Pathogen population dynamics in agricultural landscapes: The Ddal modelling framework

Infection, Genetics and Evolution

Volumn 27, Issue , 2014, Pages 509-520

  Papaïx, Julien ^a,b   Adamczyk Chauvat, Katarzyna ^b   Bouvier, Annie ^b   Kiêu, Kiên ^b   Touzeau, Suzanne ^b   Lannou, Christian ^a   Monod, Hervé ^b  

^a INRA Institut National de la Recherche Agronomique   (France)

^b UR341 National Agronomical Research Institute (INRA)   (France)

Author keywords

Landscape epidemiology; Landscape pattern indices; Metapopulation model; Model analysis; Sensitivity analysis; Tessellation models

Indexed keywords

AGRICULTURAL LAND; ARTICLE; BASIC REPRODUCTION NUMBER; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; DISEASE DYNAMIC AGRICULTURAL LANDSCAPE FRAMEWORK; HABITAT STRUCTURE; LANDSCAPE; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; POPULATION DISPERSION; POPULATION DYNAMICS; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROCESS MODEL; QUANTITATIVE ANALYSIS; SENSITIVITY ANALYSIS; SIMULATOR; AGRICULTURE; ECOSYSTEM; HOST PATHOGEN INTERACTION; THEORETICAL MODEL;

AGRICULTURE; ECOSYSTEM; HOST-PATHOGEN INTERACTIONS; MODELS, THEORETICAL;

EID: 84951908822     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2014.01.022     Document Type: Article

References (81)

