This file contains an overview of the files provided and how they are organised, details on how the files were generated and what they contain can be found in the respective methods section (and/or Supplementary Methods) of the manuscript 01_ ### --- SPECIMEN VOUCHER KEY --- ### list of specimens used for this study including specimen vouchers, species abbreviations, full species names, and sampling location with GPS coordinates 01_specimen_voucher_key.csv 02_ ### --- filtered SNP data set --- ### containing 57,751,375 SNPs 02_filtered_SNP_data.vcf.gz 03_ ### --- MITOCHONDRIAL ASSEMBLIES --- ### 03_mitochondrial_assemblies.tgz 04_ ### --- SUMMARY STATISTICS de novo GENOME ASSEMBLIES --- ### 04_genomeAssemblies_multiQC_busco.csv 04_genomeAssemblies_multiQC_quast.csv 05_ ### --- TREE FILES --- ### 05_BEAST_RAxML.tre 05_BEAST_ASTRAL.tre 05_BEAST_SNAPP.tre 05_RAxML.tre 05_SVDquartets.tre 05_SVDquartets_strictlyfiltered.tre 05_SVDquartets_strictlyfiltered_sub1.tre 05_SVDquartets_sub1.tre 05_mitogenome.tre 06_ ### --- PHENOTYPIC DATA --- ### 06_landmark_data_body_shape.tps 06_landmark_data_lower_pharyngeal_jaw.tps 06_scores_pigmentation_pattern.csv 06_stable_isotope_data.csv 07_ ### --- PHENOTYPIC DATA --- ### contains complementary graphical results on the analyses of trait evolution (phylogenetic uncertainty and analyses based on PC-scores) 07_Temporal_patterns_complementary_results.pdf 08_ ### --- TRANSPOSABLE ELEMENTS analysis --- ### contains additional graphical results of the Transposable elements characterisation 08_Transposable_elements.pdf