.2025 Aug 29;23(1):270.

doi: 10.1186/s12915-025-02343-3.

Genetic stability in the lower Yangtze River basin from Song to Qing Dynasty

Haifeng He^#¹, Xinyuan Kong^#², Le Tao^#³, Liangsai Zhu^#⁴, Xuanbo Wang⁵, Mengting Xu¹, Yuanming Chen⁴, Kongyang Zhu¹, Yu Xu¹, Haodong Chen³, Hao Ma¹, Rui Wang³, Xiaomin Yang⁶, Tianyou Bai¹, Jianxin Guo⁷, Yang Yang⁸, Xin Jia^{9 10}, Chuan-Chao Wang¹¹

Affiliations

¹ State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361005, China.
² School of Geography Science, Nanjing Normal University, Nanjing, 210023, China.
³ Ministry of Education Key Laboratory of Contemporary Anthropology, Center for Evolutionary Biology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China.
⁴ Lianyungang Institute of Cultural Relics Protection and Archaeology, Lianyungang, 222023, China.
⁵ Suqian Institute of Cultural Relics Protection and Archaeology, Suqian, 223821, China.
⁶ Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, Institute of Anthropology, Xiamen University, Xiamen, 361005, China.
⁷ State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
⁸ College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
⁹ School of Geography Science, Nanjing Normal University, Nanjing, 210023, China. jiaxin@njnu.edu.cn.
¹⁰ Institute of Environmental Archaeology, Nanjing Normal University, Nanjing, 210023, China. jiaxin@njnu.edu.cn.
¹¹ Ministry of Education Key Laboratory of Contemporary Anthropology, Center for Evolutionary Biology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China. chuanchaowang@fudan.edu.cn.

^# Contributed equally.

PMID:40877851
PMCID: PMC12395641
DOI: 10.1186/s12915-025-02343-3

Genetic stability in the lower Yangtze River basin from Song to Qing Dynasty

Haifeng He et al. BMC Biol.2025.

.2025 Aug 29;23(1):270.

doi: 10.1186/s12915-025-02343-3.

Authors

Affiliations

¹ State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361005, China.
² School of Geography Science, Nanjing Normal University, Nanjing, 210023, China.
³ Ministry of Education Key Laboratory of Contemporary Anthropology, Center for Evolutionary Biology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China.
⁴ Lianyungang Institute of Cultural Relics Protection and Archaeology, Lianyungang, 222023, China.
⁵ Suqian Institute of Cultural Relics Protection and Archaeology, Suqian, 223821, China.
⁶ Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, Institute of Anthropology, Xiamen University, Xiamen, 361005, China.
⁷ State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
⁸ College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
⁹ School of Geography Science, Nanjing Normal University, Nanjing, 210023, China. jiaxin@njnu.edu.cn.
¹⁰ Institute of Environmental Archaeology, Nanjing Normal University, Nanjing, 210023, China. jiaxin@njnu.edu.cn.
¹¹ Ministry of Education Key Laboratory of Contemporary Anthropology, Center for Evolutionary Biology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China. chuanchaowang@fudan.edu.cn.

^# Contributed equally.

PMID:40877851
PMCID: PMC12395641
DOI: 10.1186/s12915-025-02343-3

Abstract

Background: The lower Yangtze River basin holds a pivotal role in Chinese history. As previous genetic research in this region has primarily focused on modern population datasets, the limited availability of ancient human genomes has hindered our capacity to reconstruct detailed ancient population histories and evaluate the genetic impact of Yellow River-related groups. RESULTS: Here, we present the first set of ancient human genomes from the lower Yangtze River basin, comprising eight individuals from the Song to Qing Dynasties (960-1921 CE). We observed a high degree of genetic homogeneity in most samples, suggesting long-term regional genetic stability. Seven individuals were estimated to derive 69.3-100% of their ancestry from ancient Yellow River-related populations, while the remainder can be attributed to a southern East Asian substrate. Contemporary Han Chinese residing in the lower Yangtze basin can be modelled as direct genetic descendants of historical individuals from this area. Notably, one Qing Dynasty sample reveals a genetic link to the Eastern Mediterranean.

