Evolution, genomics and conservation of butterflies and moths

This zipped folder contains the necessary data (phylogenetic trees of six butterfly families) and scripts for preparing, running and visualising diversification analyses with BAMM. The phylogenetic trees of six butterfly families have been retrieved from for the following studies: Papilionidae (Allio et al. 2021: https://doi.org/10.1038/s41467-020-20507-3), Hesperiidae (Toussaint et al. in press at Systematic Biology), Pieridae (Carvalho et al. 2024: https://doi.org/10.1016/j.isci.2024.109336), Nymphalidae (Chazot et al. 2021: https://doi.org/10.1038/s41467-021-25906-8), Riodinidae (Espeland et al. 2015: http://dx.doi.org/10.1016/j.ympev.2015.08.006), and Lycaenidae (Kawahara et al. 2023: https://doi.org/10.1038/s41559-023-02041-9). For each family, a diversification analysis has been carried out with Bayesian Analysis of Macroevolutionary Mixtures (BAMM; Rabosky et al. 2013: https://doi.org/10.1038/ncomms2958) to estimate diversification rates through time and across clades.A control file (e.g. BAMM_control_file_Hesperiidae.txt) allows to set up the BAMM analysis along with the R script for BAMMtools (e.g. BAMMtools script Hesperiidae.R) to obtain the speciation and extinction priors that are put in the control file.The output files from the BAMM analyses (e.g. chain_swap_Hesperiidae.txt, event_data_Hesperiidae.txt, mcmc_out_Hesperiidae.txt, and run_info_Hesperiidae.txt) can be re-used to plot the results for each family.The results of diversification as estimated with BAMM for each family with rates through time (e.g. Rates through time for Hesperiidae.pdf) and the diversification shifts and rates across the phylogeny (e.g. Net diversification shifts and rates through time of Hesperiidae.pdf). These plots can be obtained with the R package BAMMtools using the R script for BAMMtools (e.g. BAMMtools script Hesperiidae.R). The pdf output files used to make Figure 2 of the main text are also placed in this folder.