Supplementary material: How should functional relationships be evaluated using phylogenetic comparative methods? A case study using metabolic rate and body temperature

Phylogenetic comparative methods are often used to test functional
relationships between traits. However, million-year macroevolutionary
observational datasets cannot definitively prove causal links between
traits --- correlation does not equal causation and experimental
manipulation over such timescales is impossible. While this caveat is
widely understood, it is far less appreciated that different phylogenetic
approaches make different causal assumptions about the functional
relationships of traits. In order to make meaningful inferences, it is
critical that our statistical methods make biologically reasonable
assumptions. Here we illustrate the importance of causal reasoning in
comparative biology by examining a recent study
by Avaria-Llautureo et al. (2019) that tested for the
evolutionary coupling of metabolic rate and body temperature across
endotherms and made the notable discoveries that these traits were
unlinked through evolutionary time and that body temperatures were, on
average, higher in the early Cenozoic than they are today. We argue that
the causal assumptions embedded into their models made it impossible for
them to actually test the relevant functional and evolutionary hypothesis.
We then re-analyze their data using more biologically appropriate models
and find support for the exact opposite conclusions, corroborating
previous evidence from physiology and paleontology. We highlight the vital
need for causal thinking, even when experiments are impossible.