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

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.

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Journal
iScience
Published
2025-11-27
DOI
https://doi.org/10.1016/j.isci.2025.114252
Primary Topic
Genetic and phenotypic traits in livestock
Type
article
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article

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

Adeniyi C. Adeola, Antoine Souron, George Niba, O. O. Oluwole et al.
iScience
Genetic and phenotypic traits in livestock
article

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

Adeniyi C. Adeola, Antoine Souron, George Niba, O. O. Oluwole, Joram M. Mwacharo, George Msalya, Richard P. Bishop, Chabi A. M. S. Djagoun, Bernard Agwanda, Oladipo Omotosho, Elliot Greiner, Sunday Charles Olaogun, Jianlin Han, Pam Dachung Luka, Ndifor K. Wanzie, P.M. Dawuda, Tingting Yin, Xian Shi, David H. Mauki, Olawale Festus Olaniyan, Zheng‐Fei Cai, Emmanuel Ndiema, Oscar J. Sanke, V. M. O. Okoro, Ya‐Ping Zhang, Xiaolei Liu, Yuhua Fu, Hai‐Bing Xie, Shuhong Zhao, Min-Sheng Peng, Ofelia Galman Omitogun, Lameck A. Odongo, Ruth N. Njuki
article en

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.

iScienceVol. 29(1)
Centre National de la Recherche Scientifique (FR), Université de Bordeaux (FR), National University of Lesotho (LS), University of Douala (CM), Federal University of Technology Owerri (NG), University of the Gambia (GM), University of Ibadan (NG), Kunming Institute of Zoology (CN), Yunnan University (CN), International Center for Agricultural Research in the Dry Areas (LB), Huazhong Agricultural University (CN), Sichuan University (CN), Scotland's Rural College (GB), Taraba State University (NG), West China Hospital of Sichuan University (CN), National Animal Husbandry Service (CN), Max Planck Institute for Evolutionary Anthropology (DE), Université d'Abomey-Calavi (BJ), American International University West Africa (GM), Ministère de la Culture (DZ), Sanya University (CN), Center of Hubei Cooperative Innovation for Emissions Trading System (CN), National Museums of Kenya (KE), National Veterinary Research Institute (NG), University of Chinese Academy of Sciences (CN), Obafemi Awolowo University (NG), International Livestock Research Institute (KE), Sokoine University of Agriculture (TZ), Bayero University Kano (NG)
Openalex Percentile: Top 61%
Genetic and phenotypic traits in livestock
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