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

TL;DR

The study reveals that African pigs have a complex genetic origin involving European and Asian lineages, with a rare wild boar haplogroup found in Tanzania.

Contribution

The detection of a rare Asian wild boar haplogroup in Tanzania and the genetic link between western African and Iberian pigs is a novel finding.

Findings

African pigs predominantly descend from European and East Asian lineages.

A rare Asian wild boar haplogroup A1∗ was detected in Tanzania.

Genetic link between western African and Iberian pigs dates to about 4.5 ka.

Abstract

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.

•African indigenous pigs show signatures of both European and Asian pigs•Iberian-type pigs in Africa show a spatial correlation with the Bantu dispersal•Rare mitochondrial DNA sub-haplogroup A1∗ is identified in pigs from Tanzania

African indigenous pigs show signatures of both European and Asian pigs

Iberian-type pigs in Africa show a spatial correlation with the Bantu dispersal

Rare mitochondrial DNA sub-haplogroup A1∗ is identified in pigs from Tanzania

Genomics; evolutionary ecology; evolutionary history

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