Understanding the recent colonization history of a plant pathogenic fungus using population genetic tools and Approximate Bayesian Computation

Heredity

Volumn 109, Issue 5, 2012, Pages 269-279

  Barres B ^a,b,c   Carlier, J ^a   Seguin, M ^a   Fenouillet, C ^a   Cilas, C ^a   Ravigne V ^a  

^a CIRAD   (France)

^b UMR 1202 BIOGECO   (France)

^c UNIVERSITÉ DE BORDEAUX   (France)

Author keywords

ABC; Emergent infectious disease; Microcyclus ulei; Microsatellite; Population history; SALB

Indexed keywords

MICROSATELLITE DNA;

BAYESIAN ANALYSIS; COLONIZATION; DEMOGRAPHIC HISTORY; DISEASE CONTROL; DISPERSAL; ENDEMIC SPECIES; FUNGAL DISEASE; FUNGUS; GENE FLOW; GENETIC ANALYSIS; GENETIC MARKER; GENETIC STRUCTURE; GENETIC VARIATION; INFECTIOUS DISEASE; PATHOGEN; SPORE; TWENTIETH CENTURY;

ARTICLE; ASCOMYCETES; BIOLOGICAL MODEL; GENETICS; HEVEA; HUMAN; METHODOLOGY; MICROBIOLOGY; PATHOGENICITY; PLANT DISEASE; PLANT LEAF; POPULATION GENETICS; SOUTH AMERICA;

ASCOMYCOTA; GENETICS, POPULATION; HEVEA; HUMANS; MICROSATELLITE REPEATS; MODELS, GENETIC; PLANT DISEASES; PLANT LEAVES; SOUTH AMERICA;

BRAZIL; ECUADOR; FRENCH GUIANA; GUATEMALA [CENTRAL AMERICA];

BACTERIA (MICROORGANISMS); FUNGI; HEVEA BRASILIENSIS; MICROCYCLUS ULEI;

EID: 84867869654     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2012.37     Document Type: Article

References (54)

