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Journal of Sistan and Baluchistan Studies

Journal of Sistan and Baluchistan Studies

TRACING THE ROOTS OF PLANT DISEASES: ARCHAEOLOGY, PLANT PALEOPATHOLOGY, AND THE HISTORY OF PLANT-PATHOGEN INTERACTIONS

Document Type : Review Article

Author
Department of Plant Pathology, University of Zabol, Zabol, Iran
Abstract
The study of plant diseases in archaeological contexts, known as plant paleopathology, offers critical insights into the historical interactions between plants, pathogens, and human societies. Plant diseases have significantly influenced agricultural practices, economic systems, and even the fate of civilizations, as seen in the Irish Potato Famine (caused by Phytophthora infestans) and the rust epidemics that impacted the Roman Empire. By analyzing archaeological plant remains, researchers reconstruct the history of plant pathogens, assess their societal impacts, and derive lessons for modern agriculture. This review explores the methods used to detect plant pathogens in ancient materials, including morphological analysis, ancient DNA (aDNA) sequencing, proteomics, spectroscopy, immunological assays, stable isotope analysis, and paleohistology. These techniques have enabled the identification of pathogens such as Claviceps purpurea (ergot), Puccinia graminis (wheat rust), and Phylloxera vitifoliae (grapevine pest), revealing their evolutionary and ecological histories. Case studies, such as the Irish Potato Famine and the 19th-century coffee rust epidemic in Ceylon, demonstrate how plant diseases have driven agricultural transformations, scientific advancements, and policy changes. The integration of archaeological evidence with modern biomolecular techniques provides a multidisciplinary framework for understanding long-term plant-pathogen dynamics. Future research should leverage advances in high-throughput sequencing, proteomics, and computational modeling to further explore ancient disease outbreaks, pathogen evolution, and human adaptation strategies. By bridging archaeology and plant pathology, this field enhances our ability to address contemporary challenges in food security, crop resilience, and sustainable agriculture.
Keywords

چکیده: مطالعه بیماری‌های گیاهی در زمینه‌های باستان‌شناسی، که به عنوان دیرین‌آسیب‌شناسی گیاهی شناخته می‌شود، بینش‌های مهمی در مورد تعاملات تاریخی بین گیاهان، عوامل بیماری‌زا و جوامع انسانی ارائه می‌دهد. بیماری‌های گیاهی تأثیر قابل توجهی بر شیوه‌های کشاورزی، سیستم‌های اقتصادی و حتی سرنوشت تمدن‌ها داشته‌اند، همان‌طور که در قحطی سیب‌زمینی ایرلند (ناشی از Phytophthora infestans) و همه‌گیری زنگ‌ها که امپراتوری روم را تحت تأثیر قرار داد، مشاهده می‌شود. با تجزیه و تحلیل بقایای گیاهی باستان‌شناسی، محققان تاریخچه عوامل بیماری‌زای گیاهی را بازسازی می‌کنند، تأثیرات اجتماعی آن‌ها را ارزیابی می‌کنند و درس‌هایی برای کشاورزی مدرن استخراج می‌کنند. این مرور به بررسی روش‌های مورد استفاده برای تشخیص عوامل بیماری‌زای گیاهی در مواد باستانی می‌پردازد، از جمله تحلیل ریخت‌شناسی، توالی‌یابی DNA باستانی (aDNA)، پروتئومیک‌ها، طیف‌سنجی، آزمون‌های ایمونولوژیکی، تحلیل ایزوتوپ‌های پایدار و دیرین‌بافت‌شناسی. این تکنیک‌ها شناسایی عوامل بیماری‌زایی مانند Claviceps purpurea (ارگوت)، Puccinia graminis (زنگ گندم) و Phylloxera vitifoliae (آفت مو) را ممکن ساخته و تاریخچه تکاملی و اکولوژیکی آن‌ها را آشکار کرده‌اند. مطالعات موردی، مانند قحطی سیب‌زمینی ایرلند و همه‌گیری زنگ قهوه در سیلان در قرن نوزدهم، نشان می‌دهند که چگونه بیماری‌های گیاهی منجر به دگرگونی‌های کشاورزی، پیشرفت‌های علمی و تغییرات سیاستی شده‌اند. ادغام شواهد باستان‌شناسی با تکنیک‌های زیست‌مولکولی مدرن، چارچوبی چندرشته‌ای برای درک پویایی‌های بلندمدت گیاه ـ عامل بیماری‌زا فراهم می‌کند. تحقیقات آینده باید از پیشرفت‌ها در توالی‌یابی با توان بالا، پروتئومیک‌ها و مدل‌سازی محاسباتی بهره ببرد تا به بررسی بیشتر شیوع بیماری‌های باستانی، تکامل عوامل بیماری‌زا و راهبردهای انطباق انسانی بپردازد. با پیوند باستان‌شناسی و آسیب‌شناسی گیاهی، این حوزه توانایی ما را برای مقابله با چالش‌های معاصر در امنیت غذایی، مقاومت محصولات و کشاورزی پایدار افزایش می‌دهد.

