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Life history of the Yangzi Estuary II shipwreck: environmental DNA from sediment in a 150-year-old amphora
Published online by Cambridge University Press: 11 February 2026
Abstract
Shipwrecks provide invaluable insights into human society and trade. Their unique preservation conditions also mean that they can serve as exceptional biobanks, recording traces of organisms carried aboard or arriving post wreck. Yet only limited research has explored the genetic potential of onboard sediments. Here, the authors present environmental and metagenomic analyses of sediments contained in a large amphora from the 150-year-old Yangzi Estuary II shipwreck. Weaving the results with historic texts, they reconstruct part of the history of the wrecked vessel, elucidating cargo-packing techniques, its likely season and port of sailing, and its ultimate submersion within the estuarine environment.
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- © The Author(s), 2026. Published by Cambridge University Press on behalf of Antiquity Publications Ltd
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These authors contributed equally to this work
References
Adams, J. 2001. Ships and boats as archaeological source material. World Archaeology 32: 292–310. https://doi.org/10.1080/00438240120048644
CrossRefGoogle Scholar
Allevato, E., Saracino, A., Fici, S. & Di Pasquale, G.. 2016. The contribution of archaeological plant remains in tracing the cultural history of Mediterranean trees: the example of the Roman harbour of Neapolis. The Holocene 26: 603–13. https://doi.org/10.1177/0959683615612567
CrossRefGoogle Scholar
Bass, G.F. & van Doorninck, F.H.. 1982. Yassi Ada, volume 1: a seventh-century Byzantine shipwreck. College Station: Texas A&M University Press.Google Scholar
Briggs, L. 2020. Ancient DNA research in maritime and underwater archaeology: pitfalls, promise, and future directions. Open Quaternary 6. https://doi.org/10.5334/oq.71
CrossRefGoogle Scholar
Cadet, J. & Wagner, J.R.. 2013. DNA base damage by reactive oxygen species, oxidizing agents, and UV radiation. Cold Spring Harbor Perspectives in Biology 5. https://doi.org/10.1101/cshperspect.a012559
CrossRefGoogle ScholarPubMed
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. & Madden, T.L.. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10. https://doi.org/10.1186/1471-2105-10-421
CrossRefGoogle ScholarPubMed
Carlson, D.N. 2004. Cargo in context: the morphology, stamping, and origins of the amphoras from a fifth-century B.C. Ionian shipwreck. Unpublished PhD dissertation, University of Texas at Austin.Google Scholar
Cline, E.H. 2021. 1177 BC: the year civilization collapsed: revised and updated. Princeton (NJ): Princeton University Press.Google Scholar
Coddington, J.A., Giribet, G., Harvey, M.S., Prendini, L. & Walter, D.E.. 2004. Arachnida, in Cracraft, J. & Donoghue, M.J. (ed.) Assembling the tree of life: 296–318. Oxford: Oxford University Press.10.1093/oso/9780195172348.003.0019CrossRefGoogle Scholar
Couillebault, Q., Kaniewski, D., Domínguez, A.F., Otto, T., Luce, F. & Boetto, G.. 2023. Bioarchaeology of ancient Adriatic ships: the Pula shipwrecks (Croatia). Journal of Archaeological Science: Reports 51. https://doi.org/10.1016/j.jasrep.2023.104197
Google Scholar
De Flamingh, A. et al. 2021. Sourcing elephant ivory from a sixteenth-century Portuguese shipwreck. Current Biology 31: 621–28. https://doi.org/10.1016/j.cub.2020.10.086
CrossRefGoogle ScholarPubMed
Dunlop, J.A. & Selden, P.A.. 1998. The early history and phylogeny of the chelicerates, in Fortey, R.A. & Thomas, R.H. (ed.) Arthropod relationships: 221–35. Dordrecht: Springer. https://doi.org/10.1007/978-94-011-4904-4_17
