Gene family evolution
We estimated gene turnover rates, the number of gene gains and losses
across the phylogeny lineages, and inferred gene family contractions and
expansions using BadiRate 1.7 (Librado, Vieira, & Rozas, 2012). For the
analysis we first inferred the orthogroups with OrthoFinder 2.3.8, and
we used the calibrated ultrametric tree estimated with r8s. We tested,
under the Birth-Death-Innovation (BDI) model for turnover rates, several
biological relevant hypotheses with three different branch models: Free
Rates (FR), Global Rates (GR) and Branch-specific Rates (BR), and chose
the best model based on the lowest AIC value. To ensure an appropriate
convergence we ran multiple times each model.