Table S1 Number of alleles, observed and expected heterozygosity for Maremmano, Lusitano and Italian Lipizzan horses (146 horses) based on 30 microsatellite loci.

Table S2 Nei’s standard genetic distance and Wright′s distance among 15 horse breeds.

Table S3 Estimated memberships to inferred clusters obtained by STRUCTURE and individual assignments of 549 horses according to their own predefined breed or to another breed as obtained using GeneClass2.

Figure S1 UPGMA dendrogram constructed from allele-sharing distances among 549 animals from 15 different horse breeds.

Figure S2 Graphical presentation of the population structure analyses for a sample of 549 horses from 15 different horse breeds obtained by STRUCTURE.

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