Follow this link to the zenodo repository.
This contains scripts for branch-wise analysis and gene shopping. Needs a reference species tree and gene trees. Gene trees are available on the related Zenodo repository. The branch_wise script is an early version of the script that was used for this study. A far faster version will be made available soon.
This provides the necessary inputs to estimate the time-calibrated phylogenies that were estimated in this study. In each case the treePL configuration file is provided (ending in .treePL) and the input tree file (ending in .tre)
This provides the necessary inputs to perform lineage specific diversification rate estimation on the time-calibrated phylogeny designated as main, and no maximum. In each case the BAMM input file, and input time-calibrated phylogeny is provided. Also provided is an R script used to get appropriate priors in each case, and an R script used for analysing and plotting outputs.
This contains all the scripts needed to perform ClaSSE analyses that were undertaken as part of this study. main and no_maximum contain scripts for analysis on the main and no maximum trees respectively. final_tree_and_data_frame_processing.r prunes the species tree and compiles the biome_and_region_preference into a matrix for analysis in the ClaSSE model. Note that line 118 in final_tree_and_data_frame_processing.r needs adjusting depending on which output tree from treePL you are working on. biome_and_region_preference is equivalent to Table S5 in the manuscript.
Scripts to generate the distribution map in figure 1. Source data for the distribution points is here
Scripts for plotting output from BAMM analysis (Fig. 2a and b) and biome specific speciation rates from CLASSE (Fig. 2c). Log files from BAMM and Classe here.
Scripts for plotting rates of upslode biome shifts and inter regional mountain hopping as displayed in Figure 3. Simmaps are here