Outline of the analysis of convergent adaptation to arid environment in rodents (A), which aims at quantifying convergence at different levels and phylogenetic scales (B). The methods are indicated in gray, and their main purpose is schematized (C). In particular, the EVE model and Pelican are two phylogenetic methods. EVE models the evolution of expression toward two optima depending on the condition (theta1 vs. theta2). Pelican looks for differences in amino acid usage at a given site between two conditions (here, p1 vs. p2). DESeq2, when used accounting for family effects, models a similar shift in expression level in each family regardless of the family subtree.
