Supplementary File 1Supplementary File 1. Species richness, clade ages, and stem and crown diversification rates for 72 families of squamates.Supplementary File 2Supplementary File 2. Species richness, clade ages, and stem and crown diversification rates for 505 genera of squamates.Supplementary File 3Supplementary File 3. Microhabitat data for all squamate species included in this study, including references.Supplementary File 4Supplementary File 4. Raw and logit-transformed data for proportional and strict proportions of microhabitat use for 72 squamate families.Supplementary File 5Supplementary File 5. Raw and logit-transformed data for strict proportions of microhabitat use and climatic distribution for 505 squamate generaSupplementary File 6Supplementary File 6. Climatic distribution for all squamate species analyzed in this study.Supplementary File 7Supplementary File 7. Proportional climatic distributions of species in 72 squamate families.Supplementary File 8Supplementary File 8. Microhabitat data for the MuSSE analysesSupplementary File 9Supplementary File 9. Methods and results for time-dependent diversification analysesSupplementary File 10Supplementary File 10. Results from time-dependent diversification analyses for lizards (using stem-group ages)Supplementary File 11Supplementary File 11. Results from time-dependent diversification analyses for lizards (using crown-group ages)Supplementary File 12Supplementary File 12. Results from time-dependent diversification analyses for snakes (using stem-group ages)Supplementary File 13Supplementary File 13. Results from time-dependent diversification analyses for snakes (using crown-group ages)

Patterns of species richness among clades can be directly explained by the ages of clades or their rates of diversification. The factors that most strongly influence diversification rates remain highly uncertain, since most studies typically consider only a single predictor variable. Here, we explore the relative impacts of macroclimate (i.e., occurring in tropical vs. temperate regions) and microhabitat use (i.e., terrestrial, fossorial, arboreal, aquatic) on diversification rates of squamate reptile clades (lizards and snakes). We obtained data on microhabitat, macroclimatic distribution, and phylogeny for >4000 species. We estimated diversification rates of squamate clades (mostly families) from a time-calibrated tree, and used phylogenetic methods to test relationships between diversification rates and microhabitat and macroclimate. Across 72 squamate clades, the best-fitting model included microhabitat but not climatic distribution. Microhabitat explained ∼37% of the variation in diversification rates among clades, with a generally positive impact of arboreal microhabitat use on diversification, and negative impacts of fossorial and aquatic microhabitat use. Overall, our results show that the impacts of microhabitat on diversification rates can be more important than those of climate, despite much greater emphasis on climate in previous studies.