DOI: 10.6084/m9.figshare.29315618
title: <b>Island colonisation and extinction of an insect species </b><b>revealed by mitochondrial and genome-wide nuclear variation</b>

description: <i>This README file was generated on 2025-06-13 by Víctor Noguerales.</i><br><b>GENERAL INFORMATION</b><i>1. Title of dataset</i>Island colonisation and extinction of an insect species revealed by mitochondrial and genome-wide nuclear variation<br><i>Authors and institution for correspondence:</i>Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Canary Islands, SpainDépartement de Biologie, Ecole Normale Supérieure (ENS), Paris, FranceUniversidad de La Laguna (ULL), Departamento de Biología Animal, Edafología y Geología, San Cristóbal de La Laguna, Canary Islands, Spain<b>Brent C. Emerson</b>, email: <i>bemerson@ipna.csic.es</i>, https://orcid.org/0000-0003-4067-9858<b>Alya Campedel</b>, email: <i>alya.campedel@gmail.com</i><b>Víctor Noguerales</b>, email: <i>victor.noguerales@csic.es</i>, <i>vnoguera@ull.edu.es</i>, https://orcid.org/0000-0003-3185-778X<br><br><b>SHARING/ACCESS INFORMATION</b><br><i>1. Links to publications that cite or use the data:</i>Emerson, B.C., Campedel, A. & V. Noguerales (2025). Island colonisation and extinction of an insect species revealed by mitochondrial and genome-wide nuclear variation. <i>Evolutionary Journal of the Linnean Society</i>.<br><i>2. Recommended citation for this dataset:</i>Emerson, B.C., Campedel, A. & V. Noguerales (2025). Island colonisation and extinction of an insect species revealed by mitochondrial and genome-wide nuclear variation. <i>Evolutionary Journal of the Linnean Society</i>. Figshare.<br><br><b>DATA & FILE OVERVIEW</b><br><i>1. File List:</i><br>1) 01_PCA_Structure.zip2) 02_RAXML.zip3) 03_SNAPP.zip4) 04_Heterozygosity.zip5) 05_fastsimcoal.zip<br><br>#############################################################################<b>DATA-SPECIFIC INFORMATION FOR: 01_PCA_Structure.zip</b><br>The ZIP folder "01_PCA_Structure.zip" contains the files in STRUCTURE format (.str) used for running both PCA and Structure, as detailed in Material and Methods in the manuscript.Individuals are coded in rows (2 rows per individual), with each column representing an unlinked SNP. Missing data is coded as “-9”.<br>Within the folder "a_LP_TF_GC_n240_1582SNPs", the file “inputfile_LP_TF_GC_n240_1582SNPs.str” contains the full dataset of 240 individuals from the islands of La Palma, Tenerife and Gran Canaria, including 1582 unlinked SNPs. Within the folder "b_LP_TF_n194_3700SNPs", the file “inputfile_LP_TF_n194_3700SNPs.str” contains the dataset of 194 individuals from the islands of La Palma and Tenerife, including 3700 unlinked SNPs.Within the folder "c_LP_GC_n114_3349SNPs", the file “inputfile_LP_GC_n114_3349SNPs.str” contains the dataset of 114 individuals from the islands of La Palma and Gran Canaria, including 3349 unlinked SNPs.Within the folder "d_LP_n68_20255SNPs", the file “inputfile_LP_n68_20255SNPs.str” contains the dataset of 68 individuals from the island of La Palma, including 20255 unlinked SNPs.<br>Within each of these four folders, a text file containing the scores for the first components stemming from each dataset-specific PCA is provided.<br><br>#############################################################################<b>DATA-SPECIFIC INFORMATION FOR: 02_RAXML.zip</b><br>The ZIP folder "02_RAXML.zip" contains the file in PHYLIP format (.phy) used for running RAXML, as detailed in Material and Methods in the manuscript.<br>The file "LP_TF_GC_n240_4908SNPs_phrynomics.phy" contains the full dataset of 240 individuals from the islands of La Palma, Tenerife and Gran Canaria, including 4908 concatenated linked SNPs. This input file is used to reconstruct the phylogenetic relationships among all individuals in RAXML. <br><br>#############################################################################<b>DATA-SPECIFIC INFORMATION FOR: 03_SNAPP.zip</b><br>The ZIP folder "03_SNAPP.zip" contains the inputs files for SNAPP including the subset of 90 individuals from the islands of La Palma, Tenerife and Gran Canaria, for a total of 3363 unlinked SNPs.<br>The file "LP_TF_GC_n90_3363SNPs.nex" is a NEXUS file that contains the subset of 90 individuals from the three islands, including 3363 unlinked SNPs.This file is used to the prepare the following XML file in BEAUti. Individuals are coded in rows (1 row per individual), with each subsequent column representing an unlinked SNP. Missing data is coded as “?”.<br>The file "LP_TF_GC_n90_3363SNPs.xml" contains the input in BEAST format including the subset of 90 individuals from the three islands, including 3363 unlinked SNPs. This input file is used to reconstruct the phylogenetic relationships among the three island populations in SNAPP. <br><br>#############################################################################<b>DATA-SPECIFIC INFORMATION FOR: 04_Heterozygosity.zip</b><br>The ZIP folder "04_Heterozygosity.zip" contains the files in STRUCTURE format (.str) used for calculating individual-based observed heterozygosity using R package dartR, as detailed in Material and Methods in the manuscript.Individuals are coded in rows (2 rows per individual), with each column representing an unlinked SNP. Missing data is coded as “-9”.<br>The file “inputfile_LP_TF_GC_n240_1582SNPs.str” contains the full dataset of 240 individuals from the islands of La Palma, Tenerife and Gran Canaria, including 1582 unlinked SNPs.The file “inputfile_LP_n68_20255SNPs.str” contains the dataset of 68 individuals from the island of La Palma, including 20255 unlinked SNPs.<br><br>#############################################################################<b>DATA-SPECIFIC INFORMATION FOR: "05_fastsimcoal.zip"</b><br>The ZIP folder "05_fastsimcoal.zip" contains all the required input files for running demographic analyses in FASTSIMCOAL2. <br>The folder "a_LP_TF_GC_n90" refers to the analysis regarding the subset of 90 individuals from the islands of La Palma, Tenerife and Gran Canaria.The folder "b_LP_TF_GC_n65" refers to the complementary analysis regarding the subset of 45 individuals from the islands of La Palma, Tenerife and Gran Canaria.<br>Within each of these folders, the folder "01_DNAsp_Ne" contains the DNA sequence file in IPYRAD format (.alleles files) which is used to calculate nucleotide diversity per group using DNASP, as detailed in Material and Methods in the manuscript.Within each of these folders, the folder "02_SFS" contains the VCF file which is used to estimate the SFS using easySFS, as detailed in Material and Methods in the manuscript.Within each of these folders, the folder "03_Models" contains the different demographic models, as detailed in Material and Methods in the manuscript.For each of these alternative models, two different files are provided. The .est files contain the information for model specification in terms of migration matrices and historical events. The .tpl files contains priors and rules information for each of the parameters specified in the respective .est file.<br><br>#############################################################################