Re-Evaluating the Population History of Malagasy Native Cattle Reveals Shared African Taurine-Related Ancestry but Distinct Indicine Admixture Histories Relative to East African Cattle.

East African cattle, including Malagasy native cattle (ZMA), are generally thought to have been shaped by admixture between African taurine and Asian indicine lineages, but the detailed position and formation history of ZMA within this broader diversity remain unclear. We analyzed worldwide SNP data from 145 cattle populations comprising 4093 individuals using principal component analysis (PCA), pairwise weighted FST, outgroup-f3, f4, qpWave, and qpGraph. ZMA fell along the African taurine-Asian cattle axis in PCA. Although several West African taurine populations showed the highest absolute outgroup-f3 values with ZMA, outgroup-f3 profile comparisons showed that ZMA was most closely matched by East African cattle, especially East African Shorthorn Zebu, Boran, and Sheko, consistent with a shared African taurine ancestry background. However, f4, qpWave, and qpGraph showed that these relationships are not adequately explained by a simple clade-like relationship or a single shared admixture event, but instead suggest multiple waves of gene flow from different Asian indicine populations. Our results refine African-wide models of heterogeneous indicine ancestry by showing that, in the East African-Malagasy context, ZMA are best understood as part of a shared African taurine-related ancestry background overlaid by later lineage-specific and internally heterogeneous indicine-related admixture histories.