کلیدواژه: دیرین‌آسیب‌شناسی گیاهی، DNA باستانی، باستان‌گیاه‌شناسی، بیماری‌های محصولات کشاورزی، تکامل عوامل بیماری‌زا، تاریخ کشاورزی.

Aebersold, R., & Mann, M. (2003). Mass spectrometry-based proteomics. Nature, 422(6928), 198–207.
Aebersold, R., & Mann, M. (2016). Mass-spectrometric exploration of proteome structure and function. Nature, 537(7620), 347–355.
Agrios, G. N. (2005). Plant Pathology (5th ed.). Academic Press, pp. 637–670.
Almeida, R. P. P., & Nunney, L. (2015). How do plant diseases caused by Xylella fastidiosa emerge? Plant Disease, 99(11), 1457-1467.
Allentoft, M. E., et al. (2012). The half-life of DNA in bone: Measuring decay kinetics in 158 dated fossils. Proceedings of the Royal Society B: Biological Sciences, 279(1748), 4724-4733.
Araus, J. L., Ferrio, J. P., Voltas, J., Aguilera, M., & Buxó, R. (2014). Agronomic conditions and crop evolution in ancient Near East agriculture. Nature Communications, 5, 3953.
Avelino, J., et al. (2015). The coffee rust crises in Colombia and Central America (2008–2013): Impacts, causes, and challenges. Phytopathology, 105(7), 948–960.
Bos, K. I., et al. (2011). A draft genome of Yersinia pestis from victims of the Black Death. Nature, 478(7370), 506-510.
Bourke, P. M. A. (1993). The Irish potato famine: Causes and effects. Cambridge University Press, pp. 72–130.
Briggs, A. W., et al. (2007). Patterns of damage in genomic DNA sequences from a Neandertal. Proceedings of the National Academy of Sciences, 104(37), 14616-14621.
Cappellini, E., et al. (2014). Proteomic analysis of ancient plant remains. Proceedings of the National Academy of Sciences, 111(37), 13257-13262.
Cappellini, E., et al. (2018). Biomolecular archaeology of ancient prokaryotes and eukaryotes. Nature Ecology & Evolution, 2(5), 791-796.
Cappers, R. T. J., & Neef, R. (2012). Handbook of Plant Palaeoecology. Barkhuis Publishing.
Carefoot, G. L., & Sprott, E. R. (1967). Famine on the Wind: Man's Battle Against Plant Disease. Rand McNally.
Cooper, A., & Poinar, H. N. (2000). Ancient DNA: Do it right or not at all. Science, 289(5482), 1139.
Dawson, T. E., Mambelli, S., Plamboeck, A. H., Templer, P. H., & Tu, K. P. (2002). Stable isotopes in plant ecology. Annual Review of Ecology and Systematics, 33(1), 507-559.
Der Sarkissian, C., et al. (2015). Ancient genomics. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1660), 20130387.
Derrick, M. R., Stulik, D., & Landry, J. M. (1999). Infrared Spectroscopy in Conservation Science. Getty Publications.
Edwards, H. G. M., & Vandenabeele, P. (2012). Analytical archaeometry: Selected topics. Royal Society of Chemistry.
Evershed, R. P., et al. (2001). Archaeometry, 43(4), 461-482.
Farquhar, G. D., Ehleringer, J. R., & Hubick, K. T. (1989). Carbon isotope discrimination and photosynthesis. Annual Review of Plant Physiology and Plant Molecular Biology, 40(1), 503-537.
Ferrio, J. P., Araus, J. L., Buxó, R., Voltas, J., & Bort, J. (2005). Water management practices and climate in ancient agriculture: Inferences from the stable isotope composition of archaeobotanical remains. Vegetation History and Archaeobotany, 14(4), 510-517.
Ficetola, G. F., et al. (2008). Species detection using environmental DNA from water samples. Biology Letters, 4(4), 423-425.
Fraser, R. A., Bogaard, A., Heaton, T., Charles, M., Jones, G., Christensen, B. T., ... & Styring, A. K. (2013). Crop manuring and intensive land management by Europe’s first farmers. Proceedings of the National Academy of Sciences, 110(31), 12589-12594.
