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  • Acosta-Leal, R., S. Duffy, Z. Xiong, R. W. Hammond, and S. F. Elena 2011. Advances in plant virus evolution: translating evolutionary insights into better disease management. Phytopathology 101:11361148.
  • Barton, H. D., P. Rohani, D. E. Stallknecht, B. Brown, and J. M. Drake 2013. Subtype diversity and reassortment potential for co-circulating avian influenza viruses at a diversity hot spot. Journal of Animal Ecology doi:10.1111/1365-2656.12167.
  • Basu, A. N., and B. Ganguly 1968. A note on the transmission of foorkey disease of large cardamom by the aphid, Micromyzus kalimpongensis Basu. Indian Phytopathology 21:127.
  • Burdon, J. J., and P. H. Thrall 2008. Pathogen evolution across the agro-ecological interface: implications for disease management. Evolutionary Applications 1:5765.
  • Chakraborty, S., and A. C. Newton 2011. Climate change, plant diseases and food security: an overview. Plant Pathology 60:214.
  • Chakraborty, S., R. Vanitharani, B. Chattopadhyay, and C. M. Fauquet 2008. Supervirulent pseudorecombination and asymmetric synergism between genomic components of two distinct species of begomovirus associated with severe tomato leaf curl disease in India. Journal of General Virology 89:818828.
  • Chen, L. F., M. Rojas, T. Kon, K. Gamby, B. Xoconostle-Cazares, and R. L. Gilbertson 2009. A severe symptom phenotype in tomato in Mali is caused by a reassortant between a novel recombinant begomovirus (Tomato yellow leaf curl Mali virus) and a betasatellite. Molecular Plant Pathology 10:415430.
  • Darriba, D., G. L. Taboada, R. Doallo, and D. Posada 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9:772.
  • Drummond, A. J., S. Y. W. Ho, M. J. Phillips, and A. Rambaut 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology 4:e88.
  • Drummond, A. J., M. A. Suchard, D. Xie, and A. Rambaut 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29:19691973.
  • Dugan, V. G., R. Chen, D. J. Spiro, N. Sengamalay, J. Zaborsky, E. Ghedin, J. Nolting et al. 2008. The evolutionary genetics and emergence of avian influenza viruses in wild birds. PLoS Pathogens 4:e1000076.
  • Earl, D. A., and B. M. vonHoldt 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4:359361.
  • Escriu, F., A. Fraile, and F. García-Arenal 2007. Constraints to genetic exchange support gene coadaptation in a tripartite RNA virus. PLoS Pathogens 3:e8.
  • Evanno, G., S. Regnaut, and J. Goudet 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14:26112620.
  • Excoffier, L., and H. E. Lischer 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10:564567.
  • Fu, H. C., J. M. Hu, T. H. Hung, H. J. Su, and H. H. Yeh 2009. Unusual events in Banana bunchy top virus strain evolution. Phytopathology 99:812822.
  • Fuller, T. L., M. Gilbert, V. Martin, J. Cappelle, P. Hosseini, K. J. Njabo, S. A. Aziz et al. 2013. Predicting hotspots for influenza virus reassortment. Emerging Infectious Diseases 19:5563.
  • García-Arenal, F., A. Fraile, and M. J. M. Malpica 2001. Variability and genetic structure of plant virus populations. Annual Review of Phytopathology 39:157186.
  • Ghedin, E., N. A. Sengamalay, M. Shumway, J. Zaborsky, T. Feldblyum, V. Subbu, D. J. Spiro et al. 2005. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature 437:11621166.
  • Grigoras, I., A. I. Del Cueto Ginzo, D. P. Martin, A. Varsani, J. Romero, A. C. Mammadov, I. M. Huseynova et al. 2014. Genome diversity and evidence of recombination and reassortment in Nanoviruses from Europe. Journal of General Virology 95:11781191.
  • Gu, H., C. Zhang, and S. A. Ghabrial 2007. Novel naturally occurring Bean pod mottle virus reassortants with mixed heterologous RNA1 genomes. Phytopathology 97:7986.
  • Hou, Y. M., and R. L. Gilbertson 1996. Increased pathogenicity in a pseudorecombinant bipartite geminivirus correlates with intermolecular recombination. Journal of Virology 70:54305436.
  • Hu, J. M., H. C. Fu, C. H. Lin, H. J. Su, and H. H. Yeh 2007. Reassortment and concerted evolution in banana bunchy top virus genomes. Journal of Virology 81:17461761.
