Additional file 1 of Natural clines and human management impact the genetic structure of Algerian honey bee populations
Creators: name: Salvatore, Giovanna
name: Chibani Bahi Amar, Amira
name: Canale-Tabet, Kamila
name: Fridi, Riad
name: Tabet Aoul, Nacera
name: Saci, Soumia
name: Labarthe, Emmanuelle
name: Palombo, Valentino
name: D’Andrea, Mariasilvia
name: Vignal, Alain
name: Faux, Pierre
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Pictures of A. m. sahariensis (a) and A. m. intermissa (b). Figure S2. Distribution of IBD kinship between pairs of Algerian samples. The distribution of the values of IBD kinship over 11,325 pairs of Algerian samples (N = 151) is shown in this figure. The Y axis gives the number of pairs in each bin on a logarithmic scale (a value of 1, 2 or 3 respectively means 1, 10 or 100 pairs in the corresponding bin). The red dashed line indicates the retained cut-off (0.3) to define close-related samples. For pairs beyond that cut-off value, we retained only one member in the final set (see Additional file 2: Table S1). Figure S3. Estimation of cross-validation (CV) error for 50 runs of ADMIXTURE for 2 ≤ K ≤ 12, considering Algerian and reference specimens. Among the K values with the lowest CV values, K = 4 stands out as having a significant mode that comprises 48 out of 50 runs. This mode also has the lowest mean CV value from the ADMIXTURE runs. The admixture plot for K = 4 is given along with plots for 2 ≤ K ≤ 6. Figure S4. Estimation of cross-validation (CV) error for 50 runs of ADMIXTURE for 2 ≤ K ≤ 12, only considering Algerian specimens. Figure S5. Scatter plots of genetic vs. geographic pairwise distances. The top plot displays genetic (measured as the Euclidean distance on the two first PC) and geographic distances over all pairs of samples (N = 5151). In the bottom plots, all pairs are partitioned on their type: (a) both samples from the Western cluster, (b) each sample from a different cluster, and (c) both samples from the Eastern cluster. Figure S6. PCA of the test population using each of the four panels of 96 selected SNPs. The four PCA plots show the distribution of the 63 test samples (20 Algerian bees + 13 M lineage + 30 C lineage) on the first two principal components obtained using the 96 selected SNPs with each configuration (from top to bottom, left to right: GI1, GI2, EN1 and EN2). The four scree plots correspond to the each of four PCA. In all cases the top-2 PC explain a much larger proportion of variance than the subsequent PC. Figure S7. Prediction performance of the list of 96 selected SNPs against 1000 lists of randomly-chosen SNPs. We compared the selected panel of 96 SNPs (GI1) to 1000 randomly-selected SNPs. After using each of these random panels to repeat 50 times the training of a RF classifier ({Algerian; non-Algerian}) and its application to assignment of the 63 test samples, we recorded three parameters: (a) the average classification accuracy of the test samples over the 50 runs, (b) the minimum probability of being labelled Algerian for Algerian bees, and (c) the maximum probability of being labelled Algerian for non-Algerian bees. The values of these parameters obtained with the selected panel of 96 SNPs are shown in red below each histogram. Figure S8. Assignment probability of Algerian bees and simulated hybrids. We report the probability of a test sample being labelled “Algerian” by a random forest classifier for which the training set did not include simulated hybrids, for 20 Algerian bees and 320 simulated hybrids: four types of crosses (F1 and three back-crosses – BC) on 40 per type of cross. Figure S9. Assignment probabilities, using the panel of 96 AIM vs. using all variants. We report the probability of a test sample being labelled “Algerian” by a random forest classifier trained on a population that includes simulated hybrids, using either all variants (blue boxes) or the 96 selected AIM (yellow boxes), per population or per type of hybrid.