CrossRefGoogle Scholar
Dunlop, J.A. & Webster, M.. 1999. Fossil evidence, terrestrialization and arachnid phylogeny. Journal of Arachnology 27: 86–93.Google Scholar
Goodbred, S.L. Jr & Saito, Y.. 2011. Tide-dominated deltas. In Davis, R. , Jr & Dalrymple, R. (ed.) Principles of tidal sedimentology: 129–49. Dordrecht: Springer. https://doi.org/10.1007/978-94-007-0123-6_7
Google Scholar
Green, J. 1983. The Song Dynasty shipwreck at Quanzhou, Fujian Province, People’s Republic of China. International Journal of Nautical Archaeology and Underwater Exploration 12(3): 253–61. https://doi.org/10.1111/j.1095-9270.1983.tb00140.x
CrossRefGoogle Scholar
Guo, Y. et al. 2018. Mosquito population dynamics during the construction of Three Gorges Dam in Yangtze River, China. Acta Tropica 182: 251–56. https://doi.org/10.1016/j.actatropica.2018.03.008
CrossRefGoogle ScholarPubMed
Gutaker, R.M. et al. 2020. Genomic history and ecology of the geographic spread of rice. Nature Plants 6: 492–502. https://doi.org/10.1038/s41477-020-0659-6
CrossRefGoogle ScholarPubMed
Hamilton, D.L. 1996. Basic methods of conserving underwater archaeological material culture. Washington, D.C.: US Department of Defense, Legacy Resource Management Program.Google Scholar
Hao, X.L., Zhu, T.Q., Xu, J.J., Wang, Y.R. & Zhang, X.W.. 2018. Microscopic study on the concretion of ceramics in the “Nanhai I” shipwreck of China, Southern Song Dynasty (1,127–1,279 AD). Microscopy Research and Technique 81: 486–93. https://doi.org/10.1002/jemt.23002
CrossRefGoogle Scholar
Katoh, K., Misawa, K., Kuma, K.I. & Miyata, T.. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30: 3059–66. https://doi.org/10.1093/nar/gkf436
CrossRefGoogle ScholarPubMed
Kim, M. & Moon, W.S.. 2011. Tracking 800-year-old shipments: an archaeological investigation of the Mado Shipwreck cargo, Taean, Korea. Journal of Maritime Archaeology 6: 129–49. https://doi.org/10.1007/s11457-011-9082-5
CrossRefGoogle Scholar
Kjær, K.H. et al. 2022. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 612: 283–91. https://doi.org/10.1038/s41586-022-05453-y
CrossRefGoogle ScholarPubMed
Korneliussen, T.S., Albrechtsen, A. & Nielsen, R.. 2014. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics 15. https://doi.org/10.1186/s12859-014-0356-4
CrossRefGoogle ScholarPubMed
Law, J. 1984. On the methods of long-distance control: vessels, navigation and the Portuguese route to India. The Sociological Review 32(S1): 234–63. https://doi.org/10.1111/j.1467-954X.1984.tb00114.x
CrossRefGoogle Scholar
Li, D., Liu, C.M., Luo, R., Sadakane, K. & Lam, T.W.. 2015. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31: 1674–76. https://doi.org/10.1093/bioinformatics/btv033
CrossRefGoogle ScholarPubMed
Li, J.Y., Wang, J. & Zeigler, R.S.. 2014. The 3,000 rice genomes project: new opportunities and challenges for future rice research. Gigascience 3. https://doi.org/10.1186/2047-217X-3-8
CrossRefGoogle ScholarPubMed
Ma, D., Chen, D., Li, N., Chen, Y., Du, J. & Luo, W.. 2022. Archaeometallurgical research on the bronze coins of Song Dynasty (960–1279AD) from Nanhai No. I shipwreck, the south China sea. Journal of Archaeological Science: Reports 45. https://doi.org/10.1016/j.jasrep.2022.103581
Google Scholar
Mallefet, J. et al. 2008. Belgian shipwreck: hotspots for marine biodiversity (BEWREMABI): final report. Brussels: Belgian Science Policy.Google Scholar
Massilani, D. et al. 2020. Denisovan ancestry and population history of early East Asians. Science 370: 579–83. https://doi.org/10.1126/science.abc1166
CrossRefGoogle ScholarPubMed
