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Table S1 SNP bovine genome coverage based on the Btau_4.0 bovine genome assembly

Table S2FST for each pair of populations

Table S3 Individual SNP results for CGU iHS and ZEB/CGU, AFT/CGU, EUT/CGU, AFT/EUT, AFT/ZEB and EUT/ZEB Rsb and the three Δ ancestry estimates

Table S4 Summary of AFT/EUT, AFT/ZEB and EUT/ZEB Rsb for the 23 candidate regions identified in CGU (see Table 2).

Fig. S1 Between group PCA results.

Fig. S2 Empirical distribution of CGU iHS, ZEB/CGU Rsb, AFT/CGU Rsb and EUT/CGU Rsb scores.

Fig. S3 Average local ancestry from each of the three origins (EUT, AFT and ZEB) in CGU individuals.

Fig. S4 Distribution of maximum (A) and minimum (B) Δ ancestries for the three clusters over 50 000 permutations.

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