Phylogenetic Generalised Least Squares As A Robust Causal Inference Method, 1990s – 2024

Phylogenetic Generalised Least Squares regression proposed that evolutionary associations between traits could be estimated reliably across species while accounting for shared ancestry, offering comparative biologists a principled and statistically defensible framework for their analyses. It was widely adopted across ecology and evolutionary biology, becoming a standard tool in the assessment of trait coevolution and the construction of adaptive hypotheses. For several decades it occupied a position of considerable methodological authority, appearing in thousands of comparative studies and forming the backbone of graduate training in the field. Its decline began as researchers examined the sensitivity of the method's conclusions to the assignment of variables to the dependent and independent positions — a choice that, in a genuinely robust method, ought not to determine the outcome. The terminal finding demonstrated that reversing the dependent and independent variables in a substantial proportion of published PGLS analyses yielded inconsistent or contradictory conclusions, revealing that the method had been bearing a causal interpretive weight it was not constructed to support.

It brought statistical rigour to the comparison of traits across species at a time when the alternative was largely informal, and the questions it helped researchers ask remain among the most important in evolutionary biology.