Ancient Genomics Reveals the Origin, Dispersal, and Human Management of East Asian Domestic Pigs

Abstract

Pigs are the most commercially important modern livestock animal in East Asia. Numerous aspects of their domestication history remain unclear, however, including the geographic center of their domestication, their subsequent dispersal routes, and the emergence of phenotypic traits specific to domestic pigs. To address these questions, we generated 21 nuclear genomes and 23 mitogenomes from ancient domestic pigs and wild boar from 5,800 BCE to 1,300 CE across China. Our analyses of newly generated and previously published Eurasian suid genomes confirmed Northern China and eliminated Southwestern China as the domestication origin of modern East Asian pigs. Following their association with people and the first appearance of black coat coloration, Northern Chinese domestic pigs dispersed alongside Yellow River millet farmers to the Yangtze River Basin and Southwestern China, which they admixed with local wild boar. A genome-wide loss of diversity and signatures of inbreeding in ancient Northern pigs may have been the result of intensified human management as early as 3,000 BCE. Our results reveal the geographic and temporal origins and subsequent dispersal and admixture of pigs in China, mirroring human migration and agricultural development history.