Abstract
The study of population genetics attempts to investigate evolutionary forces such as mutation, migration, genetic drift, selection and recombination, and how gene frequencies change in populations to shape their genetic structure. These evolutionary forces and the interaction among them are particularly important in plant pathogens where, combined with the pathogen’s life history characteristics, they determine the pathogen’s evolutionary potential. Advances in DNA sequencing and analytical approaches have significantly improved the accuracy of population genetic parameter estimates. In particular, coalescent-based approaches are a powerful extension of classical population genetics because it is a collection of mathematical models that can accommodate biological phenomena as reflected in molecular data. In a comparison of migration estimates of Rhynchosporium secalis, which were either derived from FST estimates, or estimated with a coalescent method, reveals that the latter are more reliable, are less dependent on population sizes being stable, are not affected by asymmetrical migration between populations, and are affected less by populations with small sample sizes. Improved analyses and their usefulness in determining the phylogeography and demography of R. secalis are discussed.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Barrett LG, Thrall PH, Burdon JJ, Linde CC (2008) Life history determines genetic structure and evolutionary potential of host-parasite interactions. Trends in Ecology & Evolution 23, 678–685. doi: 10.1016/j.tree. 2008.06.017
Beerli P (1998) Estimation of migration rates and population sizes in geographically structured populations. In ‘Advances in molecular ecology’. (Ed. G Carvalho) pp. 39–53. (NATO Science Series A: Life Sciences, IOS Press: Amsterdam)
Beerli P (2004) Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Molecular Ecology 13, 827–836. doi: 10.1111/j.1365-294X.2004. 02101.x
Brown JKM, Hovmøller MS (2002) Epidemiology — aerial dispersal of pathogens on the global and continental scales and its impact on plant disease. Science 297, 537–541. doi: 10.1126/science.1072678
Burdon JJ (1987) ‘Diseases and plant population biology.’ (Cambridge University Press: Cambridge)
Burdon JJ, Silk J (1997) Sources and patterns of diversity in plant-pathogenic fungi. Phytopathology 87, 664–669. doi: 10.1094/PHYTO.1997.87. 7.664
Eldon B, Wakeley J (2009) Coalescence times and FST under a skewed offspring distribution among individuals in a population. Genetics 181, 615–629. doi: 10.1534/genetics.108.094342
Hartl DL, Clark AG (1997) ‘Principles of population genetics.’ 3rd edn. (Sinauer Associates, Inc.: Sunderland, MA)
Hey J, Nielsen R (2004) Multilocus methods for estimation population sizes, migration rates and divergence times, with application to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167, 747–760. doi: 10.1534/genetics.103.024182
Jackson LF, Webster RK (1976) Seed and grasses as possible sources of Rhynchosporium secalis for barley in California. Plant Disease Reporter 60, 233–236.
Keiper FJ, Hayden MJ, Park RF, Wellings CR (2003) Molecular genetic variability of Australian isolates of five cereal rust pathogens. Mycological Research 107, 545–556. doi: 10.1017/S0953756203007809
Keiper FJ, Haque MS, Hayden MJ, Park RF (2006) Genetic diversity in Australian populations of Puccinia graminis f. sp. avenae. Phytopathology 96, 96–104. doi: 10.1094/PHYTO-96-0096
Lee HK, Tewari JP, Turkington TK (2001) A PCR-based assay to detect Rhynchosporium secalis in barley seed. Plant Disease 85, 220–225. doi: 10.1094/PDIS.2001.85.2.220
Linde CC, Zhan J, McDonald BA (2002) Population structure of Mycosphaerella graminicola: from lesions to continents. Phytopathology 92, 946–955. doi: 10.1094/PHYTO.2002.92.9.946
Linde CC, Zala M, Ceccarelli S, McDonald BA (2003) Further evidence for sexual reproduction in Rhynchosporium secalis based on distribution and frequency of mating-type alleles. Fungal Genetics and Biology 40, 115–125. doi: 10.1016/S1087-1845(03)00110-5
Linde CC, Zala M, McDonald BA (2009) Molecular evidence for recent founder populations and human-mediated migration in the barley scald pathogen Rhynchosporium secalis. Molecular Phylogenetics and Evolution 51, 454–464. doi: 10.1016/j.ympev.2009.03.002
Luikart G, Cornuet JM (1998) Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conservation Biology 12, 228–237. doi: 10.1046/j.1523-1739.1998. 96388.x
McDonald BA (1997) The population genetics of fungi: tools and techniques. Phytopathology 87, 448–453. doi: 10.1094/PHYTO.1997.87.4.448
McDonald BA, Linde C (2002) Pathogen population genetics, evolutionary potential, and durable resistance. Annual Review of Phytopathology 40, 349–379. doi: 10.1146/annurev.phyto.40.120501.101443
Milgroom MG, Fry WE (1997) Contributions of population genetics to plant disease epidemiology and management. Advances in Botanical Research 24, 1–30. doi: 10.1016/S0065-2296(08)60069-5
Nei M, Maruyama T, Chakrabarty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29, 1–10. doi: 10.2307/2407137
Piry S, Luikart G, Cornuet JM (1999) BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. The Journal of Heredity 90, 502–503. doi: 10.1093/ jhered/90.4.502
Rosenberg NA, Nordborg M (2002) Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews. Genetics 3, 380–390. doi: 10.1038/nrg795
Salamati S, Zhan J, Burdon JJ, McDonald BA (2000) The genetic structure of field populations of Rhynchosporium secalis from three continents suggests moderate gene flow and regular recombination. Phytopathology 90, 901–908. doi: 10.1094/PHYTO.2000.90.8.901
Shipton WA, Boyd JR, Ali SM (1974) Scald of barley. Review of Plant Pathology 53, 839–861.
Slatkin M, Barton NH (1989) A comparison of three indirect methods for estimating average levels of gene flow. Evolution 43, 1349–1368. doi: 10.2307/2409452
Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38, 1358–1370. doi: 10.2307/2408641
Whitlock MC, McCauley DE (1999) Indirect measures of gene flow and migration: FST1/(4Nm + 1). Heredity 82, 117–125. doi: 10.1038/sj.hdy. 6884960
Wright S (1951) The genetical structure of populations. Annals of Eugenics 15, 323–354.
Zaffarano PL, McDonald BA, Zala M, Linde CC (2006) Global hierarchical gene diversity analysis suggests the Fertile Crescent is not the center of origin of the barley scald pathogen Rhynchosporium secalis. Phytopathology 96, 941–950. doi: 10.1094/PHYTO-96-0941
Zaffarano PL, McDonald BA, Linde CC (2008) Rapid speciation followed host specialization in Rhynchosporium. Evolution 62, 1418–1436.
Zaffarano PL, McDonald BA, Linde CC (2009) Phylogeographical analyses reveal global migration patterns of the barley scald pathogen Rhynchosporium secalis. Molecular Ecology 18, 279–293. doi: 10.1111/j.1365-294X.2008.04013.x
Author information
Authors and Affiliations
Additional information
esented as a Keynote Address at the 17th Biennial Conference of the Australasian Plant Pathology Society, September, 2009, Newcastle.
Rights and permissions
About this article
Cite this article
Linde, C.C. Population genetic analyses of plant pathogens: new challenges and opportunities. Australasian Plant Pathology 39, 23–28 (2010). https://doi.org/10.1071/AP09061
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1071/AP09061