Fig. 2

Multivariate and admixture results based on all, neutral, and outlier SNP loci from the matrix D (3564-snps loci), which explain the highest percentage of explained variation in the analyses. a Principal component analyses (PCAs), and (b) Discriminant analyses of principal components (DAPCs) consistently recovered four genomic groups (k = 4) with all and neutral loci that are in agreement with geographic patterns but not with the previously recognized morphospecies: 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. Outlier loci resolved three groups (k = 3) where chapalae and sphyraena groups clustered together. Morphospecies are color-coded according to the genomic groups observed. In PCAs scatterplots the point clustering groups are delimited by convex hulls. In DAPC scatterplots, the point clustering groups are inside their 95% inertia ellipses, and the lines connect points to the mean value for each group. The eigenvalue bar plots are showing in the upper right of each figure. c Admixture assignment analyses estimated using all, neutral, and outlier SNPs consistently identified three well-differentiated clusters (k = 3). 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