Additional file 2 of Genome-wide species delimitation analyses of a silverside fish species complex in central Mexico indicate taxonomic over-splitting
Creators: name: Piñeros, Victor Julio
name: del R. Pedraza-Marrón, Carmen
name: Betancourt-Resendes, Isaí
name: Calderón-Cortés, Nancy
name: Betancur-R, Ricardo
name: Domínguez-Domínguez, Omar
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Supporting Methods. Figure S1. Principal Components Analyses 19 matrices with different numbers of SNPs loci, missing data, individuals, and species of the humboldtianum group. Figure S2. Principal component analyses (PCAs) based on all, neutral, and outlier SNP loci from matrices A, B, C, and E. PCAs estimated using all and neutral SNPs (~ 2 k–33 k) consistently recovered four genomic groups that are in agreement with geographic patterns but not with the previously recognized morphospecies; these are delimited with convex hulls: humboldtianum sensu stricto group (blue), from Lake Zacapu; estor group (green) from Lakes Patzcuaro and Zirahuén; chapalae group (red), from Lake Chapala; and C. sphyraena group (yellow), also from Lake Chapala. PCA analyses based on ~ 100–400 SNPs also resolved four genomic groups in matrices A and B, and in matrices C and E, chapalae and sphyraena groups clustered together. Morphospecies are color-coded according to the genomic groups observed. Figure S3. Plots of Bayesian Information Criterion (BIC) vs. number of clusters (k) of DAPC analyses for all, neutral, and outlier SNP loci from matrices A–E. Figure S4. Discriminant analyses of principal components (DAPCs) estimated using ca. 1800–33,700 SNPs resolve four well-differentiated clusters. DAPCs based on outlier SNPs recover three to four groups. These results are largely consistent across analyses based on matrices A, B, C, and E (a–d), and are also concordant with PCA analyses. In neither case, the observed genomic clusters do correspond to the morphology-based species delimitation scenario. Morphospecies are color-coded according to the genomic clusters recovered: blue, humboldtianum sensu stricto, green, estor group; red, chapalae group; yellow, C. sphyraena. Figure S5. Plots of cross-validation error of each k (number of clusters) analyzed in Admixture analyses for all, neutral, and outlier SNP loci from matrices A- E. The cross-validation procedure was performed with the folds value = 5 (the default), a block relaxation algorithm as point estimation method, and the point estimation terminated with the objective function delta &lt; 0.0001. Figure S6. Admixture assignment analyses estimated using ca. 80–33,700 neutral and outlier SNPs consistently identified three well-differentiated clusters (k = 3) using matrices A, B, C, and E (a–d). Outlier SNPs show an increased intermingling of individuals among clusters compared with analyses based on all or neutral loci. Each bar represents the probability of assignment to each cluster. Genomic clusters are color-coded as blue, humboldtianum sensu stricto, green, estor group; orange, chapalae-sphyraena group. CHA, Lake Chapala; TEP, Tepuxtepec Dam; TRI, Trinidad Fabela Dam; PAT, Lake Pátzcuaro; ZIR, Lake Zirahuén. Figure S7. Admixture assignment analyses estimated using ca. 33,700 SNP loci a) in Chapala Lake, and b) within Lakes Pátzcuaro-Zirahuén. Figure S8. Phylogenetic trees of ca. 1800–33,700 SNP loci of the humboldtianum group estimated under a maximum likelihood framework in IQ-TREE. Phylogenetic trees were estimated using all (~ 1900–33,700), neutral-only (~ 1800–33,300), and outlier (~ 80–350) SNPs. Individuals are color-coded by genetic clusters according to Fig. 2. Figure S9. Mitochondrial trees (left) and ddRADseq phylogeny (right) of the humboldtianum group. The tips in the RADseq inferences were pruned to include the same individuals present in the mitochondrial trees. Figure S10. FST versus log10-transformed posterior odds (PO) values for the global outlier detection calculated in BayeScan. The analyses were estimated considering the nine morphospecies and (A) 33,716 SNPs, where the vertical line represent the FDR threshold of q = 0.037; (B) 10,157 SNPs, q = 0.040; (C) 4821 SNPs, q = 0.025; (D) 3564 SNPs, q = 0.034; and (E) 1887 SNPs, q = 0.015. Figure S11. Mean coverage of the subset with15 samples using different values of the minimum raw reads required to form a stack (m1–m6). Figure S12. Putative loci at different combinations of de novo assembly parameters: m, minimum reads required to form a stack; M, allowed SNPs in a stack required to form a putative locus in an individual; n, allowed SNPs in a stack required to form a locus in the population. Each parameter was changed one at the time (m = 2–6, M = 0–6, and n = 0–11) while keeping the others at default values (m3M2n1). Figure S13. Genotyped loci and variant sites using a constraint on the number of minimum individuals in a population required to have that locus (r = 40, 60, and 80) based on different cutoff, as follow: (A) minimum raw reads required to form a stack (m = 2–6), (B) maximum mismatches allowed between stacks of the same individual (M = 0–6), and (C) mismatches allowed between loci of different individuals (n = 0–11). Figure S14. Flow chart of the quality control and SNP filtering steps applied to generate the final datasets.