Supplementary datasets, data analysis code, and R tutorials for: Phylogenetic analysis of adaptation in comparative physiology and biomechanics: overview and a case study of thermal physiology in treefrogs

Comparative phylogenetic studies of adaptation are uncommon in
biomechanics and physiology. Such studies require collecting data from
many species, a challenge when data collection is experimentally
intensive. Moreover, researchers struggle to employ the most biologically
appropriate phylogenetic tools for identifying adaptive evolution. Here,
we detail an established but greatly underutilized phylogenetic
comparative framework—the Ornstein-Uhlenbeck process—that explicitly
models long-term adaptation. We discuss challenges in implementing and
interpreting the model, and we outline potential solutions. We demonstrate
use of the model through studying the evolution of thermal physiology in
treefrogs. Frogs of the family Hylidae have twice colonized the temperate
zone from the tropics, and such colonization likely involved a fundamental
change in physiology due to colder and more seasonal temperatures.
However, which traits changed to allow colonization is unclear. We
measured cold-temperature tolerance and characterized thermal performance
curves in jumping for twelve species of treefrogs distributed from the
Neotropics to temperate North America. We then conducted phylogenetic
comparative analyses to examine how tolerances and performance curves
evolved and to test whether that evolution was adaptive. We found that
tolerance to low temperatures increased with the transition to the
temperate zone. In contrast, jumping well at colder temperatures was
unrelated to biogeography and thus did not adapt during dispersal.
Overall, our paper shows how comparative phylogenetic methods can be
leveraged in biomechanics and physiology to test the evolutionary drivers
of variation among species.