  • Hyder, M. Z., S. H. Shah, S. Hameed, and S. M. Naqvi 2011. Evidence of recombination in the banana bunchy top virus genome. Infection, Genetics and Evolution 11:12931300.
  • Idris, A. M., K. Mills-Lujan, K. Martin, and J. K. Brown 2008. Melon chlorotic leaf curl virus: characterisation and differential reassortment with closest relatives reveal adaptive virulence in the Squash leaf curl virus clade and host shifting by the host-restricted Bean calico mosaic virus. Journal of Virology 82:19591967.
  • Ince, W. L., A. Gueye-Mbaye, J. R. Bennink, and J. W. Yewdell 2013. Reassortment complements spontaneous mutation in influenza A virus NP and M1 genes to accelerate adaptation to a new host. Journal of Virology 87:43304338.
  • Jakobsson, M., and N. A. Rosenberg 2007. CLUMP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:18011806.
  • Kalinowksi, S. T. 2011. The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure. Heredity 106:625632.
  • Karan, M., R. M. Harding, and J. L. Dale 1994. Evidence for two groups of banana bunchy top virus isolates. Journal of General Virology 75:35413546.
  • Koehler, A. V., J. M. Pearce, P. L. Flint, J. C. Franson, and H. S. Ip 2008. Genetic evidence of intercontinental movement of avian influenza in a migratory bird: the northern pintail (Anas acuta). Molecular Ecology 21:47544762.
  • Lefeuvre, P., J.-M. Lett, B. Reynaud, and D. P. Martin 2007. Avoidance of protein fold disruption in natural virus recombinants. PLoS Pathogens 3:e181.
  • Li, H., and M. J. Roossinck 2004. Genetic bottlenecks reduce population variation in an experimental RNA virus population. Journal of Virology 78:1058210587.
  • Mandal, B. 2010. Advances in small isometric multicomponent ssDNA viruses infecting plants. Indian Journal of Virology 21:1830.
  • Mandal, B., S. Mandal, K. B. Pun, and A. Varma 2004. First report of the association of a nanovirus with foorkey disease of large cardamom in India. Plant Disease 88:428.
  • Mandal, B., S. Shilpi, A. R. Barman, S. Mandal, and A. Varma 2013. Nine novel DNA components associated with the foorkey disease of large cardamom: evidence of a distinct babuvirus species in Nanoviridae. Virus Research 178:297305.
  • Martin, D. P., E. van der Walt, D. Posada, and E. P. Rybicki 2005. The evolutionary value of recombination is constrained by genome modularity. PLoS Genetics 1:e51.
  • Martin, D. P., P. Lemey, M. Lott, V. Moulton, D. Posada, and P. Lefeuvre 2010. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26:24622463.
  • Martin, D. P., P. Biagini, P. Lefeuvre, M. Golden, P. Roumagnac, and A. Varsani 2011a. Recombination in eukaryotic single stranded DNA viruses. Viruses 3:16991738.
  • Martin, D. P., P. Lefeuvre, A. Varsani, M. Hoareau, J.-V. Semegni, B. Dijoux, C. Vincent et al. 2011b. Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologically important intragenome interaction networks. PLoS Pathogens 7:e1002203.
  • Nair, K. P. P. 2011. Agronomy and Economy of Black Pepper and Cardamom: The King and Queen of Spices. Elsevier, New York, NY.
  • Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.
  • Nelson, M. I., C. Viboud, L. Simonsen, R. T. Bennett, S. B. Griesemer, K. St George, J. Taylor et al. 2008. Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918. PLoS Pathogens 4:e1000012.
  • O'Keefe, K. J., O. K. Silander, H. McCreery, D. M. Weinreich, K. M. Wright, L. Chao, S. V. Edwards et al. 2010. Geographic differences in sexual reassortment in RNA phage. Evolution 64:30103023.
  • Oksanen, J., R. Kindt, P. Legendre, B. O'Hara, G. L. Simpson, P. Sólymos, M. H. H. Stevens et al. 2008. Vegan: Community Ecology Package. http://cran.r-project.org/web/packages/vegan/ (accessed on 29 January 2013).
  • Pearce, J. M., A. M. Ramey, P. L. Flint, A. V. Koehler, J. P. Fleskes, J. C. Franson, J. S. Hall et al. 2009. Avian influenza at both ends of a migratory flyway: characterising viral genomic diversity to optimise surveillance plans for North America. Evolutionary Applications 2:457468.
