-phylo > Subject: [R-sig-phylo] Testing for phylogenetic signal in proportions > > Hi All, > > I've tried searching the literature for this but the search terms tend to > give irrelevant papers, so I thought I'd ask for some guidance here. > > I have a set of 11 species, an ultrametric tree for the species, and for > each species I have a set of proportional data for 5 chemical traits. E.g. > for spp1 my data might be: chemicalA=10%, chemicalB=50%, chemicalC=1%, > chemicalD=19%, chemicalE=20%. The set of traits for each species always > sums to 100%, but I don't know, and can't measure, the absolute values of > the traits. Biologically speaking, this is OK, because it's the proportions > that I'm interested in. > > I want to test for phylogenetic signal in these traits, and estimate the > rate of change of each proportion along the phylogeny. Can anyone point me > to any appropriate references for the methods and pitfalls of attempting to > do this with proportion data? I can see that proportional data will have > some odd properties (non-independence of traits, bounded (i.e. > non-Brownian) evolution, etc.), but the best way of accounting for these is > not immediately apparent to me. > > Thanks, > > Rob > > -- > Rob Lanfear > Research Fellow, > Ecology, Evolution, and Genetics, > Research School of Biology, > Australian National University > > Tel: +61 2 6125 4321 > www.robertlanfear.com > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- Rob Lanfear Research Fellow, Ecology, Evolution, and Genetics, Research School of Biology, Australian National University Tel: +61 2 6125 4321 www.robertlanfear.com [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Testing for phylogenetic signal in proportions
Hi Ted, Thanks for the pointer - I wasn't aware of that paper. Phylogenetic signal might be out, but do you (or others) think it would be possible to compare rates of change in the proportions. For instance, a striking pattern in the data is that one of the proportions remains almost constant across species, while others vary a great deal. I had in mind that one way to statistically compare these would be to estimate rates of change (with an appropriate model) for each trait, and then to test for differences in rates of change by fixing rates for a given trait to the ML rate for each of the other traits, and comparing likelihoods with a likelihood ratio test. That might be overkill on the data, given that the sample size is small and the pattern is pretty obvious visually, but it would be nice to know under some reasonable null model whether the differences we see could have arisen by chance. Does something like that sound plausible? Rob On 15 March 2012 14:23, Theodore Garland Jr wrote: > It is really too few species to have a sufficiently powerful test for > phylogenetic signal. See Blomberg et al. (2003), available on my website. > > Cheers, > Ted > > Theodore Garland, Jr. > Professor > Department of Biology > University of California, Riverside > Riverside, CA 92521 > Office Phone: (951) 827-3524 > Wet Lab Phone: (951) 827-5724 > Dry Lab Phone: (951) 827-4026 > Home Phone: (951) 328-0820 > Facsimile: (951) 827-4286 = Dept. office (not confidential) > Email: tgarl...@ucr.edu > http://www.biology.ucr.edu/people/faculty/Garland.html > > Experimental Evolution: Concepts, Methods, and Applications of Selection > Experiments. 2009. > Edited by Theodore Garland, Jr. and Michael R. Rose > http://www.ucpress.edu/book.php?isbn=9780520261808 > (PDFs of chapters are available from me or from the individual authors) > > > From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] > on behalf of Rob Lanfear [rob.lanf...@gmail.com] > Sent: Wednesday, March 14, 2012 8:18 PM > To: r-sig-phylo > Subject: [R-sig-phylo] Testing for phylogenetic signal in proportions > > Hi All, > > I've tried searching the literature for this but the search terms tend to > give irrelevant papers, so I thought I'd ask for some guidance here. > > I have a set of 11 species, an ultrametric tree for the species, and for > each species I have a set of proportional data for 5 chemical traits. E.g. > for spp1 my data might be: chemicalA=10%, chemicalB=50%, chemicalC=1%, > chemicalD=19%, chemicalE=20%. The set of traits for each species always > sums to 100%, but I don't know, and can't measure, the absolute values of > the traits. Biologically speaking, this is OK, because it's the