1. Adamczyk K., Angevin F., Colbach N., Lavigne C., Le Ber F., Mari J.-F. Genexp, un logiciel simulateur de paysages agricoles pour l'étude de la diffusion de transgènes. Géomatique 2007, 17:469-487.
2. Ahlqvist O., Shortridge A. Spatial and semantic dimensions of landscape heterogeneity. Landscape Ecol. 2010, 25:573-590.
3. Arak T., Clifford P., Surgailis D. Point-based polygonal models for random graphs. Adv. Appl. Probab. 1993, 25:348-372.
4. Beaumont M.A. Approximate Bayesian computation in evolution and ecology. Annu. Rev. Ecol. Syst. 2010, 41:379-406.
5. Bousset L., Chèvre A.-M. Stable epidemic control in crops based on evolutionary principles: Adjusting the metapopulation concept to agro-ecosystems. Agric. Ecosyst. Environ. 2013, 165:118-129.
6. Bouvier A., Kiêu K., Adamczyk K., Monod H. Computation of the integrated flow of particles between polygons. Environ. Modell. Softw. 2009, 24:843-849.
7. Burdon J.J., Thrall P.H. Pathogen evolution across the agro-ecological interface. Implications for disease management. Evol. Appl. 2008, 1:57-65.
8. Burel F., Baudry J. Landscape Ecology: Concepts, Methods and Applications 2004, Science Publishers Inc., Plymouth (UK).
9. Castellazzi M.S., Matthews J., Angevin F., Sausse C., Wood G.A., Burgess P.J., Brown I., Conrad K.F., Perry J.N. Simulation scenarios of spatio-temporal arrangement of crops at the landscape scale. Environ. Modell. Softw. 2010, 25:1881-1889.
10. Caswell H. Matrix Population Models 2001, Sinauer Associates Inc. Publishers, Sunderland (USA).
11. Colbach N., Monod H., Lavigne C. A simulation study of the medium-term effects of field patterns on cross-pollination rates in oilseed rape (Brassica napus L.). Ecol. Model. 2009, 220:662-672.
12. Dalgaard T., Hutchings N.J., Porter J.R. Agroecology, scaling and interdisciplinarity. Agric. Ecosyst. Environ. 2003, 100:39-51.
13. Débarre F., Lenormand T., Gandon S. Evolutionary epidemiology of drug-resistance in space. PLoS Comput. Biol. 2009, 5(4). e1000337. http://dx.doi.org/10.1371/journal.pcbi.1000337.
14. Evans M., Grimm V., Johst K., Knuuttila T., de Langhe R., Lessells C.M., Merz M., O'Malley M.A., Orzack S.H., Weisberg M., Wilkinson D.J., Wolkenhauer O., Benton T.G. Do simple models lead to generality in ecology?. Trends Ecol. Evol. 2013, 28:578-583.
15. Fahrig L. Effects of habitat fragmentation on biodiversity. Annu. Rev. Ecol. Evol. Syst. 2003, 34:487-515.
16. Fang K.-T., Li R., Sudjianto A. Design and Modeling for Computer Experiments 2006, Chapman & Hall/CRC.
17. Forman R.T.T. Some general principles of landscape and regional ecology. Landscape Ecol. 1995, 10:133-142.
18. Fortin M.J., Boots B., Csillag F., Remmel T.K. On the role of spatial stochastic models in understanding landscape indices in ecology. Oikos 2003, 102:203-212.
19. Frantzen J., van den Bosch F. Spread of organisms: can travelling and dispersive waves be distinguished?. Basic Appl. Ecol. 2000, 1:83-91.
20. Frezal L., Robert C., Bancal M.O., Lannou C. Local dispersal of Puccinia triticina and wheat canopy structure. Phytopathology 2009, 99:1216-1224.
21. Fulford G.R., Roberts M.G., Heesterbeek J.A.P. The metapopulation dynamics of an infectious disease: tuberculosis in possums. Theor. Popul. Biol. 2002, 61:15-29.
22. Gilligan C.A. Sustainable agriculture and plant diseases: an epidemiological perspective. Philos. Trans. R. Soc. Lond. B. 2008, 363:741-759.
23. Gilligan C.A., Truscott J.E., Stacey A.J. Impact of scale on the effectiveness of disease control strategies for epidemics with cryptic infection in a dynamical landscape: an example for a crop disease. J. R. Soc. Interface 2007, 4:925-934.
24. Gustafson E.J. Quantifying landscape spatial pattern: what is the state of the art?. Ecosystems 1998, 1:143-156.
25. Hanski I. Metapopulation dynamics. Nature 1998, 396:41-49.
26. Hartig F., Calabrese J.M., Reineking B., Wiegand T., Huth A. Statistical inference for stochastic simulation models - theory and application. Ecol. Lett. 2011, 14:816-827.
27. He H.S., DeZonia B.E., Mladenoff D.J. An aggregation index (AI) to quantify spatial patterns of landscapes. Landscape Ecol. 2000, 15:591-601.
28. Iooss B. Revue sur l'analyse de sensibilité globale de modèles numériques. J. de la Société Française de Statistique 2011, 152:3-25.
