Table S1. Raw allele frequencies in the 60 populations of the PigBioDiv European project, on the 50 microsatellite loci. It is presented in a PHYLIP like format. Some loci in some population have missing values; this case is coded as a line of 0. In this table the first line gives the number of populations (60) and the number of loci (50), the second lines gives the number of alleles of the 50 loci. Then allele frequencies (resp. number of haplotypes) are given for each population. These allele frequencies were computed with variable numbers of haplotypes for each population x loci combination. These numbers are given in Table S2.

Table S2. Numbers of haplotypes used in allele frequency computation for each population x loci combination in Table S1. In this table the first line gives the number of populations (60) and the number of loci (50), the second lines gives the number of alleles of the 50 loci. Then allele frequencies (resp. number of haplotypes) are given for each population.

Table S3. Observed and expected heterozygosities, the observed and effective numbers of alleles, and the Hardy-Weinberg test for each population (PigMaP and PigBioDiv).

Table S4. F statistics for each microsatellite.

Figure S5. Clustering of the PigBioDiv breeds and lines into 12 groups, using allele sharing distance and UPGMA. The darkness is proportional to the rate of animals in each group.

Figure S6. Individual clustering of Hampshire (A), and Meishan (B) samples. MS01 and MS02 stand for French and British samples of the Meishan breed.

Figure S7. Distribution of the numbers of private alleles. Abscissa: number of private alleles found in a breed. Ordinates: number of breeds exhibiting the corresponding number of private alleles. Singletons, i.e. alleles that were found only once, were discarded.

Figure S8. Comparison of the Reynolds (PHYLIP multilocus formula, corrected here for sample size) and the standard Nei distances (PigBioDiv data).

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