proportions > that I'm interested in. > > I want to test for phylogenetic signal in these traits, and estimate the > rate of change of each proportion along the phylogeny. Can anyone point me > to any appropriate references for the methods and pitfalls of attempting to > do this with proportion data? I can see that proportional data will have > some odd properties (non-independence of traits, bounded (i.e. > non-Brownian) evolution, etc.), but the best way of accounting for these is > not immediately apparent to me. > > Thanks, > > Rob > > -- > Rob Lanfear > Research Fellow, > Ecology, Evolution, and Genetics, > Research School of Biology, > Australian National University > > Tel: +61 2 6125 4321 > www.robertlanfear.com > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- Rob Lanfear Research Fellow, Ecology, Evolution, and Genetics, Research School of Biology, Australian National University Tel: +61 2 6125 4321 www.robertlanfear.com [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Testing for phylogenetic signal in proportions
It is really too few species to have a sufficiently powerful test for phylogenetic signal. See Blomberg et al. (2003), available on my website. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026 Home Phone: (951) 328-0820 Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments. 2009. Edited by Theodore Garland, Jr. and Michael R. Rose http://www.ucpress.edu/book.php?isbn=9780520261808 (PDFs of chapters are available from me or from the individual authors) From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Rob Lanfear [rob.lanf...@gmail.com] Sent: Wednesday, March 14, 2012 8:18 PM To: r-sig-phylo Subject: [R-sig-phylo] Testing for phylogenetic signal in proportions Hi All, I've tried searching the literature for this but the search terms tend to give irrelevant papers, so I thought I'd ask for some guidance here. I have a set of 11 species, an ultrametric tree for the species, and for each species I have a set of proportional data for 5 chemical traits. E.g. for spp1 my data might be: chemicalA=10%, chemicalB=50%, chemicalC=1%, chemicalD=19%, chemicalE=20%. The set of traits for each species always sums to 100%, but I don't know, and can't measure, the absolute values of the traits. Biologically speaking, this is OK, because it's the proportions that I'm interested in. I want to test for phylogenetic signal in these traits, and estimate the rate of change of each proportion along the phylogeny. Can anyone point me to any appropriate references for the methods and pitfalls of attempting to do this with proportion data? I can see that proportional data will have some odd properties (non-independence of traits, bounded (i.e. non-Brownian) evolution, etc.), but the best way of accounting for these is not immediately apparent to me. Thanks, Rob -- Rob Lanfear Research Fellow, Ecology, Evolution, and Genetics, Research School of Biology, Australian National University Tel: +61 2 6125 4321 www.robertlanfear.com [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Testing for phylogenetic signal in proportions
Hi All, I've tried searching the literature for this but the search terms tend to give irrelevant papers, so I thought I'd ask for some guidance here. I have a set of 11 species, an ultrametric tree for the species, and for each species I have a set of proportional data for 5 chemical traits. E.g. for spp1 my data might be: chemicalA=10%, chemicalB=50%, chemicalC=1%, chemicalD=19%, chemicalE=20%. The set of traits for each species always sums to 100%, but I don't know, and can't measure, the absolute values of the traits. Biologically speaking, this is OK, because it's the proportions that I'm interested in. I want to test for phylogenetic signal in these traits, and estimate the rate of change of each proportion along the phylogeny. Can anyone point me to any appropriate references for the methods and pitfalls of attempting to do this with proportion data? I can see that proportional data will have some odd properties (non-independence of traits, bounded (i.e. non-Brownian) evolution, etc.), but the best way of accounting for these is not immediately apparent to me. Thanks, Rob -- Rob Lanfear Research Fellow, Ecology, Evolution, and Genetics, Research School of Biology, Australian National University Tel: +61 2 6125 4321 www.robertlanfear.com [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
