Modeled ranges of California plant species and scripts to run the models for Spatial phylogenetics of the native California flora (Thornhill et al. BMC Biology)

The species distribution modeling algorithm Maxent was used to model the range of each Californian species, using the cleaned species-level spatial dataset from Baldwin et al. 2017. Models were fit at the species level ; each OTU’s range was then taken to be the union of the ranges of its included species. Models were fit using four predictor variables representing major energy- and water-related variables known to be important for California plant distributions: climatic water deficit, annual precipitation, mean summer maximum temperature (June–August), and mean winter minimum temperature (December– February) as described in Thornhill et al. 2017. In addition to the standard Maxent modeling approach, we also used a second “distance hybrid” approach to model the area for each species that was both climatically suitable and geographically close to observed occurrences. The distance constraint arguably increases realism by accounting for spatial processes such as dispersal limitation and metapopulation dynamics.