1. Anderson PK, Cunningham AA, Patel NG, Morales FJ, Epstein PR, Daszak P (2004). Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers. Trends Ecol Evol 19: 535-544. (Pubitemid 39234760)
2. Arnaud-Haond S, Belkhir K (2007). GENCLONE: a computer program to analyse genotypic data, test for clonality and describe spatial clonal organization. Mol Ecol Notes 7: 15-17. (Pubitemid 46046572)
3. Aylor DE (2003). Spread of plant disease on a continental scale: Role of aerial dispersal of pathogens. Ecology 84: 1989-1997. (Pubitemid 37435673)
4. Beaumont MA, Zhang WY, Balding DJ (2002). Approximate Bayesian Computation in population genetics. Genetics 162: 2025-2035. (Pubitemid 36114682)
5. Beerli P (2004). Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Mol Ecol 13: 827-836. (Pubitemid 38390589)
6. Benjamini Y, Hochberg Y (1995). Controlling the false discovery rate - a practical and powerful approach to multiple testing. J Roy Stat Soc Ser B Met 57: 289-300.
7. Bertorelle G, Benazzo A, Mona S (2010). ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Mol Ecol 19: 2609-2625.
8. Bourassa M, Bernier L, Hamelin RC (2005). Direct genotyping of the poplar leaf rust fungus, Melampsora medusae f. sp deltoidae, using codominant PCR-SSCP markers. For Pathol 35: 245-261. (Pubitemid 41595198)
9. Brunner PC, Schurch S, McDonald BA (2007). The origin and colonization history of the barley scald pathogen Rhynchosporium secalis. J Evol Biol 20: 1311-1321. (Pubitemid 46956659)
10. Chen RS, McDonald BA (1996). Sexual reproduction plays a major role in the genetic structure of populations of the fungus Mycosphaerella graminicola. Genetics 142: 1119-1127. (Pubitemid 26115495)
11. Cornuet JM, Ravigné V, Estoup A (2010). Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0). BMC Bioinformatics 11: 401.
12. Cornuet JM, Santos F, Beaumont MA, Robert CP, Marin JM, Balding DJ et al. (2008). Inferring population history with DIYABC: a user-friendly approach to approximate Bayesian computation. Bioinformatics 24: 2713-2719. (Pubitemid 352722613)
13. Dlugosch KM, Parker IM (2008). Founding events in species invasions: genetic variation, adaptive evolution, and the role of multiple introductions. Mol Ecol 17: 431-449. (Pubitemid 350292487)
14. El Mousadik A, Petit RJ (1996). High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L) Skeels] endemic to Morocco. Theor Appl Genet 92: 832-839. (Pubitemid 26270161)
15. Estoup A, Baird SJE, Ray N, Currat M, Cornuet JM, Santos F et al. (2010). Combining genetic, historical and geographical data to reconstruct the dynamics of bioinvasions: application to the cane toad Bufo marinus. Mol Ecol Res 10: 886-901.
16. Estoup A, Guillemaud T (2010). Reconstructing routes of invasion using genetic data: why, how and so what? Mol Ecol 19: 4113-4130.
17. Evanno G, Regnaut S, Goudet J (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620. (Pubitemid 40886055)
18. Fagundes NJR, Ray N, Beaumont M, Neuenschwander S, Salzano FM, Bonatto SL et al. (2007). Statistical evaluation of alternative models of human evolution. Proc Natl Acad Sci USA 104: 17614-17619. (Pubitemid 350210884)
19. Falush D, Stephens M, Pritchard JK (2003). Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164: 1567-1587. (Pubitemid 37102217)
20. Frankham R (2005). Resolving the genetic paradox in invasive species. Heredity 94: 385.
21. Goodwin SB, Cohen BA, Fry WE (1994). Panglobal distribution of a single clonal lineage of the irish potato famine fungus. Proc Natl Acad Sci USA 91: 11591-11595. (Pubitemid 24356390)
22. Guillemaud T, Beaumont MA, Ciosi M, Cornuet JM, Estoup A (2010). Inferring introduction routes of invasive species using Approximate Bayesian Computation on microsatellite data. Heredity 104: 88-99.
23. Guyot J (2007). Analyse, a petite e'chelle, de l'influence de l'environnement, de l'inoculum et de l'hote sur la dynamique e'pide'mique de la maladie sud-amé ricaine des feuilles de l'he've'a (Microcyclus ulei) en milieu amazonien. PhD Thesis, Université Montpellier II, France.
24. Guyot J, Cilas C, Sache Y (2008). Influence of host resistance and phenology on South American Leaf Blight of the rubber tree with a special consideration for its temporal dynamics. Eur J Plant Pathol 120: 111-124.
25. Hilton RN (1955). South American Leaf Blight. a review of the literature relating to its depredation in South America, its threat to the far east, and the methods available for its control. J Nat Rubber Res 14: 287-337.
26. Holliday P (1970). South American Leaf Blight (Microcyclus ulei) of Hevea brasiliensis. Phytopatholol Papers 12: 1-31.
