Disentangling evolutionary cause-effect relationships with phylogenetic confirmatory path analysis

Abstract

Confirmatory path analysis is a statistical technique to build models of causal hypotheses among variables and test if the data conform with the causal model. However, classical path analysis techniques ignore the nonindependence of observations due to phylogenetic relatedness among species, possibly leading to spurious results. Here, we present a simple method to perform phylogenetic confirmatory path analysis (PPA). We analyzed simulated datasets with varying amounts of phylogenetic signal in the data and a known underlying causal structure linking the traits to estimate Type I error and power. Results show that Type I error for PPA appeared to be slightly anticonservative (range: 0.047–0.072) but path analysis models ignoring phylogenetic signal resulted in much higher Type I error rates, which were positively related to the amount of phylogenetic signal (range: 0.051 for λ = 0 to 0.916 for λ = 1). Further, the power of the test was not compromised when accounting for phylogeny. As an example of the application of PPA, we revisit a study on the correlates of aggressive broodmate competition across seven avian families. The use of PPA allowed us to gain greater insight into the plausible causal paths linking species traits to aggressive broodmate competition.