Fig 1.
Map of the wild and cultivated Agave angustifolia collected in the states of Sonora and Oaxaca.
The localities are colored as cultivated (dark orange) and wild (dark blue). In the left corner is a picture of cultivated Espadín collected in the Oaxaca state. In the right corner is a map of Mexico, with the Sonora and Oaxaca states marked in blue, showing all sampled localities in black, using triangles for Sonora and circles for Oaxaca.
Table 1.
Diversity estimates with corresponding standard deviation values (SD) for wild and cultivated Agave angustifolia in the Oaxaca and Sonora states estimated using 51,560 SNPs.
Fig 2.
Scatter plot of LD decay (r2) against the distance in base pairs for pairs SNP for: (A) wild Sonoran populations, (B) managed Sonoran populations, (C) wild populations from Oaxaca, and (D) managed Espadín from Oaxaca.
Fig 3.
The diagram of relatedness coefficient as estimated within vcftools for: (A) 56 wild and (B) 42 managed A. angustifolia individuals from the state of Sonora, (C) 62 wild, and (D) 47 managed A. angustifolia individuals from the state of Oaxaca.
Fig 4.
Population genetic structure of wild and cultivated A. angustifolia from Sonora and Oaxaca states, Mexico, based on 51,560 genome-wide SNPs.
(A) Principal component analysis (PCA) of the individuals of A. angustifolia. (B) Neighbor-joining (NJ) network of 207 individuals of A. angustifolia. PCA and NJ tree tips are colored according to the management type of the samples: dark blue for wild and dark orange for managed. Shapes on PCA and NJ tree tips correspond to the state where samples were collected: circles to Oaxaca and triangles to Sonora. (C) Pairwise FST differences among wild and cultivated samples of A. angustifolia from Sonora and Oaxaca states, Mexico. Colors represent FST values from the lowest of 0 in white to the highest of 0.12 in orange. Abbreviations: OW- Oaxaca Wild, OM – Oaxaca Managed, SW – Sonora Wild, and SM – Sonora managed.
Fig 5.
Comparison of the allele frequencies (A) and (B) the distribution of allele frequency differences between wild and managed A. angustifolia from the Sonora state and (C) and (D) between wild and managed A. angustifolia from the Oaxaca state.
Fig 6.
The number of alleles identified as shared, private to domesticated populations, and private to the wild samples for managed (A) A. angustifolia in Sonora and (B) managed Espadín in Oaxaca.