Fig. 1

Genetic variation and divergence. a PCA of the genetic distance was performed to assess the clustering of sequences according to their genome of origin, taurine (blue), indicine (orange) or admixed (green). For PCA breed composition, (see Additional file 1: Figure S2). b Proportion and number of private and shared SNPs for the taurine (blue), indicine (orange) or admixed (green) cattle datasets. c Estimated nucleotide diversity in 20-kb genomic bins for the taurine (blue), indicine (orange) or admixed (green) sequences. d–f Correlations between estimated reference allele frequencies (RAF) between taurine (blue) and indicine (orange) (d), admixed (green) and indicine (orange) (e) and admixed (green) and taurine (blue) (f). An increasing number of SNP counts is related to warmer colours