A deep thought on this topic, from a mind run aground amidst grading papers.
While I am a big fan of using multiple trees, we should keep in mind
that phylogenetic uncertainty makes signal into a rather snaky
concept. By this, I mean that there could have only been one true
history (which may or may not be captured within our sample of
potentially true-ish phylogenetic reconstructions). Thus, even if
phylogenetic signal was perfect in a given trait, we would
underestimate the extent of that signal on all trees except for the
true tree. It should be very hard for a trait with less than perfect
signal to appear to have higher amounts of signal than reality, as
that would require a phylogeny that perfectly matches the distortions
from the expectation under true signal. Thus, whatever distribution of
signal estimates we obtain from a distribution of trees, we should
probably expect the upper tail to be closer to reality than the mean
(Something similar should also be true of rates, where inaccurate
trees are probably more likely to upwardly bias rate estimates, rather
than downward. Slow rates should be much harder to accurately measure.
In both cases, based on my experience looking at how parameter
estimates vary in simulations with different dating methods, I think
the effects will be partly exacerbated by variation in the dating
(i.e. branch lengths) and affected less by differences in topology
that don't greatly impact the divergence times.)
...Or maybe I'm just crazy.
On Thu, Dec 8, 2016 at 9:53 AM, Brian O'Meara <omeara.br...@gmail.com> wrote:
> Well, since 1000 are a sample, 100 sampled from those is a somewhat more
> manageable sample.
> As to using, say, an 80% cutoff is a valid procedure, one question is what
> you're doing this for. I'd be tempted to just show or report the
> distribution of K, lambda, and p values and talk about what they mean in
> terms of your biological question: "We don't know the tree exactly, but
> it's clear that for most feasible trees, related things are similar" or
> something like that. If it's a question of scaling trees for later
> analyses, you can just (using a script, or built in functions) choose the
> particular scaling to be appropriate for each tree, and so the distribution
> across them doesn't matter in that case.
> Brian O'Meara, http://www.brianomeara.info, especially Calendar
> <http://brianomeara.info/calendars/omeara/>, CV
> <http://brianomeara.info/cv/>, and 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)
> Communication Director, Society of Systematic Biologists
> On Thu, Dec 8, 2016 at 11:26 AM, Carturan, Bruno <bruno.cartu...@ubc.ca>
>> Hello R-sig-phylo community,
>> I am trying to measure the phylogenetic signal of functional traits with
>> the Blomberg’s K and Pagel’s λ methods. My problem is that I don’t have one
>> phylogenetic tree but 1000 (the trees were created by first combining
>> different molecular, morphologic and taxonomic trees, then by conducting a
>> MCMC analysis and finally by selecting the 1000 trees – work made by Huang
>> and Roy 2015).
>> Is there a way to proceed to test the significance of the K and λ values
>> for each trait with these 1000 trees?
>> An idea I have is to run the test and obtain a p value for each of the
>> 1000 trees, which would give me a distribution of p values, and then
>> consider that if 80% (for instance) of the p values are significant, the K
>> or λ value is significant. This is computationally very demanding (I have
>> 735 species) and I don’t know if this could be considered as a valid
>> I am looking forward for you answer.
>> Bruno Carturan
>> PhD Candidate
>> Complex Environmental Systems Lab
>> University of British Columbia
>> Okanagan Campus
>> From: Liam J. Revell [liam.rev...@umb.edu]
>> Sent: Wednesday, December 07, 2016 6:54 AM
>> To: Carturan, Bruno
>> Subject: Re: A question about phylogenetic signal significance with 1000
>> This is an interesting question. Since this doesn't pertain specifically
>> to phytools, perhaps you should pose it to the R-sig-phylo email
>> list-serve. You may get a good answer there.
>> All the best,
>> 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 12/6/2016 6:16 PM, Carturan, Bruno wrote:
>> > Hello Dr. Revell,
>> > I am a PhD student from the Complex Environmental Systems Lab, from the
>> > University of British Columbia and I would like to ask you question.
>> > I am trying to measure the phylogenetic signal of functional traits with
>> > the Blomberg’s K and Pagel’s λ methods. My problem is that I don’t have
>> > one phylogenetic tree but 1000 (the trees were created by first
>> > combining different molecular, morphologic and taxonomic trees, then by
>> > conducting a MCMC analysis and finally by selecting the 1000 trees –
>> > work made by Huang and Roy 2015).
>> > Is there a way to proceed to test the significance of the K and λ values
>> > for each trait with these 1000 trees?
>> > An idea I have is to run the test and obtain a p value for each of the
>> > 1000 trees, which would give me a distribution of p values, and then
>> > consider that if 80% (for instance) of the p values are significant, the
>> > K or λ value is significant. This is computationally very demanding (I
>> > have 735 species) and I don’t know if this could be considered as a
>> > valid procedure.
>> > I am looking forward for you answer.
>> > Best regards,
>> > Bruno Carturan
>> > PhD Candidate
>> > Complex Environmental Systems Lab
>> > University of British Columbia
>> > Okanagan Campus
>> > <http://www.ubc.ca/okanagan/>
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