Phylogenetic biogeography inference using dynamic paleogeography models and explicit geographic ranges

Supplementary data for the manuscript entitled "Phylogenetic Biogeography Inference Using Dynamic Paleogeography Models and Explicit Geographic Ranges". This dataset contains the supplementary figures as well as the basic setup for the simulation used to test the method described in the manuscript,and an empirical example using the plant family Sapindaceae, analyzed with the program PhyGeo.

Methods
Paleogeographic model
The plate motion model is Muller et al. (2022). The paleolandscape model is based on an unrotated version of Cao et al. (2017) for the 0-400 Ma period, and an unrotated version of the PaleoMap model (Scotese and Wright 2018), for the period 405-540 Ma. Then the pixels were rotated using the Muller et al. (2022) plate motion model.

Phylogeny
The phylogenetic tree for the empirical dataset was built using the Sapindaceae branch from the phylogenomic analysis of the Sapindales by Joyce et al. (2023), which is quite similar in content (at genus level) to previous biogeographic analyses of the group (Buerki et al. 2011, 2013). As the original publication does not provide a machine-readable file, the relationships and ages were extracted manually from the figures. The phylogeny was augmented with a few terminals from Buerki et al. (2013), mostly to enlarge the sampling of a few genera. The species Matayba tenax was excluded, as it does not match any Maytaba species or synonym in the Plants of the World database, as this particular terminal float in a previous analysis (Buerki et al., 2021), and the genus Matayba did not appear as monophyletic in previous studies (Buerki et al. 2011, 2013).

Distribution records
Specimen data were obtained from a search of geo-referenced preserved specimens of Sapindaceae in GBIF. The initial number of records was 387.463 occurrences.

Data analysis
See the readme for the data analysis.