2026-10-06T18:38:17Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33511723 2026-09-18T17:26:51Z category_24247 category_24271 category_24277 category_24244 category_24310 category_24436 item_type_3 month_year_09_2026

Data matrices used for the analysis performed in the study: Genome-wide SNPs reveal two novel species in Orotettix: different pathways to speciation in a heterogeneous mountainous landscape Diego Caraballo (12766454) Viviana Andrea Confalonieri (8853084) Maria Marta Cigliano (8856714) Martina E. Pocco (4515463) Claudio Slamovits (99256) Noelia Guzman (11084994) Elio Castillo (8856713) Biogeography and phylogeography Phylogeny and comparative analysis Speciation and extinction Animal systematics and taxonomy Genomics Invertebrate biology Orotettix RAD-Sequencing phylogenomics population genomics species delimitation hybridization pseudocryptic species Andean grasshoppers Matrix 1. Matrix obtained with STACKS (min-mac=3, keeping the first SNP of each locus). This dataset contains 7.00 × 10⁵ loci, 1.52 × 10⁵ SNPs, and 93 individuals. This matrix was used to obtain all subsequent matrices and downstream analyses.Matrix 2. Input for species tree inference with SNAPPER. Obtained from Matrix 1 (93 individuals and 1.52 × 10⁵ SNPs), filtered down to 5,412 SNPs present in at least one individual per species.Matrix 3. Input for ADMIXTURE and PCA for all Orotettix species. 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).Matrix 4. Input for ADMIXTURE and PCA for Orotettix andeanus. 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. 2026-09-18T17:26:51Z Dataset Dataset 10.6084/m9.figshare.33511723.v1 https://figshare.com/articles/dataset/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/33511723 CC BY 4.0 Open Access after 2027-09-18