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. 2026 May 5;24(2):100704. doi: 10.1016/j.jgeb.2026.100704

Ancient DNA reveals pig domestication history in Northeastern China☆

Hualin Tao a,b,1, Mingmin Zheng a,b,1, Bo Xiao a,b, Shiwen Song a,b, Fancheng Xing c, Rong Guan d, Yan Zhu a,b, Shan Jiang a,b, Xulong Lai a,e, Junxia Yuan a,f,⁎, Guilian Sheng a,b,⁎
PMCID: PMC13157208  PMID: 42309607

Abstract

Pigs (Sus scrofa) were independently domesticated in the Near East and East Asia about 10,000 years ago. As one of the earliest livestock, their domestication process is closely intertwined with human activities. Previous studies have identified the Qinghai-Tibet Plateau, the Yellow River basin, and the middle-lower reaches of the Yangtze River as major domestication centers for indigenous Chinese pig breeds. However, whether Northeast China served as another independent center remains debated. To address this issue, we obtained ten near-complete mitochondrial genomes from pig teeth collected from Northeast China. Using phylogenetic analysis, we examined the maternal genetic relationships between these ancient individuals and other pig populations across different historical periods in China. Our results reveal the presence of an ancient, now-extinct lineage of domestic pigs in Northeast China, with no genetic links between ancient and modern pig populations in this region. These findings suggest that the available molecular data do not support Northeast China as an independent pig domestication center. Moreover, we demonstrate that the continuous and diverse human cultures in China significantly influenced the effective population size dynamics of domestic pigs over time.

Keywords: Sus scrofa, Ancient DNA, Mitochondrial genome, Northern China, Domestication, Human culture

1. Introduction

Pigs (Sus scrofa) have played a significant role in human history as an important livestock species. Previous studies integrating archaeological, isotopies, morphological and pathological evidence have confirmed that their initial domestication occurred about 9,000–10,000 years ago in the Near East and East Asia.1, 2, 3, 4, 5 Additional independent domestication events have also been proposed in several other regions, including Central Europe, Italy, India, Southeast Asia, and Oceania.3 In East Asia, China is widely regarded as one of the major centers of pig domestication. Genomic and zooarchaeological studies suggest that pigs were domesticated in multiple regions across China, particularly in the Yangtze River Basin in the south and the Yellow River Basin in the north.2, 5, 6, 7.These areas, which also cradled early Chinese civilizations, were pivotal to the development of agriculture.8 Other regions such as the Tibetan Plateau have also been proposed as potential sites of local domestication.9, 10, 11

Besides these regions, Manzhouli and the broader Northeast China have also been proposed as potential centers of pig domestication, from which domestic pigs may have subsequently expanded southward to Hebei and Henan.12, 13 In contrast, Wang et al. (2022) espoused that domestic pigs in this region were more likely introduced from the North China Plain.14 Zhang and Fu (2020) also support this viewpoint. Based on genetic analysis of ancient human populations, they suggested frequent interaction and possible population movements between Northeast China and the Yellow River Basin, it implies that introduction of domesticated pigs from other regions to Northeast China was a possibility.15 Therefore, it remains uncertain whether an independent domestication process took place in Northeast China.

In this study, we collected pig remains from Northeast China to explore their maternal genetic components and phylogenetic relationships with contemporary pigs from other regions of China. We aimed to elucidate the genetic domestication history of pigs in Northeast China through genetic evidence.

2. Material and methods

2.1. Sampling

We obtained 10 pig skeletal samples from Harbin and Suihua in Heilongjiang Province, and from New Barag East County in Inner Mongolia, Northeast China (Fig. 1). Detailed descriptions and photographs of the analyzed pig remains are provided in Table S1 and Fig. S1. One sample (CADG1024) was sent to the Beta Analytic Laboratory (Miami, USA) for accelerator mass spectrometry (AMS) radiocarbon dating, while the remaining samples were dated using molecular clock tip calibration. Additionally, to assess the domestication status of these samples, we conducted morphological identification based on mandibular third molar (M3) measurements, as this trait exhibits distinct and stable size differences between wild boars and domestic pigs and has been widely applied in zooarchaeological and domestication studies.16, 17, 18

Fig. 1.