McLaren, C.G., Bruskiewich, R.M., Portugal, A.M. & Cosico, A.B.. 2005. The International Rice Information System. A platform for meta-analysis of rice crop data. Plant Physiology 139: 637–42. https://doi.org/10.1104/pp.105.063438
CrossRefGoogle ScholarPubMed
Meyer, M. & Kircher, M.. 2010. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor Protocols 2010(6). https://doi.org/10.1101/pdb.prot5448
CrossRefGoogle ScholarPubMed
Niu, W., Zhao, L., Switzer, A.D., Zhai, Y., Zhang, W. & Wang, Z.. 2021. Sedimentary evidence for a period of rapid environmental change in the Yangtze River Delta, China around 150 years ago. Continental Shelf Research 229. https://doi.org/10.1016/j.csr.2021.104552
CrossRefGoogle Scholar
Pearsall, D. 2018. Case studies in paleoethnobotany: understanding ancient lifeways through the study of phytoliths, starch, macroremains, and pollen. London: Routledge.10.4324/9781351009683CrossRefGoogle Scholar
Pirazzoli-t’Serstevens, M. 2011. The Brunei shipwreck: a witness to the international trade in the China Sea around 1500. The Silk Road 9: 5–17.Google Scholar
Poinar, H.N. et al. 2006. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311: 392–94. https://doi.org/10.1126/science.1123360
CrossRefGoogle ScholarPubMed
Powell, W. et al. 2022. Tin from Uluburun shipwreck shows small-scale commodity exchange fueled continental tin supply across Late Bronze Age Eurasia. Science Advances 8. https://doi.org/10.1126/sciadv.abq3766
CrossRefGoogle ScholarPubMed
Pulak, C. 1988. The Bronze Age shipwreck at Ulu Burun, Turkey: 1985 campaign. American Journal of Archaeology 92: 1–37. https://doi.org/10.2307/505868
CrossRefGoogle Scholar
Pulak, C. 1998. The Uluburun shipwreck: an overview. The International Journal of Nautical Archaeology 27: 188–224. https://doi.org/10.1111/j.1095-9270.1998.tb00803.x
CrossRefGoogle Scholar
R Core Team. 2021. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available at: https://www.R-project.org/
Google Scholar
Schubert, M., Lindgreen, S. & Orlando, L.. 2016. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes 9. https://doi.org/10.1186/s13104-016-1900-2
CrossRefGoogle ScholarPubMed
Selden, P.A., Dunlop, J.A. & Edgecombe, G.D.. 1998. Fossil taxa and relationships of chelicerates, in Edgecombe, G. (ed.) Arthropod fossils and phylogeny: 303–31. New York: Columbia University Press.Google Scholar
Stuiver, M., Reimer, P. & Reimer, R.. 2021. CALIB radiocarbon calibration 8.2 [software]. Available at: http://calib.org
Google Scholar
Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S.. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30: 2725–29. https://doi.org/10.1093/molbev/mst197
CrossRefGoogle ScholarPubMed
Thomsen, P.F. & Willerslev, E.. 2015. Environmental DNA – an emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation 183: 4–18. https://doi.org/10.1016/j.biocon.2014.11.019
CrossRefGoogle Scholar
Wang, A., Wang, Z., Liu, J., Xu, N. & Li, H.. 2021. The Sr/Ba ratio response to salinity in clastic sediments of the Yangtze River Delta. Chemical Geology 559. https://doi.org/10.1016/j.chemgeo.2020.119923
CrossRefGoogle Scholar
Wang, Y. et al. 2021. Late Quaternary dynamics of Arctic biota from ancient environmental genomics. Nature 600: 86–92. https://doi.org/10.1038/s41586-021-04016-x
CrossRefGoogle ScholarPubMed
Willerslev, E. et al. 2003. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300: 791–95. https://doi.org/10.1126/science.1084114
CrossRefGoogle ScholarPubMed
Zhu, K. et al. 2022. Cultural and demic co-diffusion of Tubo Empire on Tibetan Plateau. iScience 25. https://doi.org/10.1016/j.isci.2022.105636
CrossRefGoogle ScholarPubMed
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