Unscrambling the history of African indicine cattle genomes

African cattle's genetic heritage reflects millennia of relationships between African and Asian human societies and civilizations. By analysing genome-wide SNP data from 1,043 individuals representing 38 breeds, including 36 from Africa, in an Approximate Bayesian Computation framework coupled with random forest classification, we show that this history was characterised by at least two independent arrivals of zebu (indicine) cattle from the Indian subcontinent. Time estimates coincide with major cultural transitions across Africa, including state formation, iron technology spread, and pastoral intensification, exemplified by developments such as the Aksumite Empire and Swahili civilization. Moreover, we show that sanga cattle are the result of admixture between native African taurine and zebu cattle from the first arrival. These findings provide a refined chronology of cattle movements and pastoralism into Africa, reveal how human cultural transitions structured livestock genomes, and highlight Africa’s central role in shaping global cattle diversity.