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 http://home.uchicago.edu/~dwbapst/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