29. Iooss B., Ribatet M. Global sensitivity analysis of computer models with functional inputs. Reliab. Eng. Syst. Saf. 2009, 94:1194-1204.
30. Johnson T. Man-guided evolution in plant rusts. Science 1961, 10:357-362.
31. Kareiva P.M., Watts S., McDonald R., Boucher T. Domesticated nature: shaping landscapes and ecosystems for human welfare. Science 2007, 316:1866-1869.
32. Keesing F., Holt R.D., Ostfeld R.S. Effects of species diversity on disease risk. Ecol. Lett. 2006, 9:485-498.
33. Kiêu K., Adamczyk-Chauvat K., Monod H., Stoica R.S. A completely random T-tessellation model and Gibbsian extensions. Spat. Stat. 2013, 6:118-138.
34. Kirkpatrick S., Gelatt C.D., Vecchi M.P. Optimization by simulated annealing. Science 1983, 220:671-680.
35. Lannou C., Soubeyrand S., Frezal L., Chadoeuf J. Autoinfection in wheat leaf rust epidemics. New Phytol. 2008, 177:1001-1011.
36. Lavigne C., Klein E.K., Mari J.-F., Le Ber F., Adamczyk K., Monod H., Angevin F. How do genetically modified (GM) crops contribute to background levels of GM pollen in an agricultural landscape?. J. Appl. Ecol. 2008, 45:1104-1113.
37. Le Ber F., Benoît M., Schott C., Mari J.-F., Mignolet C. Studying crop sequences with CarrotAge, a HMM-based data mining software. Ecol. Modell. 2006, 191:170-185.
38. Le Ber F., Lavigne C., Adamczyk K., Angevin F., Colbach N., Mari J.-F., Monod H. Neutral modelling of agricultural landscapes by tessellation methods - application for gene flow simulation. Ecol. Modell. 2009, 220:3536-3545.
39. Levins R. Some demographic and genetic consequences of environmental heterogeneity for biological control. Bull. Entomol. Soc. Am. 1969, 15:237-240.
40. Li H., Reynolds J.F. On definition and quantification heterogeneity. Oikos 1995, 73:280-284.
41. Li H., Wu J. Use and misuse of landscape indices. Landscape Ecol. 2004, 19:389-399.
42. Loreau M., Mouquet N., Holt R.D. Meta-ecosystems: a theoretical framework for a spatial ecosystem ecology. Ecol. Lett. 2003, 6:673-679.
43. Madden L.V., Hughes G., van den Bosch F. The Study of Plant Disease Epidemics 2008, APS Press, St. Paul (USA).
44. Massol F., Calcagno V., Massol J. The metapopulation fitness criterion: proof and perspectives. Theor. Popul. Biol. 2009, 75:183-200.
45. Melbourne B.A., Cornell H.V., Davies K.F., Dugaw C.J., Elmendorf S., Freestone A.L., Hall R.J., Harrison S., Hastings A., Holland M., Holyoak M., Lambrinos J., Moore K., Yokomizo H. Invasion in a heterogeneous world: resistance, coexistence or hostile takeover?. Ecol. Lett. 2007, 10:77-94.
46. Monod H., Naud C., Makowski D. Uncertainty and sensitivity analysis for crop models. Working with Dynamic Crop Models: Evaluation, Analysis, Parameterization, and Applications 2006, 55-100. Elsevier, chapter 4. D. Makowski, D. Wallach, J.W. Jones (Eds.).
47. Mundt C.C. Use of multiline cultivars and cultivar mixtures for disease management. Annu. Rev. Phytopathol. 2002, 40:381-410.
48. Mundt C.C., Brophy L.S. Influence of number of host genotype units on the effectiveness of host mixtures for disease control: a modeling approach. Phytopathology 1988, 78:1087-1094.
49. Mundt C.C., Sackett K.E., Wallace L.D. Landscape heterogeneity and disease spread: experimental approaches with a plant pathogen. Ecol. Appl. 2011, 21:321-328.
50. Okabe A., Boots B., Sugihara K. Spatial Tessellations: Concepts and Applications of Voronoi Diagrams 1992, Wiley.
51. O'Neill R.V. Indices of landscape pattern. Landscape Ecol. 1988, 1:153-162.
52. Papaïx, J., 2011. Landscape Structure and Epidemic Risk, a Demo-Genetic Approach (Ph.D. thesis). AgroParisTech - ABIES.
53. Papaïx J., David O., Lannou C., Monod H. Dynamics of adaptation in spatially heterogeneous metapopulations. PLoS One 2013, 8:e54697.
54. Park A.W., Gubbins S., Gilligan C.A. Invasion and persistence of plant parasites in a spatially structured host population. Oikos 2001, 94:162-174.
55. Pautasso M., Holdenrieder O., Stenlid J. Susceptibility to fungal pathogens of forests differing in tree diversity. Ecol. Stud. 2005, 176:263-289.
56. Peng J., Wang Y., Zhang Y., Wu J., Li W., Li Y. Evaluating the effectiveness of landscape metrics in quantifying spatial patterns. Ecol. Indic. 2010, 10:217-223.