Fig. 1

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Geographical locations of ancient Chinese pig individuals. Sampling locations in this study are represented by red triangles. The ancient Chinese pigs used in this study are represented by blue squares, with shades of color distinguishing different ages. The size of the square represents number of samples from one site. The map draft (chart no. GS (2016)2957) was downloaded from the National Administration of Surveying, Mapping and Geoinformation of China (http://bzdt.ch.mnr.gov.cn). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

2.2. Sample handling and DNA extraction

The whole experimental processes were carried out in dedicated ancient DNA laboratory facilities at China University of Geosciences (Wuhan, CUG). Instruments and consumables used in the process are sterilized and irradiated with UV light. First, we removed the surface layer of each sample to prevent potential contamination and subsequently selected the inter part of the samples and grounded each one to powder. Approximately 100–150 mg of powder for each sample was then mixed with extraction buffer consisting of 3 mL EDTA (0.5 M, pH = 8) and 0.04 mL Proteinase K (20 mg/mL) in a 15 mL centrifuge tube. After 16 h incubation in a rotating hybridization at 37 °C, the mixture was centrifuged at 7,000 rpm for 10 min and the supernatant was transferred into an ultrafiltration tube and concentrated to 150 µL by centrifugation at 7,000 rpm. The purification step was carried out by using MinElute PCR Purification Kit (Qiagen, Germany). Finally, 50 µL of DNA extract was obtained.

2.3. Library preparation and sequencing

Double-stranded libraries were constructed for the Illumina sequencing platform. A volume of 20 µL of DNA extract for each sample was used for subsequent library construction according to the protocol by Meyer and Kircher19. After blunt-end repairing, adapter ligation, and fill-in steps, indexing PCR amplifications were performed using Q5 High-Fidelity DNA Polymerase (New England Biolabs) and dual primers (P5 and P7 for Illumina sequencing platform). PCR amplification was performed under the following conditions: 120 s at 95 °C and 17 cycles of 15 s denaturation at 95 s, 30 s annealing at 60 °C and 30 s elongation at 68 °C. DNA concentration was measured by Qubit 4.0 (Invitrogen). Next-generation sequencing was conducted on Illumina NovaSeq6000 platform in Annoroad Gene Technology Co., Ltd, Beijing, China.

2.4. Sequence data processing and data sets

Sequencing raw reads were trimmed with fastp-0.22.0,20 and low-quality reads shorter than 30 bp were discarded. Reads were mapped against a Sus scrofa mitogenome (GenBank: NC_000845.1) using bwa-0.7.1521 with ‘aln’ algorithm and default options except for disabled seed. SAMtools-1.3.122 was used to sort mapped reads and remove duplicates with options ‘sort’ and ‘rmdup’. The final mitochondrial consensus sequence was produced using ‘-doFasta 2′ in ANGSD-0.938,23 setting a minimum base depth of 2 (−setMinDepthInd 2) to avoid DNA damage and sequencing errors. Reads coverage across the reference was calculated using Qualimap-2.2.1.24 MapDamage2.025 was used to analyze the damage pattern in the fragments.

We downloaded all available complete mitogenome sequences of Suidae from three currently recognized centers of pig domestication in China from GenBank (Table S2), including a total number of 90 sequences, among which 5 are wild boars, 84 are domestic pigs that contains 29 ancient individuals, and one Sus verrucosus used as outgroup. All ancient individuals are from the Yellow River Basin since there are no available complete mitochondrial sequences of ancient pigs from either the Yangtze River Basin or the Tibet Plateau. We classified these individuals into nine groups based on their original geographic region, status (wild or domestic). Ten newly obtained mitochondrial genomes were aligned with sequences above by using MAFFT online with ClustalW algorithm in the EMBL-EBI (https://www.ebi.ac.uk). Finally, besides our ten newly obtained sequences, a data set of wild and domestic pigs homologous sequences with a length of 11,958 bp were obtained using Gblock-0.91b26 with default parameters for subsequent analyses. We used this data set to perform a detailed phylogenetic analysis using divergence time information, and to explore the possible connection between ancient pigs from Northeast China and their counterparts from other three centers. We randomly chose 8 modern S. scrofa sequences from Europe, 5 modern S. scrofa sequences from China, and kept 29 ancient domestic pig sequences with no more than 20% sequencing gaps as a dataset for molecular dating (Table S3).

