Data matrices used for the analysis performed in the study: Genome-wide SNPs reveal two novel species in <i>Orotettix</i>: different pathways to speciation in a heterogeneous mountainous landscape

Input for ADMIXTURE and PCA for all <i>Orotettix species</i>. Starting from Matrix 1, to reduce redundancy due to linkage disequilibrium (LD), SNP pruning was performed using a sliding-window approach in PLINK, corresponding to a window of 50 SNPs, a step size of 10 SNPs, and an r² threshold of 0.2 (--indep-pairwise 50 10 0.2); SNP pairs exceeding this threshold were removed, producing a final pruned dataset containing 6,164 independent SNPs (26,987 variants removed).</p><p dir="ltr"><b>Matrix 4</b>.

Input for ADMIXTURE and PCA for <i>Orotettix andeanus</i>. Starting from Matrix 1, individuals assigned to this lineage were extracted, resulting in a subset of 40 samples. SNP filtering was subsequently applied using a missing data threshold of 50% and a minor allele frequency threshold of 0.05, yielding 19,219 SNPs that passed quality control.

Linkage disequilibrium pruning using a sliding-window approach (50 SNP windows, 10 SNP step size, and r² = 0.2) retained a final dataset of 3,331 SNPs.</p>