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.附加文件3：表S1。墨西哥高原中部采样点信息：采样点、湖泊、样本量（n）、地理坐标（纬度与经度）及海拔（以海平面为基准的米数，m.o.s.l.）。 表S2。单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据库过滤方案。其中以粗体标注的数据库将用于后续过滤流程。 表S3。基于Tassel过滤流程生成的数据库，用于评估基因组模式与单核苷酸多态性（SNP）数量、个体数、物种类别及缺失数据占比的一致性。基因组分析中使用的矩阵以粗体标注。 表S4。针对Barbour[10]提出的9个形态种间的3482个单核苷酸多态性（SNP）位点，开展基因组两两群体分化系数（Fixation Index, FST）比较。经序列邦费罗尼校正后，粗体数值表示两两比较在α=0.0014水平下具有统计学显著性。 表S5。针对Betancourt-Resendes等人[11]提出的5个线粒体核基因组分组间的3482个SNP位点，开展基因组两两FST比较。经序列邦费罗尼校正后，粗体数值表示两两比较在α=0.005水平下具有统计学显著性。 表S6。通过主成分判别分析（Discriminant Analysis of Principal Components, DAPC）在humboldtianum类群中检测到的4个基因组簇间的3842个SNP位点的基因组两两FST比较。经序列邦费罗尼校正后，粗体数值表示两两比较在α=0.0083水平下具有统计学显著性。 表S7。通过群体遗传结构分析（Admixture）与系统发育分析在humboldtianum类群中检测到的3个基因组簇间的3482个SNP位点的基因组两两FST比较。经序列邦费罗尼校正后，粗体数值表示两两比较在α=0.017水平下具有统计学显著性。 表S8。各湖泊内生态型间的3482个SNP位点的基因组两两FST比较。经序列邦费罗尼校正后，粗体数值表示两两比较在α=0.005水平下具有统计学显著性。 表S9。通过BayeScan软件开展的FST离群位点分析所检测到的与基因区域相关的离群位点。