Abstract:
The questions addressed by macroevolutionary biologists are often impervious to
experimental approaches, and alternative methods have to be adopted. The phylogenetic
comparative approach is a very powerful one since it combines a large
number of species and thus spans long periods of evolutionary change. However,
there are limits to the inferences that can be drawn from the results, in part due to
the limitations of the most commonly employed analytical methods. In this
chapter, we show how confirmatory path analysis can be undertaken explicitly
controlling for non-independence due to shared ancestry. The phylogenetic path
analysis method we present allows researchers to move beyond the estimation of
direct effects and analyze the relative importance of alternative causal models
including direct and indirect paths of influence among variables. We begin the
chapter with a general introduction to path analysis and then present a step-by-step
guide to phylogenetic path analysis using the d-separation method. We also show
how the known statistical problems associated with non-independence of data
points due to shared ancestry become compounded in path analysis. We finish with
a discussion about the potential effects of collinearity and measurement error, and
a look toward possible future developments.