Phylogenetic Principal Components Analysis and Geometric Morphometrics

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mvmorph: an r package for fitting multivariate evolutionary models to morphometric data (2015, methodology): “…methods in phylogenetic comparative analysis should deserve more attention in the future as common approaches used to reduce the dimensionality of such data sets (e.g. principal component analysis) are prone to several biases (Monteiro 2013; Polly et al. 2013; Uyeda, Caetano & Pennell 2015).”
Phylogenetic Comparative Methods and the Evolution of Multivariate Phenotypes (2019, methodology): “Because this procedure is based on a decomposition of S, the axes of the phylomorphospace are orthogonal (Polly et al. 2013), and the method is thus a rigid rotation of the original phenotype space. www.annualreviews.org • Evolution of Multivariate Phenotypes 409 A nn u.”
Statistical Issues and Assumptions of Phylogenetic Generalized Least Squares (2014, background): “…more about principal component and factor analysis, see, e.g., Budaev 2010, and for phylogenetic principal components analysis see Revell 2009 and Polly et al. 2013); and (3) exclude predictors based on collinearity (i.e., the variance inflation factors revealed for them; see section about…”