Data from Louis M., Galimberti M, Archer F., Berrow S., Brownlow A., Fallon R., O'Brien J., Robertson K., Rosel P. E., Simon-Bouhet B., Wegmann D., Fontaine M. C. , Foote A. D., Gaggiotti O. E.*. 2021. Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. (*these authors contributed equally). See materials and methods and supplementary material for details on data generation. This data archive includes 4 main files : The VCF file (called genotypes) 1_TtmappednewTtvar_biallelic.vcf.gz: Variant calling format (VCF) file including the biallelic single nucleotide variants (SNVs or SNPs) used in Louis et al. The sample names are in the vcf file header. See the materials and methods and supplementary material of the manuscript for details on data generation. Genotype likelihood Linkage-disequilibrium pruned input file 2_Tursiops_unlinkedSNPs.beagle.gz: Note that the sample order (Ind0 to Ind55) is given in the file Tursiops_samples_no7Tt182.bamlist. Sample 7Tt182 is not included in the beagle file due to its low coverage but clusters with the other NWAp. See materials and methods and supplementary material for details on data generation. haplo file (pseudo-haploid random call) 3_Tursiops_ALL.haplo: Individual order is given in Tursiops_samples_ALL.bamlist. Note that 7Tt182 is included there but was not included in the analyses, which are based on a subset of individuals (one coastal individual and all allopatric pelagic individuals except from 7Tt192).See materials and methods and supplementary material for details on data generation. GhostAncestry-master compressed folder (4_GhostAncestry-master.tar.gz) contains the codes written by Benoit Simon-Bouhet to generate the input files for the ghost ancestry analyses - also available at https://github.com/besibo/GhostAncestry ## The folder 1_One Scaffold contains the code to test the script on one scaffold only ## The folder 2_All scaffolds contains the code to run the script on all scaffolds # R code is FileMaker.R, note that you will need the script Custom_functions.R as well # Example input files are in _infiles # Example output files are in _outfiles - the input files for the ghost ancestry analyses from Skov et al. 2018. See materials and methods and supplementary material for details on data generation.

These data and scripts are accompanying the manuscript "Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum" by Ben Chehida Y., Thumloup J., Schumacher C., Harkins T., Aguilar A., Borrell A., Ferreira M., Rojas-Bracho L., Robertson K.M., Taylor B.L., Vikingsson G.A., Weyna A., Romiguier J., Morin P.A., & Fontaine M.C. The archive here includes the final alignment of complete mitogenome sequences (16,302 bp) from 71 cetaceans (63 from the different porpoise species and 7 outgroup sequences) and various scripts used for the bioinformatics and data analyses.