This supplementary material contains data and scripts for (1) a simulation study assessing the performance of our phylogenetic comparative method on trait data generated using an actual species network, and (2) a comparative analysis of how Polemonium leaflet size covaries with geographical predictors, assuming either a reticulate or non-reticulate time-calibrated phylogeny, accounting for or ignoring within-species variation.

There are two top-level folders:

(1) simulations: contains scripts to replicate the simulation study and associated figures in the subfolder "scripts", and results from the simulations in the subfolder "data".

(2) polemonium: contains uncalibrated/calibrated species phylogenies (.tre), gene trees (.t, .tre) and genetic distance estimates (.csv) used for calibration, morphological and geographical data for Polemonium (.csv), and model estimates (.csv) in the subfolder "data"; and scripts to do calibration, preprocess the trait data, fit models and save estimates, and recreate figures from the article in the subfolder "scripts".

The archive and each top-level folder contain their own README file with more detailed information.

The Julia and R programming languages (RStudio is additionally needed to open .Rmd) are required to run the scripts (.jl, .R, .Rmd) provided. Further instructions on how to initialize the working directory and package environment are provided in the README files.