2.5. Phylogenetic analysis

To explore the phylogenetic relationships between pig remains from Northeast China and the three pig domestication centers, we constructed a time-calibrated phylogenetic tree using BEAST v1.10.4. The best evolutionary model ‘HKY + I + G’ was chosen for BEAST analysis using jModelTest 2 under the Bayesian Inference Criterion. A strict molecular clock and constant population size were employed, with the divergence time between Sus verrucosus and S. scrofa set to 2.575 million years ago (Ma).27 The Markov chain Monte Carlo (MCMC) was run for 80 million generations, sampling every 1,000 generations. The above calculations were performed on CIPRES portal (https://www.phylo.org). The effective sample size (ESS) of values was ensured to be greater than 200. The phylogenetic tree was visualized in FigTree (v1.4.0), where 20% of the trees were discarded due to burn-in. Meanwhile, we performed maximum-likelihood (ML) phylogenetic analysis with IQ-TREE2.28 ML tree was generated using “iqtree −s example.phy −m MFP −st CODON”. Moreover, we performed Bayesian skyline plots (BSPs) with the same data set except the outgroup to construct the maternal demographic history of Chinese pigs by performing using BEAST v1.10.4. We set a clock rate of 1.2612 × 10⁻7 substitutions/site/year and used the HKY + I + G evolutionary model. Other parameters were set as described above. The BSPs were visualized using Tracer v1.6.

To molecularly estimate our specimens, we used root and tip-dating methods to calibrate the Bayesian tree based on the selected data set. We determined the most suitable model by jModelTest 2 and molecularly dated the samples with Beast1.10.4. All S. scrofa specimens with definite ages were used as tip-date calibrating to estimate the median age of our specimens. We set a clock rate of 1.2612 × 10-7 substitutions/site/year and evolutionary model of ‘HKY + I + G’. We ran a total of 10 million MCMC chains, sampling every 1000 steps. We randomly selected an ancient sequence with known dating information to be placed in Taxa of the year to be determined. The above parameter setting was considered reliable if the final obtained molecular age was nearly the same as the known age. Our sample sequences were then added one by one for molecular dating sequentially under these parameters.

3. Results

3.1. Data overview and molecular dating

Shotgun sequencing of individual libraries yielded 3.7–8.8 Mb raw reads. From these, we obtained 787–19,399 unique reads across ten S. scrofa specimens. Ten mitochondrial sequences were successfully generated, ranging in lengths from 7,359 to 16,595 bp, with mean coverage varying between 3-fold and 102-fold. Specific sequence information for each sample is provided in Table S4.

Molecular dating placed the samples from around 4,000 years ago to near-modern times (Table 1). These time frames correspond to historical periods spanning the Middle-Late Neolithic through the Northern and Southern Dynasties, to the late Tang–Five Dynasties period and near-modern, which were characterized by large-scale human migrations. The M3 measurement results are shown in Table S5. The mandibular third molars of CADG1013, CADG1018, and CADG1200 had not yet erupted and can thus be considered most likely domestic pigs, as domestic pigs are typically slaughtered at 1-2 years of age or earlier 10. In contrast, CADG1226, CADG692, CADG695, and CADG721 are represented by single isolated teeth and cannot be reliably identified. Furthermore, the length distribution of the M3 from domestic pigs at northern Chinese cultural sites and in our samples indicated that the tooth sizes generally fell within the typical range observed for domestic pigs (Fig. S2).

Table 1.

Molecular dating of ten DNA containing samples.

Laboratory No. Molecular age and confidence interval
CADG692 2,987 (1,784–3,791) cal BP
CADG695 2,658 (3,477–1,263) cal BP
CADG721 214 (35–339) cal BP
CADG1012 3,876 (2,006–6,493) cal BP
CADG1013 4,150 (2,861–6,653) cal BP
CADG1018 1,096 (83–1,719) cal BP
CADG1022 1,669 (861–3,461) cal BP
CADG1024* 31 (28–89) cal BP
CADG1200 1,507 (874–2,687) cal BP
CADG1226 3,047 (2,569–5,588) cal BP
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Sample marked with an asterisk (*) were analyzed for AMS radiocarbon dating.

Damage patterns and cytosine deamination frequencies vary with sample age (Table 1). Older specimens (CADG1012, CADG1013, CADG1226, CADG692, CADG695) exhibited short DNA fragments (35-70 bp; Fig. S3) and pronounced C to T misincorporation at read ends (Fig. S4), consistent with typical ancient DNA damage pattern. In contrast, more recent samples (CADG1018, CADG1022, CADG1024, CADG1200, CADG721) showed minimal misincorporation, suggesting they might be classified as historical or near-modern.

