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

Liam J. Revell liam.revell at umb.edu
Thu Nov 10 21:49:22 CET 2011

Hi David.

In general it is inconsequential whether X or Y are biologically 
inherited traits; but whether the residual error in Y given X is 
correlated or independent among species.  In the case of "growth rate as 
a function of habitat degradation" this corresponds to:

Growth Rate = beta0 + beta1*Habitat Degradation + e

It seems highly plausible that the residual error in Growth Rate (e), 
that is error not explained by Habitat Degradation, is phylogenetically 
correlated.  This would imply only that closely related species have 
growth rates that deviate from the mean relationship between growth rate 
and habitat degradation in similar ways.  In this case, PIC or some 
other phylogenetic method should be used.  To be clear also, contrasts 
need to be computed for both X & Y regardless of whether or not there is 
phylogenetic autocorrelation in both X & Y!  (See Revell 2010, MEE; or, 
better yet, Stone 2011, Syst. Biol. doi:10.1093/sysbio/syq098.)

Regarding extinction probability, perhaps someone else on the list can 
address that specific example.

All the best, Liam

Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.revell at umb.edu
blog: http://phytools.blogspot.com

On 11/10/2011 3:36 PM, David Bapst wrote:
> 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

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