Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

PCR amplification of the Irish potato famine pathogen from historic specimens


Late blight, caused by the oomycete plant pathogen Phytophthora infestans, is a devastating disease of potato and was responsible for epidemics that led to the Irish potato famine in 1845 (refs 1,2,3,4,5). Before the 1980s, worldwide populations of P. infestans were dominated by a single clonal lineage, the US-1 genotype or Ib mitochondrial DNA (mtDNA) haplotype, and sexual reproduction was not documented outside Mexico, the centre of diversity of the pathogen6,7. Here we describe the amplification and sequencing of 100-base-pair fragments of DNA from the internal transcribed spacer region 2 from 28 historic herbarium samples including Irish and British samples collected between 1845 and 1847, confirming the identity of the pathogen. We amplified a variable region of mtDNA that is present in modern Ib haplotypes of P. infestans, but absent in the other known modern haplotypes (Ia, IIa and IIb)8. Lesions in samples tested were not caused by the Ib haplotype of P. infestans, and so theories that assume that the Ib haplotype is the ancestral strain need to be re-evaluated4,7. Our data emphasize the importance of using historic specimens when making inferences about historic populations.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

Figure 1: Specimen of potato infected with P. infestans.
Figure 2: Amplified PCR products obtained using HERB1 and PINF from historic herbarium samples infected with P. infestans and collected between 1845 and 1886.
Figure 3: Amplified PCR products (P2F4/P2R4) from a variable region near the 3′ end of the Nad4 gene in the P2 region of mtDNA from herbarium specimens infected with P. infestans.

Accession codes



Data deposits

DNA sequence data can be found in GenBank under accession nos AF004277AF004280 (ITS and rDNA of four modern isolates); AY027652AY027655, AF349576AF349587 (PINF/Herb amplification of spacer region 2 from four modern isolates and herbarium specimens); AY003908AY003919 (mtDNA P2 region for three modern isolates of each haplotype); AF348598AF348609 (mtDNA P4 region for three modern isolates of each haplotype); and AF349588349601 (P2F4/R4 amplification of mtDNA from four modern haplotypes and herbarium specimens).


  1. Berkeley, M. J. Observations, botanical and physiological on the potato murain. J. Hort. Soc. Lond. 1, 9– 34 (1846).

    Google Scholar 

  2. de Bary, M. Researches into the nature of the potato fungus—Phytophthora infestans. J. R. Agr. Soc. 2, 239– 269 (1876).

    Google Scholar 

  3. Gunderson, J. H., Elwood, H., Ingold, H., Kindle, A. & Sogin, M. L. Phylogenetic relationships between chlororphytes, chrysophytes, and oomycetes. Proc. Natl Acad. Sci. USA 84, 5823– 5827 (1987).

    Article  ADS  CAS  Google Scholar 

  4. Fry, W. & Goodwin, S. B. Resurgence of the Irish potato famine fungus. Bioscience 47, 363– 371 (1997).

    Article  Google Scholar 

  5. Goodwin, S. B., Cohen, B. A., Deahl, K. L. & Fry, W. E. Migration from Northern Mexico as the probable cause of recent genetic changes in populations of Phytophthora infestans in the United States and Canada. Phytopathology 84, 553– 558 (1994).

    Article  Google Scholar 

  6. Gallegly, M. E. & Galindo, J. Mating types and oospore of Phytophthora infestans in nature in Mexico. Phytopathology 48, 274– 277 (1958).

    Google Scholar 

  7. Goodwin, S., Cohen, B. & Fry, W. Panglobal distribution of a single clonal lineage of the Irish potato famine fungus. Proc. Natl Acad. Sci. USA 91, 11591– 11595 (1994).

    Article  ADS  CAS  Google Scholar 

  8. Griffith, G. W. & Shaw, D. S. Polymorphisms in Phytophthora infestans: four mitochondrial haplotypes are detected after PCR amplification of DNA from pure cultures or from host lesions. Appl. Env. Microbiol. 64, 4007– 4014 (1998).

    Article  ADS  CAS  Google Scholar 

  9. Ristaino, J. B. The importance of archival and herbarium materials in understanding the role of oospores in late blight epidemics of the past. Phytopathology 88, 1120– 1130 (1998).

    Article  CAS  Google Scholar 

  10. Drancourt, M., Aboudharam, G., Signoli, M., Dutour, O. & Raoult, D. Detection of 400-year-old Yersinia pestis in human dental pulp: An approach to the diagnosis of ancient septicemia. Proc. Natl Acad. Sci. USA 95, 12637– 12640 (1998).

    Article  ADS  CAS  Google Scholar 

  11. Taylor, J. W. & Swann, E. in Ancient DNA: Recovery and Analysis of Genetic Information from Paleontological, Archaeological, Museum, Medical, and Forensic Specimens (eds Herrmann, B. & Hummel, S.) 166– 181 (Springer, New York, 1994).