3.2. Phylogeny of S. Scrofa in Northeast China

The mitochondrial MCC tree (Fig. 2) and ML tree (Fig. S5) yielded consistent topologies, indicating that domestic and wild pigs from China do not form distinct clades, which is consistent with previous studies 5, 29. Moreover, no obvious phylogeographic pattern was observed. Regarding the phylogenetic relationship between the Northeast Chinese pig remains and their counterparts from three major domestication centers in China, we find that: three individuals (CADG695, CADG692 and CADG721) form an independent, relatively basal clade; three others (CADG1013, CADG1226 and CADG1012) settle in a clade predominantly composed of ancient pigs from the Yellow River basin, with CADG1013 joining together with an individual dated to 5,000–4,500 BP, while CADG1226 and CADG1012 clustering with several pigs dated to 7,000–5,500 BP; CADG1018 and CADG1024 fall within a clade consisting exclusively of modern pigs from either the Yangtze or from the Yellow River Basin; CADG1200 and CADG1022 form a separate sub-clade sister to ancient Yellow River pigs dated between 7,000–3,900 BP.

Fig. 2.

Fig. 2

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Maximum clade credibility (MCC) tree of Sus scrofa based on 11,958 bp mitogenome sequences, with S. verrucous as the outgroup. Different colors represent geographic origins: solid-colored circles represent modern domestic pigs, slash-colored circles denote modern wild boars, blue squares indicate ancient individuals from the Yellow River basin, and red triangles mark the ancient samples analyzed in this study. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

3.3. Temporal dynamics of maternal effective population size

The Bayesian skyline plot shows the maternal effective population size dynamics of Chinese domestic pigs and wild boars over the past 50,000 years (Fig. 3). The population maintained relatively stable until around 12 Ka, then experienced a slight decline, reaching its lowest point around 9 Ka. A rapid increase occurred from 8 to 3 Ka, followed by a slowdown in growth over the last 3,000 years.

Fig. 3.

Fig. 3

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Bayesian skyline plot based on 11,958 bp homologous mitogenome sequences of S. scrofa individuals. The x axis shows years before present; the y axis stands for the estimated effective female population size (Ne). Black line represents median value, and blue area is the 95% HPD limits. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

4. Discussion

4.1. An extinct maternal lineage of domestic pigs in Northeast China

In this study, three ancient individuals (CADG721, CADG695 and CADG692) from Northeast China form a distinct and relatively early-diverging clade that does not include any known modern domestic pigs. This suggests the presence of an ancient maternal lineage unique to this region that has since gone extinct. Such extinct genetic clades are not uncommon in domesticated animals. For example, certain ancient horse genealogies in Western Europe did not persist into modern times 30; and both European taurine cattle (Bos taurus) and Indian zebu cattle (B. indicus) have experienced genetic loss during domestication 31, 32. The disappearance of pig lineages may be attributed to genetic drift, selective breeding by humans, or adaptations to shift in agricultural systems, environmental pressures, or cultural practices such as warfare, farming intensity, and animal management strategies.

4.2. Genetic connections between pig populations from Northeast and the other regions in China

Previous studies have identified three major pig domestic centers in China. At the approximately 8000-year-old Cishan site in the Yellow River Basin, domestic pig bones accounted for a substantial proportion of the 48 types of animal remains uncovered.1 Over 60% of the pigs were slaughtered between 0.5 and 1 year of age, and their average mandibular third molars (M3) length was close to 40 mm—consistent with dimensions typical of domestic pigs.1 Additionally, evidence from sites such as Jiangzhai in Shaanxi and Erlitou in Henan indicates a gradual reduction in pig body size from the early to late Neolithic 33. More recently, Han et al.5 analyzed 21 ancient pig nuclear genomes from 14 archaeological sites across China, dating to approximately 8,000–800 years BP. Their results support northern China as an independent center of pig domestication and do not support southwestern China as a domestication origin for modern East Asian pigs, while also revealing a close association between domestic pigs and millet-based agricultural communities. These archaeological findings support the view that the middle-lower reaches of the Yellow River Basin was one of the earliest regions for pig domestication, coinciding with the rise of agricultural civilization in this region 1, 5, 34.

In the Lower Yangtze River Basin, analyses of starch grains, phytoliths, and parasite remains from pig dental calculus suggest a mixed management pattern involving both domesticated and wild pigs around 8,000 years ago.35 Meanwhile, Yang et al. proposed the Tibetan highlands as another potential center of pig domestication.36

Based on a combined dataset of 239 bp cytb and control region sequences, Xiang et al. suggested an independent domestication event in Northeast China, supporting in situ origin of local pigs from 8,000 to 3,500 years ago, followed by genetic replacement after that period 12. In our study, however, the ten pig individuals from Northeast China did not form a monophyletic clade in the phylogenetic tree that constructed on mitochondrial genome dataset with > 60% coverage (Fig. 2). Three individuals older than 3,500 years (CADG1226, CADG1012 and CADG1013) cluster within a clade mainly composed of ancient domestic pigs from the Yellow River Basin. This finding contradicts the hypothesis of in situ domestication in Northeast China prior to 3,500 BP. Nevertheless, our phylogeny supports a lack of genetic continuity between pig populations in Northeast China before and after 3,500 BP, consistent with Xiang et al.’s proposal of a genetic replacement around that time 37.