27. Hovmøller MS, Justesen AF, Brown JKM (2002). Clonality and long-distance migration of Puccinia striiformis f. sp tritici in north-west Europe. Plant Pathol 51: 24-32. (Pubitemid 34172018)
28. Hovmøller MS, Yahyaoui AH, Milus EA, Justesen AF (2008). Rapid global spread of two aggressive strains of a wheat rust fungus. Mol Ecol 17: 3818-3826.
29. Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009). Inferring weak population structure with the assistance of sample group information. Mol Ecol Res 9: 1322-1332.
30. Junqueira NTV, Chaves GM, Zambolin L, Romeiro RS, Gasparotto L (1984). Isolamento, cultivo e esporulaçao de Microcyclus ulei, agente etiologico do mal-das-folhas da seringueira. Rev Ceres 31: 322-331.
31. Le Guen V, Garcia D, Mattos CRR, Clement-Demange A (2002). Evaluation of field resistance to Microcyclus ulei of a collection of Amazonian rubber tree (Hevea brasiliensis) germplasm. Crop Breed Appl Biotech 2: 141-148.
32. Le Guen V, Rodier-Goud M, Troispoux V, Xiong TC, Brottier P, Billot C et al. (2004). Characterization of polymorphic microsatellite markers for Microcyclus ulei, causal, agent of South American leaf blight of rubber trees. Mol Ecol Notes 4: 122-124. (Pubitemid 38261330)
33. Lespinasse D, Grivet L, Troispoux V, Rodier-Goud M, Pinard F, Seguin M (2000). Identification of QTLs involved in the resistance to South American leaf blight (Microcyclus ulei) in the rubber tree. Theor Appl Genet 100: 975-984. (Pubitemid 30263897)
34. Lieberei R (2007). South American leaf blight of the rubber tree (Hevea spp.): New steps in plant domestication using physiological features and molecular markers. Ann Bot 100: 1125-1142. (Pubitemid 47614296)
35. Liyanage AdS (1981). Long distance transport and deposition of spores of Microcyclus ulei in tropical America - a possibility. Bull Rubber Res Inst Sri Lanka 16: 3-8.
36. Marin JM, Pillai N, Robert CP, Rousseau J (2011). Relevant statistics for Bayesian model choice. arXiv: 1110.4700.
37. Marin DH, Romero RA, Guzman M, Sutton TB (2003). Black sigatoka: An increasing threat to banana cultivation. Plant Dis 87: 208-222. (Pubitemid 36247218)
38. McDonald BA, Linde C (2002). Pathogen population genetics, evolutionary potential, and durable resistance. Annu Rev Phytopathol 40: 349-379. (Pubitemid 35235585)
39. Mundt CC, Sackett KE, Wallace LD, Cowger C, Dudley JP (2009). Long-Distance Dispersal and accelerating waves of disease: Empirical relationships. Am Nat 173: 456-466.
40. Pan Z, Yang XB, Pivonia S, Xue L, Pasken R, Roads J (2006). Long-term prediction of soybean rust entry into the continental United States. Plant Dis 90: 840-846.
41. Paradis E, Claude J, Strimmer K (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290. (Pubitemid 38195693)
42. Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945-959. (Pubitemid 30397141)
43. Qiagen (2006). DNeasy Plant Handbook. Qiagen: New-York, pp 32-36.
44. R Development Core Team (2004). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing: Vienna, Austriahttp://www.Rproject.org).
45. Raboin LM, Selvi A, Oliveira KM, Paulet F, Calatayud C, Zapater MF et al. (2007). Evidence for the dispersal of a unique lineage from Asia to America and Africa in the sugarcane fungal pathogen Ustilago scitaminea. Fungal Genet Biol 44: 64-76. (Pubitemid 46016969)
46. Rivas GG, Zapater MF, Abadie C, Carlier J (2004). Founder effects and stochastic dispersal at the continental scale of the fungal pathogen of bananas Mycosphaerella fijiensis. Mol Ecol 13: 471-482. (Pubitemid 38143388)
47. Robert CP, Cornuet JM, Marin JM, Pillai NS (2011). Lack of confidence in approximate Bayesian computation model choice. Proc Natl Acad Sci USA 108: 15112-15117.
48. Rousset F (2008). GENEPOP ' 007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Res 8: 103-106. (Pubitemid 350231212)
49. Rozen S, Skaletsky H (2000). Primer 3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds). Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press: Totowa, NJ, pp 365-386.
50. Sakai AK, Allendorf FW, Holt JS, Lodge DM, Molofsky J, With KA et al. (2001). The population biology of invasive species. Annu Rev Ecol Syst 32: 305-332. (Pubitemid 34043164)
51. Storey JD (2002). A direct approach to false discovery rates. J Roy Stat Soc Ser B Stat Meth 64: 479-498.
52. Ule E (1905). Kautschukgewinnung und kautschuckhandel am Amazonen-strome. Tropenpflanzer-Beihefte 6: 1-71.
53. Vercken E, Fontaine MC, Gladieux P, Hood ME, Jonot O, Giraud T (2011). Glacial Refugia in pathogens: European genetic structure of anther smut pathogens on Silene latifolia and Silene dioica. PLoS Pathog 6: e1001229.
54. Weir BS, Cockerham CC (1984). Estimating F-statistics for the analysis of populationstructure. Evolution 38: 1358-1370.