title: Interpretation of the results of common principal components analyses.
abstract: Common principal components (CPC) analysis is a new tool for the comparison of phenotypic and genetic variance-covariance matrices. CPC was developed as a method of data summarization, but frequently biologists would like to use the method to detect analogous patterns of trait correlation in multiple populations or species. To investigate the properties of CPC, we simulated data that reflect a set of causal factors. The CPC method performs as expected from a statistical point of view, but often gives results that are contrary to biological intuition. In general, CPC tends to underestimate the degree of structure that matrices share. Differences of trait variances and covariances due to a difference in a single causal factor in two otherwise identically structured datasets often cause CPC to declare the two datasets unrelated. Conversely, CPC could identify datasets as having the same structure when causal factors are different. Reordering of vectors before analysis can aid in the detection of patterns. We urge caution in the biological interpretation of CPC analysis results.
authors: Department of Zoology, University of Toronto, ON, Canada. dhoule@bio.fsu.edu
authors: David
authors: D
authors: Houle
authors: Jason
authors: J
authors: Mezey
authors: Paul
authors: P
authors: Galpern
mesh_terms: D000704:Analysis of Variance; D005075:Biological Evolution; D014644:Genetic Variation; D008954:Models, Biological; D010641:Phenotype; D015203:Reproducibility of Results