This project contains supplement files associated with the manuscript entitled 'Whole chloroplast genomes reveal a complex genetic legacy of lost lineages, past radiations and secondary contacts in the dominant temperate deciduous tree genus Fagus" by Worth et al. available as a preprint 10.1101/2025.06.03.653586 posted on bioRxiv (https://www.biorxiv.org/cgi/content/short/2025.06.03.653586v1).