57. Plantegenest M., Le May C., Fabre F. Landscape epidemiology of plant diseases. J. R. Soc. Interface 2007, 4:963-972.
58. Priestley R.H., Bayles R.A. Varietal diversification as a means of reducing the spread of cereal disease in the United Kingdom. J. Nat. Inst. Agric. Bot. 1980, 15:205-214.
59. Rickelfs R.E. Community diversity: relative roles of local and regional processes. Science 1987, 235:167-171.
60. Riitters K.H., O'Neill R.V., Hunsaker C.T., Wickham J.D., Yankee D.H., Timmins S.P., Jones K.B., Jackson B.L. A factor analysis of landscape pattern and structure metrics. Landscape Ecol. 1995, 10:23-39.
61. Sackett K.E., Mundt C.C. The effects of dispersal gradient and pathogen life cycle components on epidemic velocity in computer simulations. Phytopathology 2005, 95:992-1000.
62. Saltelli A., Tarantola S., Campolongo F. Sensitivity analysis as an ingredient of modeling. Stat. Sci. 2000, 15:377-395.
63. Saltelli A., Ratto M., Andres T., Campolongo F., Cariboni J., Gatelli D., Saisana M., Tarantola S. Global sensitivity analysis. The primer 2008, Wiley, Chichester (UK).
64. Sapoukhina N., Tyutyunov Y., Sache I., Arditi R. Spatially mixed crops to control the stratified dispersal of airborne fungal diseases. Ecol. Modell. 2010, 221:2793-2800.
65. Seppelt R., Muller F., Schroder B., Volk M. Challenges of simulating complex environmental systems at the landscape scale: a controversial dialogue between two cups of espresso. Ecol. Modell. 2009, 220:3481-3489.
66. Shennan C. Biotic interactions, ecological knowledge and agriculture. Philos. Trans. R. Soc. Lond. B. 2008, 363:717-739.
67. Skelsey P., Rossing W.A.H., Kessel G.J.T., Powell J., van der Werf W. Influence of host diversity on development of epidemics: an evaluation and elaboration of mixture theory. Phytopathology 2005, 95:328-338.
68. Skelsey P., Rossing W.A.H., Kessel G.J.T., van der Werf W. Invasion of Phytophthora infestans at the landscape level: how do spatial scale and weather modulate the consequences of spatial heterogeneity in host resistance?. Phytopathology 2010, 100:1146-1161.
69. Sobol I.M. Sensitivity estimates for non linear mathematical models. Matematicheskoe Modelirovanie 1990, 2:112-118. (in Russian). English translation in: Mathematical Modeling and Computational Experiment, 1993, 1, 407-414.
70. Soubeyrand S., Enjalbert J., Sanchez A., Sache I. Anisotropy, in density and in distance, of the dispersal of yellow rust of wheat: experiments in large field plots and estimation. Phytopathology 2007, 97:1315-1324.
71. Stukenbrock E.H., McDonald B.A. The origins of plant pathogens in agro-ecosystems. Annu. Rev. Phytopathol. 2008, 46:75-100.
72. Sudret B. Global sensitivity analysis using polynomials chaos expansions. Reliab. Eng. Syst. Saf. 2008, 93:964-979.
73. Thrall P.H., Oakeshott J.G., Fitt G., Southerton S., Burdon J.J., Sheppard A., Russell R.J., Zalucki M., Heino M., Denison R.F. Evolution in agriculture: the application of evolutionary approaches to the management of biotic interactions in agro-ecosystems. Evol. Appl. 2011, 4:200-215.
74. Tilman D. Global environmental impacts of agricultural expansion: the need for sustainable and efficient practices. Proc. Natl. Acad. Sci. USA 1999, 96:5995-6000.
75. Tischendorf L. Can landscape indices predict ecological processes consistently?. Landscape Ecol. 2001, 16:235-254.
76. Turner M.G. Landscape ecology: what is the state of the science?. Annu. Rev. Ecol. Evol. Syst. 2005, 36:319-344.
77. Turner M.G., Gardner R.H. Quantitative Methods in Landscape Ecology: An Introduction 1991, Springer-Verlag, New York (USA).
78. van den Bosch F., Gilligan C.A. Measures of durability of resistance. Phytopathology 2003, 93:616-625.
79. van den Driessche P., Watmough J. Reproduction numbers and sub-threshold endemic equilibria for compartmental models of disease transmission. Math. Biosci. 2002, 180:29-48.
80. Viaud V., Monod H., Lavigne C., Angevin F., Adamczyk K. Spatial sensitivity of maize gene-flow to landscape pattern: a simulation approach. Landscape Ecol. 2008, 23:1067-1079.
81. Zhu Y., Chen H., Fan J., Wang Y., Li Y., Chen J., Fan J.X., Yang S., Hu L., Leung H., Mew T.W., Teng P.S., Wang Z., Mundt C.C. Genetic diversity and disease control in rice. Nature 2000, 406:718-722.