DOI: 10.5061/dryad.fqz612k5n
title: Data from: Genetic and environmental similarities drive repeated genomic evolution in island lizards

description: Repeated adaptation provides valuable insights into the predictability of
 evolution. Population history, selection and stochastic processes can
 concur to generate a continuum from distinct to highly parallel
 evolutionary trajectories across replicate populations. Yet, the role of
 genetic and environmental factors in shaping this continuum remains
 underexplored. We quantified repeated genetic adaptation in lizards that
 colonized multiple islands with comparable environmental gradients,
 investigating whether environmental-dependent and divergence-dependent
 processes can explain the degree of repeated adaptation (genetic reuse and
 trajectory similarity). We found 149 genes exhibiting repeated adaptation
 in multiple islands, some of which are likely involved in thermal
 physiology and developmental processes. Genetic reuse was stronger at the
 functional level than at the mutation level and exceeded random
 expectations, highlighting that different genetic combinations can
 generate similar functional outcomes. Adaptive trajectories were more
 similar between islands with low genetic differentiation and similar
 environmental conditions, but the effects of genetic and environmental
 factors vary across the diverse facets of repeatability. Overall, our
 findings reveal the extent and conditions under which local adaptation is,
 in part, predictable.
description: # Data accompanying Sherpa et al. Genetic and environmental similarities
 drive repeated genomic evolution in island lizards # Experiment ``` Double
 digest restriction associated DNA sequencing (ddRADseq) ``` # Description
 of the data ## Dataset 1: Global SNP dataset
 ('Sherpa_et_al_2025_Mol_Ecol_Dataset_1.vcf') ``` - 245
 individuals; sample characteristics and raw data accession numbers in
 Population file 1. - 343,545 SNPs (filtered for non-biallelic sites, minor
 allele frequency &lt; 1%, and heterozygosity &gt; 0.6). - 91,383 loci
 (filtered for &gt; 25% missing data per SNP overall and &gt; 25% missing
 data within each island group). - Format: VCF; alelle model: P. siculus
 reference genome. Missing genotypes ('./.') denote both uncalled
 genotypes, and genotype calls with depth of coverage &lt; 5 and &gt; 100.
 Used for detection of signatures of selection. ``` ## Dataset 2: Neutral
 SNP dataset ('Sherpa_et_al_2025_Mol_Ecol_Dataset_2.vcf') ``` -
 245 individuals; sample characteristics and raw data accession numbers in
 Population file 1. - 88,401 SNPs (filtered for physical LD (one random SNP
 per locus) and environmental association). - Format: same as Dataset 1.
 Used for population genetic structure and diversity, and neutral genetic
 trajectories. ``` ## Population file 1: Sample characteristics for
 Datasets 1 and 2
 ('Sherpa_et_al_2025_Mol_Ecol_Population_map_Dataset_1_Dataset_2.txt') ``` - Group affiliation (i.e., island); Geographic coordinates. - Raw data accession numbers: European Nucleotide Archive repository (project PRJEB85261). ``` ## SNP annotation and genome correspondence for Dataset 1 ('Sherpa_et_al_2025_Mol_Ecol_Annotation_Dataset_1.txt') ``` - Psic: Podarcis siculus ddRADseq loci (Psic_locusID) and position using P. siculus reference genome. - Pmur: position and annotation of Psic loci aligned to the reference genome of Podarcis muralis. - Praf : position and annotation of Psic loci aligned to the reference genome of Podarcis raffonei. - Gene, Amino_acids, Codons, Distance, Feature and SO_term (Sequence Ontology) based on Variant Effect Predictor. ``` ## Dataset 3: Combined SNP dataset generated by merging previous data (Sherpa et al. 2024) with the data produced in this study (‘Sherpa_et_al_2025_Mol_Ecol_Dataset_3.vcf’) ``` - 72 individuals; sample characteristics and raw data accession numbers in Population file 2. - 3,825 SNPs (filtered for non-biallelic sites, minor allele frequency &lt; 1%, and heterozygosity &gt; 0.6, physical LD). - 3,825 loci (filtered for &gt; 25% missing data per SNP overall and &gt; 50% missing data within each 2015-2021 dataset). - Format: same as Dataset 1. Used to confirm genetic relationships among the islands and with the ancestral Sicilian population. ``` ## Population file 2: Sample characteristics for Dataset 3 ('Sherpa_et_al_2025_Mol_Ecol_Population_map_Dataset_3.txt') ``` - Group affiliation (i.e., island, dataset). - Raw data accession numbers: European Nucleotide Archive repository (projects PRJEB62841 for 2015 data and PRJEB85261 for 2021 data). ``` # Access information ``` Podarcis siculus reference genome: UCBerk_Psic_1 (GenBank accession GCA_034642415.1; release date: 2023-12-26; access date: 2024-01-03; Sabolić et al. 2024). Podarcis muralis reference genome: PodMur_1.0 (RefSeq assembly GCF_004329235.1; release date: 2019-03-07; Andrade et al. 2019; RefSeq annotation GCF_004329235.1; release date: 2019-04-12). Podarcis raffonei reference genome: rPodRaf1.pri (RefSeq assembly GCF_027172205.1; release date: 2022-12-27; Gabrielli et al. 2023; RefSeq annotation GCF_027172205.1-RS_2023_02; release date: 2023-02-25). European Nucleotide Archive raw data - 2015 dataset: https://www.ebi.ac.uk/ena/browser/view/PRJEB62841. European Nucleotide Archive raw data - 2021 dataset: https://www.ebi.ac.uk/ena/browser/view/PRJEB85261. ```