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.