Additional file 3 of Genome-wide species delimitation analyses of a silverside fish species complex in central Mexico indicate taxonomic over-splitting

Additional file 3: Table S1. Information of the sampling localities in the central Mexico plateau: localities, lakes, number of samples (n), geographic coordinates (Latitude and Longitude) and Altitude (meters over sea level, m.o.s.l.). Table S2. Filters applied to SNP databases. The databases highlighted in bold were selected for further filtering. Table S3. Databases generated with Tassel filters used to evaluate the consistency of the genomic patterns to the number of SNPs, individuals, species, and missing data percentage. The matrices used in the genomic analyzes are indicated in bold. Table S4. Genomic pairwise FST comparisons for 3482 SNP loci among the nine morphospecies proposed by Barbour [10]. Values in bold indicate significance at α = 0.0014 for pairwise comparisons, following sequential Bonferroni corrections. Table S5. Genomic pairwise FST comparisons for 3482 SNP loci among the five mitonuclear groups proposed by Betancourt-Resendes et al. [11]. Values in bold indicate significance at α = 0.005 for pairwise comparisons, following sequential Bonferroni corrections. Table S6. Genomic pairwise FST comparisons for 3842 SNP loci among the four genomic clusters detected in humboldtianum group by DAPC analyses. Values in bold indicate significance at α = 0.0083 for pairwise comparisons, following sequential Bonferroni corrections. Table S7. Genomic pairwise FST comparisons for 3482 SNP loci among the three genomic clusters detected in the humboldtianum group by Admixture and phylogenetic analyses. Values in bold indicate significance at α = 0.017 for pairwise comparisons, following sequential Bonferroni corrections. Table S8. Genomic pairwise FST comparisons for 3482 SNP loci among the ecotypes in each lake. Values in bold indicate significance at α = 0.005 for pairwise comparisons, following sequential Bonferroni corrections. Table S9. Outlier loci detected by the FST outlier analysis performed in BayeScan related to gene regions.