The dataset contains the files associated with the study "Integrating three comprehensive datasets shows that mitochondrial DNA variation is linked to species traits and palaeogeographic events in European butterflies." The files are described below: >Appendix S2.R. The R script used to carry out the analyses of the study >data_specimens.txt. Contains the data for each specimen included in the analysis >data_sequences.fas. Contains the COI sequences of the specimens in the same order as in the previous file >traits.txt. Contains the traits used to identify phylogenetic signals and to carry out the phylogenetic regressions. >Butterflies_Europe_tree.nwk. A Newick multi-locus tree for all the European butterfly species. >ne_10m_ocean (series of associated files) is a Ocean leyer used to plot the results of the zoogeographic regionalization Some files generated by the analysis are also provided: >data_specimens_with_areas.txt. The same as data_specimens.txt but it also contains attribution of specimens to the 2.5x2.5 degree grid >tabfinal.txt. The same as traits.txt but it contains the values for teh indices of genetic diversification and the factors for phenology and ecophysiology variables. >Butterflies_Europe_tree_ultrametric.nwk. The same as "Butterflies_Europe_tree.nwk." after transformation to an ultramtric tree with the "force.ultrametric" R function