Fuller, D. Q., & Lucas, L. (2017). Archaeobotany and the Archaeology of Plants. In Encyclopedia of Geoarchaeology (pp. 1–10). Springer.
Gilbert, M. T. P., & Willerslev, E. (2007). Ancient DNA: The first three decades. Philosophical Transactions of the Royal Society B: Biological Sciences, 362(1482), 3-11.
Gilbert, M. T. P., et al. (2005). Assessing ancient DNA studies. Trends in Ecology & Evolution, 20(10), 541-544.
Gobbin, D., et al. (2006). Genetic structure and evolution of Plasmopara viticola populations in Europe. Molecular Ecology, 15(1), 49-60.
Hendy, J., et al. (2018). Ancient protein analysis in archaeology. Science Advances, 4(6), eaau4806.
Hendy, J., et al. (2018). Proteomic evidence of dietary sources in ancient dental calculus. Proceedings of the Royal Society B, 285(1883), 20180977.
Hofreiter, M., et al. (2001). Ancient DNA. Nature Reviews Genetics, 2(5), 353-359.
Iriti, M., Faoro, F. (2008). Ancient plant diseases in Roman Age. Acta Phytopathol Entomol Hungarica, 43: 15–21.
Kenward, H. K., & Hall, A. R. (1995). Biological Evidence from Anglo-Scandinavian Deposits at 16-22 Coppergate. Council for British Archaeology.
Knapp, M., & Hofreiter, M. (2010). Next-generation sequencing of ancient DNA: Requirements, strategies, and perspectives. Genes, 1(2), 227-243.
Krings, M., Taylor, T. N., & Dotzler, N. (2017). Fungal endophytes as a driving force in land plant evolution: Evidence from the fossil record. In Fungi in Biogeochemical Cycles (pp. 5-28). Cambridge University Press.
Labandeira, C.C., Prevec, R. (2014). Plant paleopathology and the roles of pathogens and insects. International Journal Paleopathology, 4:1-16.
Large, E. C. (1940). The Advance of the Fungi. Jonathan Cape.
Lister, D. L., et al. (2009). Latent infection of ancient wheat remains by Barley stripe mosaic virusJournal of Archaeological Science, 36(10), 2215-2222.
Marciniak, S., & Poinar, H. N. (2018). Ancient pathogens through human history: A paleogenomic perspective. Nature Reviews Genetics, 19(6), 355-370.
Martin, F. M., & Kamoun, S. (Eds.). (2012). Effectors in Plant-Microbe Interactions. Wiley-Blackwell.
Martin, F., Kohler, A., Murat, C., Veneault-Fourrey, C., & Hibbett, D. S. (2016). Unearthing the roots of ectomycorrhizal symbioses. Annual Review of Phytopathology, 54(1), 1-23.
Martin, M. D., & Cappellini, E. (2015). Ancient genomics of plant pathogens. Nature Reviews Genetics, 16(10), 591-602.
Martin, M. D., et al. (2013). Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nature Communications, 4, 2172.
McCook, S. (2019). Coffee is not forever: A global history of the coffee leaf rust. Ohio University Press, pp. 45–104.
McNeill, J. R. (2012). The Global Environmental Footprint of the Habsburg Empire, 1526–1918. Environmental History, 17(4), 725–746.
McNeill, W. H. (1976). Plagues and Peoples. Anchor Books, pp. 41–89.
Nesvizhskii, A. I. (2014). Proteogenomics: Concepts, applications, and computational strategies. Nature Methods, 11(11), 1114–1125.
Nunney, L., et al. (2014). Population genomic analysis of Xylella fastidiosa: Insights into the emergence of plant pathogens. Molecular Ecology, 23(7), 1513-1528.
Orlando, L., et al. (2015). Reconstructing ancient genomes and epigenomes. Nature Reviews Genetics, 16(7), 395-408.
Orlando, L., et al. (2021). Ancient DNA analysis. Nature Reviews Methods Primers, 1(1), 14.
