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It is widely accepted that modern pigs were domesticated independently at least twice, and Chinese native pigs are deemed as direct descendants of the first domesticated pigs in the corresponding domestication centers. By analyzing mitochondrial DNA sequences of an extensive sample set spanning 10,000 years, we find that the earliest pigs from the middle Yellow River region already carried the maternal lineages that are dominant in both younger archaeological populations and modern Chinese pigs. Our data set also supports early Neolithic pig utilization and a long-term in situ origin for northeastern Chinese pigs during 8,000–3,500 BP, suggesting a possibly independent domestication in northeast China. Additionally, we observe a genetic replacement in ancient northeast Chinese pigs since 3,500 BP. The results not only provide increasing evidence for pig origin in the middle Yellow River region but also depict an outline for the process of early pig domestication in northeast China.

The origin of domesticated pigs is of interest to the general public. Technology to analyze ancient DNA can provide direct scientific evidence to address this question. It has been reported that modern Chinese pigs were domesticated in an independent pattern in the area of the middle and lower reaches of the Yellow River; however, ancient pig samples from the upper reaches of the Yellow River have never been tested. In this study, 14 unearthed ancient pig samples were collected from three archaeological sites in the upper and middle reaches of the Yellow River. Using DNA extraction, PCR amplification and DNA sequencing, these ancient samples were analyzed and compared with gene information from ancient pig samples from the middle and lower reaches of the Yellow River and from modern wild boars and domesticated pigs. We succeeded in generating a 179 bp sequence of mitochondrial D-loop from five ancient pig samples respectively, including three samples from the Qinglongquan archaeological site in Hubei Province and two samples from the Lajia archaeological site in Qinghai Province. Sequence alignment analysis indicated that ancient samples from Qinglongquan and Lajia were sorted into different haplotypes. Compared with previous data from ancient DNAs, modern pig breeds and wild boars, the two Qinglongquan samples shared one haplotype with one sample from the Jiahu site, and the Lajia samples shared a haplotype with four samples from the Gaohong archaeological site and with three samples from the Taosi archaeological site, which are both located in Shanxi Province. The two haplotypes were consistent with the four main types of modern Chinese pigs. The results indicate that pigs in the upper reaches of the Yellow River originated from the same domestic center as the pigs in the middle and lower reaches of the Yellow River did. These findings further our understanding of the origin of pig domestication in China.

The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig ( Sus scrofa ) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as “cryptic domestication,” given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East.