  • Pita, J. S., V. N. Fondong, A. Sangare, G. W. Otim-Nape, S. Ogwal, and C. M. Fauquet 2001. Recombination, pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of severe cassava mosaic disease in Uganda. Journal of General Virology 82:655665.
  • Plantegenest, M., C. Le May, and F. Fabre 2007. Landscape epidemiology of plant diseases. Journal of the Royal Society Interface 4:963972.
  • Prasanna, H. C., D. P. Sinha, A. Verma, M. Singh, B. Singh, M. Rai, and D. P. Martin 2010. The population genomics of begomoviruses: global scale population structure and gene flow. Virology Journal 7:220.
  • Pritchard, J. K., M. Stephens, and P. Donnelly 2000. Inference of population structure using multilocus genotypic data. Genetics 155:945959.
  • Quantum GIS Development Team. 2014. Quantum GIS geographic information system. Open source geospatial foundation project. http://www.qgis.org (accessed on 25 February 2014).
  • R Development Core Team. 2013. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/ (accessed on 30 April 2012).
  • Rambaut, A. 2009. FigTree v. 1.3.1. Computer program and documentation distributed by the author at http://tree.bio.ed.ac.uk/software/ (accessed on 7 September 2012).
  • Rambaut, A., and A. J. Drummond. 2007. Tracer v.1.5. Computer program and documentation distributed by the authors at http://beast.bio.ed.ac.uk/Tracer (accessed on 7 September 2012).
  • Rambaut, A., O. G. Pybus, M. I. Nelson, C. Viboud, J. K. Taubenberger, and E. C. Holmes 2008. The genomic and epidemiological dynamics of human influenza A virus. Nature 453:615619.
  • Ramey, A. M., J. M. Pearce, C. E. Ely, L. M. Guy, D. B. Irons, D. V. Derksen, and H. S. Ip 2010. Transmission and reassortment of avian influenza viruses at the Asian-North American interface. Virology 406:352359.
  • Rokyta, D. R., and H. A. Wichman 2009. Genic incompatibilities in two hybrid bacteriophages. Molecular Biology and Evolution 26:28312839.
  • Rosenberg, N. A. 2004. Distruct: a program for the graphical display of population structure. Molecular Ecology Notes 4:137138.
  • Rozas, J., and R. Rozas 1999. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174175.
  • Savory, F. R., and U. Ramakrishnan 2014. Asymmetric patterns of reassortment and concerted evolution in Cardamom bushy dwarf virus. Infection, Genetics and Evolution 24:1524.
  • Stainton, D., S. Kraberger, M. Walters, E. J. Wiltshire, K. Rosario, M. Halafihi, S. Lolohea et al. 2012. Evidence of inter-component recombination, intra-component recombination and reassortment in Banana bunchy top virus. Journal of General Virology 93:11031119.
  • Strange, R. N., and P. R. Scott 2005. Plant disease: a threat to global food security. Annual Review of Phytopathology 43:83116.
  • Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Molecular Biology and Evolution 28:27312739.
  • Thrall, P. H., J. G. Oakeshott, G. Fitt, S. Southerton, J. J. Burdon, A. Sheppard, R. J. Russell et al. 2011. Evolution in agriculture: the application of evolutionary approaches to the management of biotic interactions in agro-ecosystems. Evolutionary Applications 4:200215.
  • Timchenko, T., L. Katul, Y. Sano, F. de Kouchkovsky, H. J. Vetten, and B. Gronenborn 2000. The master rep concept in nanovirus replication: identification of missing genome components and potential for natural genetic reassortment. Virology 274:189195.
  • Tsompana, M., J. Abad, M. Purugganan, and J. W. Moyer 2005. The molecular population genetics of the tomato spotted wilt virus (TSWV) genome. Molecular Ecology 14:5366.
  • Varma, P. M., and S. P. Capoor 1964. ‘Foorkey’ disease of large cardamom. Indian Journal of Agricultural Science 34:5662.
  • Wang, H.-I., C.-H. Chang, P.-H. Lin, H.-C. Fu, C. Tang, and H.-H. Yeh 2013. Application of motif-based tools on evolutionary analysis of multipartite single-stranded DNA viruses. PLoS ONE 8:e71565.
  • Weir, B. S., and C. C. Cockerham 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:13581370.
  • Wille, M., G. J. Robertson, H. Whitney, M. A. Bishop, J. A. Runstadler, and A. S. Lang. 2011. Extensive geographic mosaicism in avian influenza viruses from gulls in the northern hemisphere. PLoS ONE 6:e20664.