Integrated mitogenome and Y chromosome analysis untangles the complex origin of African pigs

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The genetic history of African indigenous pigs remains poorly documented due to scarce archaeological and genomic data. Here, we analyzed 473 mitogenomes and 202 Y chromosome sequences from indigenous pigs in Africa, alongside 901 published mitogenomes and 715 Y chromosome sequences from Eurasian pigs and wild boars. Our results reveal that African pigs predominantly descend from European (haplogroup E, 44.8%) and East Asian (haplogroup D, 53.3%) lineages. Interestingly, there was a novel detection of Asian wild boar haplogroup A∗ (1.9%) in Tanzania. This pattern is congruent with that of Y chromosome analysis. Further maternal analyses confirm a genetic link between western African and Iberian pigs dating to about 4.5 ka, and dispersal into eastern Africa coinciding with the Bantu expansion around 2 ka. Our findings demonstrate complex human-mediated dispersal routes, highlighting the role of Bantu societies in shaping the genetic architecture of African indigenous pigs.