This is the supplematary data for "Endemic but not eroded: Genomic distinctiveness and conservation genomics of the British swallowtail butterfly (Papilio machaon britannicus Seitz, 1907)" Information in ReadMe.txt Authors Benoit Nabholz1,2*, Eliette L. Reboud1,3,, Bérénice J. Lafon1, Adam M. Cotton4, Martin G. Partridge5, N. Mark Collins5 & Fabien L. Condamine1* Affiliations 1 Institut des Sciences de l’Evolution de Montpellier, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier, France 2 Institut Universitaire de France, Paris, France 3 Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, CNRS, IRD, 91190 Gif-sur-Yvette, France 4 86/2 Moo 5, Tambon Nong Kwai, Hang Dong, Chiang Mai, Thailand 5 Swallowtail and Birdwing Butterfly Trust, ℅ Stephenson Smart, Queens Head House, The Street, Acle, Norfolk, NR13 3DY, UK. Authors for correspondence (*): Benoit Nabholz (benoit.nabholz@umontpellier.fr) and Fabien L. Condamine (fabien.condamine@gmail.com) (In ReadMe.txt)#### Explanation of the content of files and folders to uncompress archive use tar -xzvf command such as:tar -xzvf Scripts.tar.gz ### ScriptsScripts/ – Folder containing scripts Script_britannicus.bash – Script to reproduce genomic analyses britannicus_popGen.R – Script to reproduce figures and statistical analyses ### AssembliesPapilionini_Papilio_machaon_FC3013_pool_megahit_asm_purged.fasta.gz = megahit+purge_dups assembly of FC3013 individualsPapilionini_Papilio_machaon_FC3013_pool_megahit_purged_ragtag_GCF912999745_asm.fasta.gz = RAG-TAG guided assembly using GCF_912999745.1_ilPapMach1.1 assembly as guide ### Data All_machaon_noindels_nosexchr.recode.vcf.gz – VCF with all individuals, without indels and sex chromosomes All_machaon_Q200_noindels_goodSNP_nomissing_nosexchr.vcf.gz – VCF after filtering for high-quality SNPs Analyses/ GADMA/ – GADMA analysis folder Geno/ – Geno files for PCA analyses PnPs/ – Results of the Pn/Ps analyses RoH/ – Results of the RoH analyses Scan/ – Population genetics statistics SNPEFF/ – Results of the SNPEFF SNP annotation Treemix/ – Treemix analysis folder Fasta/ – Whole-genome alignments split into 100 kb windows FastaCDS/ – CDS alignments Heterozygosity/ – Results of the heterozygosity analysis ncbi_dataset/ – Papilio machaon annotations downloaded from NCBI and used in SNPEFF Papilio_machaon_hardmasked.fasta – Repeat-masked reference genome quantile.cov.txt – File with coverage quantiles