This ZENODO archive publication contains extra data used in the analyses of the study "Pervasive horizontal transmission of Wolbachia in natural populations of closely related and widespread tropical skipper butterflies". Following you can find a list with the description of the data provided here. EVERY FILE CAN AND WILL BE SHARED UPON REQUEST BEFORE THE EMBARGO DATE MAKES THEM PUBLICLY AVAILABLE. combined_nuclearPCG_forSECAPR.fasta 406 curated nuclear protein coding genes (PCGs) used in the SECAPR pipeline for the extraction, from every studied specimen, of the contigs containing these PCGs. 406_nuclearPCG.fasta.tar.gz Individual FASTA files of the 406 PCGs, used for the obtention of exonic regions from the contigs of every studied specimen. aln_mitoPCG_concatenated.phy Final concatenated alignment of mitochondrial PCGs used for mitochondrial phylogenetic inference. aln_nuclearPCG_concatenated.phy Final concatenated alignment of nuclear PCGs used for nuclear phylogenetic inference. MLST_Concatenated.phy Final concatenated alignment of Wolbachia MLST markers and the wsp marker used for the phylogenetic inference of the Wolbachia supergroups infecting our studied specimens. aln_fbpa_NoStopCodons.phy Wolbachia fbpA MLST marker alignment used for the investigation of potential lateral gene transfer, including specimens that have pseudogenized (stop codons) sequences. Here, the regions containing stop codons where removed, leaving only their conserved part. aln_fbpa_StopCodons.phy Wolbachia fbpA MLST marker alignment showing the pseudogenized sequences that contain stop codons. This alignment was not used for phylogenetic inference due to the noise generated by stop codons, but it shows how the pseudogenized sequences look. fastqcHTMLresults.tar.gz Results from FastQC for all samples in HTML format. all_samples_blastx_TSV.tar.gz Results from the BLASTX search analysis used to identify Wolbachia proteins in the studied specimens' contigs. The results are in TSV format, and the files are the "raw", non-filtered tables directly resulting from the BLASTX analyses. These tables were filtered as described in the Methods - Confirmation of Wolbachia infection section. MLST_tree.best_model.nex Best models found by IQTree2 using the -m MFP option for the concatenated MLST alignment. NuclearTree_tree.best_model.nex Best models found by IQTree2 using the -m MFP option for the concatenated nuclear loci alignment. PCGsMitogenome_tree.best_model.nex Best models found by IQTree2 using the -m MFP option for the mitogenome loci alignment. wolbSubsetConcatenated.phy Final concatenated alignment of a subset of 108 Wolbachia protein coding loci used for Wolbachia supergroups phylogenetic inference. wolbSubset.best_model.nex Best evolutionary models found for the inference of the Wolbachia supergroups phylogenetic tree. The usage of each one of these files is described in the manuscript/publication in the specific section where the analysis is explained or the results shown. Authors: Pedro Ribeiro, Anzhelika Butenko,Daniel Linke, Hamid Reza Ghanavi, Joana Meier, Niklas Wahlberg, Pável Matos-Maraví.