Data from: Phylogenetic ANOVA: group-clade aggregation, biological challenges, and a refined permutation procedure

Phylogenetic regression is frequently utilized in macroevolutionary
studies, and its statistical properties have been thoroughly investigated.
By contrast, phylogenetic ANOVA has received relatively less attention,
and the conditions leading to incorrect statistical and biological
inferences when comparing multivariate phenotypes among groups remains
under-explored. Here we propose a refined method of randomizing residuals
in a permutation procedure (RRPP) for evaluating phenotypic differences
among groups while conditioning the data on the phylogeny. We show that
RRPP displays appropriate statistical properties for both phylogenetic
ANOVA and regression models, and for univariate and multivariate datasets.
For ANOVA, we find that RRPP exhibits higher statistical power than
methods utilizing phylogenetic simulation. Additionally, we investigate
how group dispersion across the phylogeny affects inferences, and reveal
that highly aggregated groups generate strong and significant correlations
with the phylogeny, which reduce statistical power and subsequently affect
biological interpretations. We discuss the broader implications of this
phylogenetic group aggregation, and its relation to challenges encountered
with other comparative methods where one or a few transitions in discrete
traits are observed on the phylogeny. Finally, we recommend that
phylogenetic comparative studies of continuous trait data utilize RRPP for
assessing the significance of indicator variables as sources of trait
variation.