# Phylogenetic dependent variables: ANOVA?

I understand deriving a covariance matrix from phylogenetic data to make $cov(X,Y) = 0$ for two variables you're making a regression on. But what happens if you have one continuous variable, that you've previously shown to be dependent on phylogeny, and one ordinal variable? The latter being ordinal, I'm not sure how to relate this to the way in which phylogenetic dependence results in biased test statistics.

Is it meaningful to calculate Felsenstein's Phylogenetic Independent Contrasts on your continuous variable and use these for your ANOVA?

The PIC value is: $$C_{ij} = \frac{(X_i - X_j)}{\sqrt{d_{ij}}}$$

Where $X_i$ is $X$ for species $i, X_j$ is $X$ for species $j$, and $d_{ij}$ is the pairwise distance between species $i$ and $j$ on the phylogenetic tree.

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There are enough applied statisticians at CrossValidated that we may want to consider migrating this to the stats site. –  Daniel Standage Feb 1 '12 at 20:32
I'd recommend the r-sig-phylo mailing list (stat.ethz.ch/mailman/listinfo/r-sig-phylo). Even if you are not using R for your analysis, you will get very good answers to your question. –  kmm Feb 1 '12 at 21:38