Data from: A genomic approach for distinguishing between recent and ancient admixture as applied to cattle

Genomic data facilitate opportunities to track complex population histories of divergence and gene flow. We developed a metric, scaled block size (SBS), that uses the unrecombined block size of introgressed regions of chromosomes to differentiate between recent and ancient admixture, and applied it to reconstructing admixture in cattle. Cattle are descendants of two independently domesticated lineages, taurine and indicine, that diverged 200,000 or more years ago. Several breeds have hybrid ancestry between these divergent lineages. Using 47,506 SNPs, we analyzed the genomic architecture of ancestry of 1369 indivduals. We focussed on four groups with admixed ancestry, including two anciently admixed African breeds (n=58; n=43), New World cattle of Spanish origin (n=51), and known recent hybrids (n=46). We estimated ancestry of chromosomal regions for each individual and used the SBS metric to differentiate timing of admixture among groups and among individuals within groups. By comparing SBS values of test individuals to standards with known recent hybrid ancestry, we were able to differentiate individuals of recent hybrid origin from other admixed cattle. We also estimated ancestry at the chromosomal scale. The X chromosome exhibits reduced indicine ancestry in recent hybrid, New World, and western African cattle, with virtually no evidence of indicine ancestry in New World cattle.