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Additional file 2: Table S2. Marginal estimated means of each diversity index per group of populations. The letters and grey color stand for significant pairwise differences between groups (Tukey correction for multiple tests).

Additional file 3: Figure S1. Correlation matrix of population molecular or demographic diversity indices for breeds involved in a management program (Group 1). Values correspond to Pearson’s correlation coefficients. Colored cells stand for significant correlations (p < 0.05) either positive (blue) or negative (red), the intensity depending on the strength of the correlation between estimates. White cells represent non-significant correlations. Nb.Generation stands for the number of generations since the start of the management program and Fixed for the proportion of fixed alleles.

Additional file 5: Figure S3. Mean assignment probability of populations to each of the two clusters. The Asian and European clusters are colored in red and blue, respectively.

Additional file 4: Figure S2. Matrix of pairwise Fst between populations. Darker blue indicates a stronger pairwise Fst.

Additional file 6: Figure S4. Unrooted neighbor-joining tree of the Hergnie breed. The colors of the surrounding circle represent the different breeders.