    Book  Google Scholar 

  12. Cooper, A. et al. Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 404, 704– 707 (2001).

    Article  ADS  Google Scholar 

  13. Paabo, S., Higuchi, R. & Wilson, A. C. Ancient DNA and the polymerase chain reaction. J. Biol. Chem. 264, 9709– 9712 (1989).

    Article  CAS  Google Scholar 

  14. White, T. J., Bruns, T., Lee, S. & Taylor, J. in PCR Protocols: A Guide to Methods and Applications (eds Innis, M. A., Gelfand, D. H., Sninshy, J. J. & White, T. J.) 315– 322 (Academic, New York, 1990).

    Google Scholar 

  15. Poinar, G. Ancient DNA. Am. Sci. 87, 446– 457 (1999).

    Article  ADS  Google Scholar 

  16. Krings, M. et al. Neanderthal DNA sequences and the origin of modern humans. Cell 90, 19– 30 (1997).

    Article  CAS  Google Scholar 

  17. Salo, W. L., Aufderheide, A. C., Buikstra, J. & Holcomb, T. A. Identification of Mycobacterium tuberculosis DNA in a pre-Columbian Peruvian mummy. Proc. Natl Acad. Sci. USA 91, 2091– 2094 (1994).

    Article  ADS  CAS  Google Scholar 

  18. Trout, C. L., Ristaino, J. B., Madritch, M. & Wangsomboondee, T. Rapid detection of Phytophthora infestans in late blight infected potato and tomato using PCR. Plant Dis. 81, 1042– 1048 (1996).

    Article  Google Scholar 

  19. Erwin, D. C. & Ribiero, O. K. Phytophthora Diseases Worldwide (Am. Phytopathol. Soc. Press, St. Paul, MN, 1996)

    Google Scholar 

  20. Higgins, D. G. & Sharp, P. M. Fast and sensitive multiple sequence alignments on a microcomputer. CABIOS 5, 151– 153 (1989).

    CAS  PubMed  Google Scholar 

  21. Carter, D. A., Archer, S. A., Buck, K. W., Shaw, D. S. & Shattock, R. C. Restriction fragment length polymorphisms of mitochondrial DNA of Phytophthora infestans. Mycol. Res. 94, 1123– 1128 (1990).

    Article  Google Scholar 

  22. Goodwin, S. B. in Phytophthora (eds Lucas, J. A., Shattock, R. C., Shaw, D. S. & Cooke, L. R.) 256– 271 (Cambridge Univ. Press, New York. 1991).

    Google Scholar 

  23. Gavino, P. D. Mitochondrial DNA evolution and its utility for population genetic studies of Phytophthora infestans. Thesis, Cornell Univ. (1999).

    Google Scholar 

  24. Lang, B. F. & Forget, L. in Genetic Maps. Locus Maps of Complex Genomes (ed. O'Brien, S. J.) 3.133– 3.135 (Cold Spring Harbor Laboratory Press, Plain View, New York, 1993).

    Google Scholar 

  25. Paquin, B. et al. The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression. Curr. Genet. 31, 320– 395 (1997).

    Article  Google Scholar 

  26. Day, J. P. & Shattock, R. C. Aggressiveness and other factors relating to the displacement of populations of Phytophthora infestans in England and Wales. Eur. J. Plant Path. 103, 379– 391 (1997).

    Article  Google Scholar 

  27. Lebreton, L., Laurent, C. & Andrivon, D. Evolution of Phytophthora infestans populations in the two most important potato production areas of France during 1992–1996. Plant Pathol. 47, 427– 439 (1998).

    Article  Google Scholar 

  28. Wangsomboondee, T,, Groves, C. T., Shoemaker, P. B., Cubeata, M. A. & Ristaino, J. B. Genetic diversity of isolates of Phytophthora infestans from tomato and potato in North Carolina. Phytopathology 90, S65 (2000).

    Google Scholar 

  29. Penny, D., Steel, M., Waddell, P. J. & Hendy, M. D. Improved analysis of human mtDNA sequences support a recent African origin of Homo sapiens. Mol. Biol. Evol. 12, 863– 882 (1995).

    CAS  PubMed  Google Scholar 

Download references


This research was supported in part by a grant from the National Geographic Society and in part by the North Carolina State University Agricultural Research Service and the North Carolina State University Office of International Programs. We thank K. May for producing the gels for final publication; J. Thomas, NCSU for use of the Phytotron Facility Laboratory; M. Chase, Jodrell Laboratory, Royal Botanic Gardens, Kew, England, for use of his lab facilities; and D. Pegler and B. Spooner, Mycology Herbarium, Royal Botanic Gardens, Kew, England; A. Rossman, US National Fungus Collections, USDA; M. Jebb, National Botanic Gardens, Glasnevin, Dublin, Ireland; and D. Pfister, Farlow Herbarium, Harvard University for providing access to specimens. Statistical advice from J. Thorne is appreciated.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Jean B. Ristaino.

Supplementary Information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Ristaino, J., Groves, C. & Parra, G. PCR amplification of the Irish potato famine pathogen from historic specimens. Nature 411, 695–697 (2001).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing