Ancient introgression drives wild boar expansion and phenotypic diversification of domestic pigs

Despite the ubiquity of wild boar populations across Eurasia, their origins, routes of dispersal, and phenotypic evolution remain uncertain. Here, using 745 genomes representing populations across Eurasia, we demonstrate that wild boar expanded from South Asia during the Middle Pleistocene. This expansion was preceded by a Pliocene introgression (~3 to 5 million years ago) in South Asia from an archaic Suinae lineage that introduced a ~43 megabase X-chromosomal haplotype into the ancestral wild boar population. This haplotype includes loci associated with increased body size and adaptation to cold climates. During domestication, this region was selected at least three times independently to develop modern large-bodied breeds. Our findings reveal a long-lasting evolutionary legacy of this ancient introgression, which provided genetic material that was later shaped by natural and artificial selection.

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Journal
Science
Published
2026-09-24
DOI
https://doi.org/10.1126/science.adq7553
Primary Topic
Genetic and phenotypic traits in livestock
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article
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article

Ancient introgression drives wild boar expansion and phenotypic diversification of domestic pigs

Jie Zhong, Lingzhao Fang, Faiz‐ul Hassan, Neena Amatya Gorkhali et al.
Science
Genetic and phenotypic traits in livestock
article

Ancient introgression drives wild boar expansion and phenotypic diversification of domestic pigs

Jie Zhong, Lingzhao Fang, Faiz‐ul Hassan, Neena Amatya Gorkhali, Jianhai Chen, Malavanh Chittavong, Greger Larson, Richard P. Bishop, Luan Fu, B D P Soewandi, S. M. Farhad Vahidi, Laurent Frantz, Nicholas W. VanKuren, Thuy Nhien Thi Tran, Mukesh Kumar Thakur, Matthew W. Hahn, Xiaoyong Du, Jianlin Han, Ivan Jakovlić, Edward S. Rice, Changyi Xiao, Xinyun Li, Guanglin He, Abdullah Ibne Omar, Yalan Yang, Shuhong Zhao, Amali Malshani Samaraweera, Pradeepa Silva, Kevin G. Daly, Nikica Šprem, Hidayat Ashari, Mikhail Sablin, Supamit Mekchay, David W. G. Stanton, Jeffrey P. Spence, Daniel Falush, Md. Omar Faruque, Xiaolei Liu, Saroj Sapkota, Mingshan Wang, Zhuofan Yan, Xuewen Xu, Shilin Zhu, Jingjin Li, Zhuqing Zheng, Ali Akbar Bhuiyan, Debabrata Phukon, Fan Jiang, Pan Ni, San San Hmwe, Le Thi Thuy
article en

Abstract

Despite the ubiquity of wild boar populations across Eurasia, their origins, routes of dispersal, and phenotypic evolution remain uncertain. Here, using 745 genomes representing populations across Eurasia, we demonstrate that wild boar expanded from South Asia during the Middle Pleistocene. This expansion was preceded by a Pliocene introgression (~3 to 5 million years ago) in South Asia from an archaic Suinae lineage that introduced a ~43 megabase X-chromosomal haplotype into the ancestral wild boar population. This haplotype includes loci associated with increased body size and adaptation to cold climates. During domestication, this region was selected at least three times independently to develop modern large-bodied breeds. Our findings reveal a long-lasting evolutionary legacy of this ancient introgression, which provided genetic material that was later shaped by natural and artificial selection.

ScienceVol. 393(6818)
University College Dublin (IE), University of Peradeniya (LK), Zoological Survey of India (IN), Queen Mary University of London (GB), University of California, San Francisco (US), University of Zagreb (HR), Kunming Institute of Zoology (CN), Chinese Academy of Sciences (CN), Aarhus University (DK), Huazhong Agricultural University (CN), Trinity College Dublin (IE), Bangladesh Agricultural University (BD), Sichuan University (CN), Government of India (IN), Zoological Institute (RU), Bangladesh Medical Research Council (BD), Dagon University (MM), University of Oxford (GB), University of Chicago (US), Animal Husbandry & Veterinary (IN), Soil Conservation and Watershed Management Research (IR), West China Hospital of Sichuan University (CN), National Institute of Animal Sciences (VN), Shanghai Institute of Materia Medica (CN), Indiana University Bloomington (US), Ministry of Agriculture (ID), Chinese Academy of Agricultural Sciences (CN), Oxford Archaeology (GB), Agricultural Research & Education Organization (IR), Nepal Agricultural Research Council (NP), Agricultural Biotechnology Research Institute of Iran (IR), Sanya University (CN), Center of Hubei Cooperative Innovation for Emissions Trading System (CN), Hubei Academy of Agricultural Sciences (CN), National University of Laos (LA), Chiang Mai University (TH), Uva Wellassa University (LK), China Agricultural University (CN), International Livestock Research Institute (KE), Indiana University (US), Lanzhou University (CN), University of Missouri (US), Cardiff University (GB), University of Veterinary and Animal Sciences (PK), Ludwig-Maximilians-Universität München (DE)
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Genetic and phenotypic traits in livestock
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