Hi Russell,
And, for a fully PGLS and Bayesian model, see this:
https://pubmed.ncbi.nlm.nih.gov/17344851/
Best, Chris
On Thu, Jul 1, 2021 at 1:10 AM Theodore Garland
wrote:
>
> Russell,
> Please read this paper:
> https://pubmed.ncbi.nlm.nih.gov/10718731/
> Cheers
> Ted
>
>
> On Wed, Jun 30, 2021, 9:21 PM Russell Engelman
> wrote:
>
> > Dear All,
> >
> > What you see is the large uncertainty in “ancestral” states, which is part
> >> of the intercept here. The linear relationship that you overlaid on top of
> >> your data is the relationship predicted at the root of the tree (as if such
> >> a thing existed!). There is a lot of uncertainty about the intercept, but
> >> much less uncertainty in the slope. It looks like the slope is not affected
> >> by the inclusion or exclusion of monotremes. (for one possible reference on
> >> the greater precision in the slope versus the intercept, there’s this:
> >> http://dx.doi.org/10.1214/13-AOS1105 for the BM).
> >
> >
> > Yes, that sounds right from the other data I have. The line approximates
> > what would be expected for the root of Mammalia, and the signal in the PGLS
> > is more due to shifts in the y-intercept than shifts in slope, which in
> > turn is supported by the anatomy of the proxy.
> >
> > My second cent is that the phylogenetic predictions should be stable. The
> >> uncertainty in the intercept —and the large effect of including monotremes
> >> on the intercept— should not affect predictions, so long as you know for
> >> which species you want to make a prediction. If you want to make prediction
> >> for a species in a small clade “far” from monotremes, say, then the
> >> prediction is probably quite stable, even if you include monotremes: this
> >> is because the phylogenetic prediction should use the phylogenetic
> >> relationships for the species to be predicted. A prediction that uses the
> >> linear relationship at the root and ignores the placement of the species
> >> would be the worst-case scenario: for a mammal species with a completely
> >> unknown placement within mammals.
> >
> >
> > This is what I'm a bit confused about. I was always told (and it seemingly
> > implies this in some of the PGLS literature I read like Rohlf 2011 and
> > Smaers and Rohlf 2016) that it isn't possible to include phylogenetic data
> > from the new data points into the prediction in order to improve
> > predictions. I'm a little confused as to whether it's possible or not (see
> > below).
> >
> > There’s probably a number of software that do phylogenetic prediction. I
> >> know of Rphylopars and PhyloNetworks.
> >
> >
> > I will take a look into those.
> >
> > I think that Cécile' and Theodore' point is important and too often
> >> overlooked. Using GLS models, the BLUP (Best Linear Unbiased Prediction) is
> >> not simply obtained from the fitted line but should incorporates
> >> information from the (evolutionary here) model.
> >
> >
> > There’s a way to impute phylogenetic signal back into a PGLS model? I
> > am super surprised at that. I’ve talked to at least three different
> > colleagues who use PGLS about this issue, and all of them had told me that
> > there is no way to input phylogenetic signal back into the model for new
> > data points and I should just go with the single regression line the model
> > gives me (i.e., the regression line for the ancestral node).
> >
> > I tried looking around to see what previous researchers used when
> > using PCM on body mass (Esteban-Trivigno and Köhler 2011, Campione and
> > Evans 2012, Yapuncich 2017 thesis) and it looks like all of them just went
> > with the best fit line with the ancestral node, i.e., looking at their
> > reported results they give a simple trait~predictor equation that does not
> > include phylogeny when calculating new data. Campion and Evans 2012 used
> > PIC versus PGLS, which I know are technically equivalent but it doesn't
> > seem like they included phylogenetic information when they predicted new
> > data: they used their equations on dinosaurs but there are no dinosaurs in
> > the tree they used. I know that it’s possible to incorporate phylogenetic
> > signal into the new data using PVR but PVR has been criticized for other
> > reasons.
> >
> > This is something that seems really, really concerning because if
> > there is a method of using phylogenetic covariance to adjust the position
> > of new data points it seems like a lot of workers don’t know these methods
> > exist, to the point that even published papers overlook it. This was
> > something I was hoping to highlight in a later paper on the data, but it
> > sounds like people might have discussed it already. I remember talking with
> > my colleagues a lot about "isn't there some way to incorporate phylogenetic
> > information back into the model to improve accuracy of the prediction if we
> > know where the taxon is positioned?" and they just thought there wasn't a
> > way.
> >
> > Regarding the model compari