Notably, among the three recognized domestication centers, only the Yellow River Basin has yielded ancient individuals with complete mitochondrial genomes available. In this study, five out of ten individuals show genetic connections to ancient pigs from this center, while relationships with pigs from the other two centers remain unsolved due to limited ancient genomic data.

4.3. Impacts of human activities on pig dispersal and population dynamics

The demographic history of domestic pigs in China reflects not only the process of domestication but also the broad influence of human migration and subsistence transitions. Our Bayesian skyline plot indicates a rapid increase in the effective population size of domestic pigs from 8,000 to 3,000 BP, followed by slower growth over the last 3,000 years. This trend is consistent with findings by Zhang et al., who examined pig population dynamics in the Yellow River Basin between 7000 and 4000 BP.7 This pattern aligns with the north China pig domestication origin, their dispersal with agricultural populations, and intensified management practices, mirroring the interplay between pig demography and human-agricultural history in East Asian.5 Similar short-time demographic expansions have also been observed in other East Asian domesticates, such as Chinese goats and dogs.38, 39

We propose that the rapid growth and subsequent stabilization of domestic pigs and other livestock populations reflect not only advances in agricultural technology and farmland expansion, but also a continuity and interaction of ancient human cultures in China, from the Middle-Late Neolithic through the Northern and Southern Dynasties, to the late Tang–Five Dynasties period. During the Middle-Late Neolithic, the Dawenkou Culture maintained connections with the Yangshao and Hongshan Cultures via corridors spanning the Yellow River Basin, the Haidai region, and the Liao River Basin, as evidenced by shared ceramic techniques and jade exchanges.40, 41 By the Northern and Southern Dynasties, large-scale migrations, including the Sinicization of the Xianbei, further promoted cultural and genetic integration across Northern China.42 During the late Tang and Five Dynasties, warfare in the Central Plains prompted many northern Han families to migrate into Khitan-controlled territories, while others were forcibly relocated to the Northeast.43, 44 These cultural continuities and large-scale population movements likely facilitated genetic exchange among pig populations in ancient China.

5. Conclusions

In this study, we analyzed the genetic relationships between pig remains from Northeast China and those from other regions and explored the changes in the maternal effective population size of Chinese domestic pigs over time. Our results reveal an extinct maternal lineage of domestic pigs in Northeast China. We conclude that current molecular evidence does not support the existence of an independent domestication center in this region. Instead, most domestic pigs in Northeast China likely originated from the expansion of domestic lineages from the Yellow River Basin. Furthermore, we demonstrate a correlation between the continuity of human culture in China from around 8000 to 3000 years ago and the demographic dynamics of domestic pigs.

CRediT authorship contribution statement

Hualin Tao: Writing – review & editing, Writing – original draft, Validation, Investigation, Formal analysis, Data curation, Conceptualization. Mingmin Zheng: Writing – review & editing, Visualization, Investigation, Formal analysis, Data curation, Conceptualization. Bo Xiao: Software, Methodology, Investigation. Shiwen Song: Resources, Investigation. Fancheng Xing: Resources. Rong Guan: Resources. Yan Zhu: Investigation. Shan Jiang: Investigation. Xulong Lai: Writing – review & editing, Supervision. Junxia Yuan: Resources, Project administration, Methodology, Funding acquisition. Guilian Sheng: Writing – review & editing, Writing – original draft, Validation, Supervision, Resources, Methodology, Funding acquisition, Conceptualization.

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgements

We would like to express our gratitude to Guoqing Peng for his assistance with sample collection.

Formatting of funding sources

This research was funded by the National Natural Science Foundation of China (Nos. 42572005, 42472008) and the Local Government Service Program (No. 2021046702).

Footnotes

☆

This article is part of a special issue entitled: ‘Ancient DNA’ published in Journal of Genetic Engineering and Biotechnology.

Appendix A

Supplementary data to this article can be found online at https://doi.org/10.1016/j.jgeb.2026.100704.

Contributor Information

Junxia Yuan, Email: yuanjx@cug.edu.cn.

Guilian Sheng, Email: glsheng@cug.edu.cn.

Appendix A. Supplementary data

The following are the Supplementary data to this article:

Supplementary Data 1
mmc1.docx (1.8MB, docx)

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