Conclusions: Our findings illustrate enduring genetic continuity in the lower Yangtze River basin throughout historical times. These findings underscore the region's role as a genetic bridge between northern and southern East Asia, retaining local rice-farming ancestry while being shaped by southward expansions of Yellow River-related ancestry.

Keywords: Historical Jiangsu; Population history; Rice farming-related ancestry; The lower Yangtze River basin.

PubMed Disclaimer

Conflict of interest statement

Declarations. Ethics approval and consent to participate: All procedures performed in studies involving human participants were approved by the local archaeological institutions and Xiamen University (XDYX202412K88) reviewed and approved the study. Consent for publication: Not applicable. Competing interests: The authors declare that they have no competing interests.

Figures

**Fig. 1**
Geographic location and principal components analysis of newly sampled individuals in this study. Each symbol stands for a population or individual inA andB, respectively.A Geographic location of newly sampled individuals and published ancient populations from East Asia used in this study. Made with Natural Earth. Free vector and raster map data @naturalearthdata.com.B Principal components analysis (PCA) of East Asian individuals. Ancient individuals (colored symbols) were projected onto the PCs calculated by modern East Asians (grey symbols)

**Fig. 2**
Genetic structure of ancient individuals in the lower Yangtze River basin.A Genetic homogeneity analysis using pairwiseqpWave; the number in cell stands for thep-value of Rank = 0qpWave modelling based on 1240 k datasets.B Unsupervised ADMIXTURE at K = 4. See also Additional file 6: Figure S3.C Outgroup-f₃ analysis to evaluate which population shared the most alleles with our newly sampled individuals. We plotted the top 10 populations from our study to provide visual context for our findings. See also Additional file 4: Table S2A

**Fig. 3**
Ancestry components modelled byqpAdm. Each color represents an ancient population used in the analysis. See also Additional file 7: Table S4A

**Fig. 4**
Relationships between modern East Asian and ancient individuals in the lower Yangtze River basin.A Geographic location of modern populations in this study. Each symbol stands for a population or individual inA andB, respectively.B PCA of East Asian individuals. Ancient individuals were projected onto the PCs, which were calculated by modern East Asians.C Outgroup-f₃ analysis to evaluate which modern East Asian population shared the most alleles with our newly sampled individuals. To provide visual context for our findings, we plotted the top 10 populations from our analysis. See also Additional file 4: Table S2B

See this image and copyright information in PMC

References

1. Zhang J, Jiang L, Yu L, Huan X, Zhou L, Wang C, et al. Rice’s trajectory from wild to domesticated in East Asia. Science. 2024;384(6698):901–6. - PubMed
1. Jia X, Zhao D, Storozum MJ, Shi H, Bai G, Liu Z. The “2.8 ka BP cold event” indirectly influenced the agricultural exploitation during the late Zhou Dynasty in the coastal areas of the Jianghuai Region. Front Plant Sci. 2022;13: 902534. - PMC - PubMed
1. He K, Lu H, Zhang J, Wang C, Huan X. Prehistoric evolution of the dualistic structure mixed rice and millet farming in China. The Holocene. 2017;27(12):1885–98.
1. Tang Y, Marston JM, Fang X. Early millet cultivation, subsistence diversity, and wild plant use at Neolithic Anle, Lower Yangtze. China. Holocene. 2022;32(10):1003–14.
1. Hayashi M. The iconography of gods and beasts: ancient Chinese deities [in Chinese]. Beijing: Sanlian Press; 2009. p. 259.

Publication types

Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

Substances

Actions

LinkOut - more resources

Full Text Sources
- BioMed Central
- PubMed Central
Research Materials
- NCI CPTC Antibody Characterization Program

Movatterモバイル変換

Account

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Full text links

Actions

Genetic stability in the lower Yangtze River basin from Song to Qing Dynasty

Affiliations

Genetic stability in the lower Yangtze River basin from Song to Qing Dynasty

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Substances

LinkOut - more resources

Full Text Sources

Research Materials