[R-sig-phylo] R: Comparative Methods and Pseudo-Traits

pasquale.raia at libero.it pasquale.raia at libero.it
Fri Nov 11 00:06:32 CET 2011

Hi all,

David, I'd say yes, PICs or P-GLS or any other? related PCM could be applied 
to quasi-traits in principle. On the mathematical grounds, I think most of us 
will be content with Liam's explanation. On the theoretical grounds, I think 
that for most quasi-traits the correct answer is in your own words: hidden 
correlations may justify PCMs as applied to quasi traits. Let's take the growth 
rate/habitat degradation (by humans) relationship.  If you assume similar/close 
habitats are similarly affected by humans, and take niche conservatism 
seriously, than you will find yourself assuming that closely related species 
most probably experience similar habitat conditions, or degradation thereof. 
This means that you'd expect that the quasi trait "habitat degradation by 
anthropogenic disturbance" takes closer than expected values among closely 
related species, which is what PCMs do test or account for. One way to look at 
evolutionary models is that they describe the path of evolution in the simplest 
yet most reasonable way. Another way to look at them, is that they provide a 
basic, quantitative hypothesis about character divergence given the 
(phylogenetic) history of the species you consider. In the latter sense, to 
appy PICs to a quasi-trait is much easier to swallow, besides being 
mathematically feasible.


>----Messaggio originale----
>Da: dwbapst at uchicago.edu
>Data: 10/11/2011 21.36
>A: "R Sig Phylo Listserv"<r-sig-phylo at r-project.org>
>Ogg: [R-sig-phylo] Comparative Methods and Pseudo-Traits
>Hello all,
>A recent discussion set my mind thinking on a particular issue and, once
>again, I decided to ask for the general opinion of R-Sig-Phylo denizens. It
>may be easier to start with an example.
>Let's say that there exists a worker who is measuring several different
>traits across a number of species and then testing for correlations among
>these traits. The first test is body size versus growth rate and they use
>independent contrasts or PGLS to test for a the correlation, accounting for
>phylogeny. Both of these traits are inherited, evolving variables. Now
>let's say they'd like to test for the relationship between growth rate and
>some metric of the anthropogenic degradation of that species' habitat. Now
>what? It is even valid to apply PIC to the habitat degradation metric even
>though it is not an inherited, evolving trait? It's unclear to me.
>Let's consider a paleontological example, one which I have found myself
>both strongly agreeing and disagreeing with at times. Essentially, how
>should we test for extinction selectivity on some trait at a mass
>extinction event? Let's say we think body size is a predictor of the risk
>of extinction during that event and so we want to test for a correlation
>between them (please ignore that extinction would be a discrete variable
>for the moment). Do we treat these variable with PIC or PGLS? Is it really
>proper to refer to the probability of going extinct during a mass
>extinction as an evolving trait? Let's say we did and we got different
>results than when we used an analysis which did not account for the
>phylogenetic covariance. How should we interpret these results?
>One explanation I know of is that when we apply phylogenetic comparative
>methods to these quasi-traits to consider their relationship to another
>trait, we are assuming that these variables are actually the result of some
>underlying, unobserved set of traits which are evolving along the
>phylogeny. This makes sense, maybe in the extinction event case, which
>would mean that any PCM analysis would be testing for an evolutionary
>relationship between body size and these unobserved traits which predict
>extinction. Of course, if extinction risk is largely a function of
>non-inherited traits, then the initial assumption may be incorrect (that
>extinction risk itself is an evolving trait). Regardless, I don't see how
>to apply that explanation to the habitat degradation example.
>So, what do people think? How should we test for correlation when
>non-evolving quasi-traits are involved? I'm very interested to hear
>people's thoughts on this matter.
>-Dave Bapst, UChicago
>David Bapst
>Dept of Geophysical Sciences
>University of Chicago
>5734 S. Ellis
>Chicago, IL 60637
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