Paabo, S., et al. (2004). Genetic analyses from ancient DNA. Annual Review of Genetics, 38, 645-679.
Panagiotakopulu, E. (2001). New records for ancient pests: Archaeoentomology in Egypt. Journal of Archaeological Science, 28(11), 1235-1246.
Pearsall, D. M. (2015). Paleoethnobotany: A Handbook of Procedures (3rd ed.). Routledge.
Rakhshani, M. R., & Mansouri-Birjandi, M. A. (2018). A high-sensitivity sensor based on three-dimensional metal–insulator–metal racetrack resonator and application for hemoglobin detection. Photonics and Nanostructures - Fundamentals and Applications, 32, 28–34.
Rasmussen, M., et al. (2017). Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. Cell, 163(3), 571-582.
Reader, J. (2009). Potato: a history of the propitious esculent. New Haven: Yale University Press.
Redman, C. L. (1999). Human Impact on Ancient Environments. University of Arizona Press.
Ristaino, J. B., et al. (2001). PCR amplification of the Irish potato famine pathogen from historic specimens. Nature, 411(6838), 695-697.
Rouxel, M., et al. (2013). Geographic distribution and evolutionary history of Plasmopara viticola lineages. Phytopathology, 103(6), 564-573.
Schmid, E., Schmid, U., & Schweingruber, F. H. (2017). Atlas of Woody Plant Stems: Evolution, Structure, and Environmental Modifications. Springer.
Schweingruber, F. H. (1990). Anatomy of European Woods. Paul Haupt.
Shackley, M. S. (2011). X-Ray Fluorescence Spectrometry (XRF) in Geoarchaeology. Springer.
Shapiro, B., & Hofreiter, M. (2014). A paleogenomic perspective on evolution and gene function: New insights from ancient DNA. Science, 343(6169), 1236573.
Shevchenko, A., et al. (2001). Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Analytical Chemistry, 73(13), 2500–2514.
Smith, O., et al. (2014). Sedimentary DNA from a submerged site reveals wheat in the British Isles 8,000 years ago. Science, 345(6194), 998-1001.
Taylor, T. N., Krings, M., & Taylor, E. L. (2015). Fossil Fungi. Academic Press.
Van der Veen, M. (2007). Formation processes of desiccated and carbonized plant remains – the identification of routine practice. Journal of Archaeological Science, 34(6), 968-990.
Wales, N., et al. (2016). Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement. Evolutionary Applications, 9(9), 1191-1201.
Warinner, C., et al. (2014). Pathogens and host immunity in the ancient human oral cavity. Nature Genetics, 46(4), 336-344.
Warinner, C., et al. (2017). A robust framework for microbial archaeology. Annual Review of Genomics and Human Genetics, 18, 321-356.
Willerslev, E., & Cooper, A. (2005). Ancient DNA. Proceedings of the Royal Society B: Biological Sciences, 272(1558), 3-16.
Wilkins, M. R., et al. (1996). Proteome research: New frontiers in functional genomics. Springer-Verlag.
Yates, J. R., Ruse, C. I., & Nakorchevsky, A. (2009). Proteomics by mass spectrometry: Approaches, advances, and applications. Annual Review of Biomedical Engineering, 11, 49–79.
Yoshida, K., et al. (2013). The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. eLife, 2, e00731.
Zhou, X., & Li, X. (2019). Ancient plant diseases: A review of paleopathological approaches. Journal of Archaeological Science, 101, 1–10.
Zohary, D., Hopf, M., & Weiss, E. (2012). Domestication of Plants in the Old World (4th ed.). Oxford University Press, pp. 157–174.
Volume 5, Issue 1
June 2025
Pages 49-57

  • Receive Date 09 February 2025
  • Revise Date 02 April 2025
  • Accept Date 18 April 2025
  • Publish Date 01 April 2025