Dog breeds used in molecular analyses. (A) Geographic representation of the region of origin for the 23 Mediterranean breeds. The (B) smooth-coated and (C) rough-coated varieties are both recognized in Fonni’s Dogs. Breed abbreviations are listed in Table 1.
STRUCTURE analysis of (A) Mediterranean and (B) Italian dog breeds. Colors indicate separate STRUCTURE group signatures for individual dogs. Maximum likelihood predicts groupings of K = 15 and K = 3 for Mediterranean and Italian breeds, respectively.
Weir and Cockerham’s weighted FST values based on breed-to-breed comparisons of SNP genotypes. (A) Scores of 0 (yellow) indicate perfect identity, scores of 0.3 (blue) indicate the highest level of divergence observed in this set of breeds. (B) Distribution of breed-specific FST values.
PCA of SNP-chip data for (A and B) Mediterranean breeds (PC1 = 5.54, P = 1.33 × 10−46; PC2 = 4.89, P = 5.68 × 10−42; PC3 = 4.70, P = 5.68 × 10−51; PC4 = 4.49, P = 2.78 × 10−62), (C and D) all Italian breeds (PC1 = 3.84, P = 2.41 × 10−27; PC2 = 2.71, P = 1.40 × 10−23; PC3 = 2.03, P = 1.83 × 10−13; PC4 = 1.65, P = 1.88 × 10−05), and (E and F) regional Italian breeds (PC1 = 1.51, P = 0.51; PC2 = 1.46, P = 0.32; PC3 = 1.40, P = 0.19; PC4 = 1.40, P = 0.04). Breed clusters are denoted with ellipses of 2 SD. Breed abbreviations are listed in Table 1.
SNP-based neighbor-joining cladograms for (A) Mediterranean and (B) Italian breeds. Clade coloration reflects the designations assigned by FastSTRUCTURE (Figure 4). Branch numbers indicate the bootstrapping values from 100 repetitions. *, the nine Cane Corso dogs did not form a single clade, however the bootstrap values for their phylogenetic locations relative to each other are each 100. Breed abbreviations are listed in Table 1.
(A) Admixture predictions by three computational algorithms. TreeMix three_pop analysis (green arrow) identified Fonni’s Dog contribution to the Portuguese Water Dog/Cane Paratore clade at 17.43% with P = 0.00723. ANGSD (red dashed line) calculated significant values of D(O, Fonni’s Dog; Komondor, Cane Corso) = 0.039, Z = 4.366; D(O, Komondor; Fonni’s Dog, Cane Corso) = 0.031, Z = 3.920; D(O, Fonni’s Dog; Saluki, Cane Corso) = 0.033, Z = 3.893; D(O, Saluki; Fonni’s Dog, Cane Corso) = 0.040, Z = 5.075. AdmixTools (blue dashed line) supports the findings of TreeMix with significant D-statistic values for Fonni’s Dog and Portuguese Water Dog of D(O, Portuguese Water Dog; Fonni’s Dog, X) = −0.0139 to −0.1287, Z = −3.737 to −25.274; D(O, Fonni’s Dog; Portuguese Water Dog, X) = −0.0127 to −0.1309, Z = −3.078 to −25.797; D(O, Fonni’s Dog; X, Portuguese Water Dog) = 0.0100–0.0767, Z = 3.016–22.189; Cane Paratore of D(O, Cane Paratore; Fonni’s Dog, X) = −0.0104 to −0.1317, Z = −3.108 to −26.025; D(O, Fonni’s Dog; Cane Paratore, X) = −0.0096 to −0.1289, Z = −3.055 to −25.805; D(O, Fonni’s Dog; X, Cane Paratore) = 0.0104–0.0811, Z = 3.643–22.974; Komondor of D(O, Fonni’s Dog; Komondor, X) = −0.0116 to −0.1123; D(O, Fonni’s Dog; X, Komondor) = 0.0116–0.1280, Z = 3.142–25.720; and Saluki of D(Saluki, X; Fonni’s Dog, Y) = 0.007–0.131, Z = 3.047–29.352. TreeMix predicted phylogenies with (B) 1 or(C) 25 allowed introgression events, and corresponding standard error residuals for (D) 1 and (E) 25 introgressions.