(Poaceae) shows multiple origins of C4 photosynthesis. Am J Bot 88, 1993–2012. Grasso, C. & Lee, C. (2004). Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics 20, 1546–1556. Guindon, S. & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696–704. Heath, L., van der Walt, E., Varsani, A. & Martin, D. P. (2006). Recombination patterns in aphthoviruses mirror those found in other picornaviruses. J Virol 80, 11827–11832. Hughes, F. L., Rybicki, E. P. & Kirby, R. (1993). Complete nucleotide sequence of sugarcane streak Monogeminivirus. Arch Virol 132, 171–182. Jeske, H., Lutgemeier, M. & Preiss, W. (2001). DNA forms indicate rolling circle and recombination-dependent replication of Abutilon mosaic virus. EMBO J 20, 6158–6167. Lefeuvre, P., Martin, D. P., Hoareau, M., Naze, F., Delatte, H., Thierry, M., Varsani, A., Becker, N., Reynaud, B. & Lett, J. M. (2007a). Begomovirus ‘melting pot’ in the south-west Indian Ocean islands: molecular diversity and evolution through recombination. J Gen Virol 88, 3458–3468. Lefeuvre, P., Lett, J. M., Reynaud, B. & Martin, D. P. (2007b). Avoidance of protein fold disruption in natural virus recombinants. PLoS Pathog 3, e181. Martin, D. & Rybicki, E. (2000). RDP: detection of recombination amongst aligned sequences. Bioinformatics 16, 562–563. Martin, D. P. & Rybicki, E. P. (2002). Investigation of Maize streak virus pathogenicity determinants using chimaeric genomes. Virology 300, 180–188. Martin, D. P., Willment, J. A. & Rybicki, E. P. (1999). Evaluation of maize streak virus pathogenicity in differentially resistant Zea mays genotypes. Phytopathology 89, 695–700. Martin, D. P., Willment, J. A., Billharz, R., Velders, R., Odhiambo, B., Njuguna, J., James, D. & Rybicki, E. P. (2001). Sequence diversity and virulence in Zea mays of Maize streak virus isolates. Virology 288, 247–255. Martin, D. P., Posada, D., Crandall, K. A. & Williamson, C. (2005a). A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 21, 98–102. Martin, D. P., Williamson, C. & Posada, D. (2005b). RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21, 260–262. Martin, D. P., van der Walt, E., Posada, D. & Rybicki, E. P. (2005c). The evolutionary value of recombination is constrained by genome modularity. PLoS Genet 1, e51. McClean, A. P. D. (1947). Some Forms of Streak Virus Occurring in Maize, Sugar-Cane and Wild Grasses. Pretoria: South Africa Government Printers. Mesfin, T., den Hollander, J. & Markham, P. G. (1991). Cicadulina species and maize streak virus in Ethiopia. Trop Pest Manage 37, 240–244. Monci, F., S a´nchez-Campos, S., Navas-Castillo, J. & Moriones, E. (2002). A natural recombinant between the geminiviruses Tomato yellow leaf curl Sardinia virus and Tomato yellow leaf curl virus exhibits a novel pathogenic phenotype and is becoming prevalent in Spanish populations. Virology 303, 317–326. Ndunguru, J., Legg, J. P., Aveling, T. A., Thompson, G. & Fauquet, C. M. (2005). Molecular biodiversity of cassava begomoviruses in http://vir.sgmjournals.org MSV diversity in African grasses Tanzania: evolution of cassava geminiviruses in Africa and evidence for East Africa being a center of diversity of cassava geminiviruses. Virol J 2, 21. Olmstead, R. G. & Sweere, J. A. (1994). Combining data in phylogenetic systematics: an empirical approach using three molecu- lar data sets in the Solanaceae. Syst Biol 43, 467–481. Oluwafemi, S., Varsani, A., Monjane, A. L., Shepherd, D. N., Owor, B. E., Rybicki, E. P. & Martin, D. P. (2008). A new African streak virus species from Nigeria. Arch Virol 153, 1407–1410. Owor, B. E., Shepherd, D. N., Taylor, N. J., Edema, R., Monjane, A. L., Thomson, J. A., Martin, D. P. & Varsani, A. (2007a). Successful application of FTA classic card technology and use of bacteriophage phi29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes. J Virol Methods 140, 100–105. Owor, B. E., Martin, D. P., Shepherd, D. N., Edema, R., Monjane, A. L., Rybicki, E. P., Thomson, J. A. & Varsani, A. (2007b). Genetic analysis of maize streak virus isolates from Uganda reveals widespread distribution of a recombinant variant. J Gen Virol 88, 3154–3165. Padidam, M., Sawyer, S. & Fauquet, C. M. (1999). Possible emergence of new geminiviruses by frequent recombination. Virology 265, 218–225. Penny, D., White, W. T., Hendy, M. D. & Phillips, M. J. (2007). A bias in ML estimates of branch lengths in the presence of multiple signals. Mol Biol Evol 25, 239–242. Peterschmitt, M., Reynaud, B., Sommermeyer, G. & Baudin, P. (1991). Characterization of maize streak virus isolates using monoclonal and polyclonal antibodies and by transmission to a few hosts. Plant Dis 75, 27–32. Peterschmitt, M., Granier, M., Frutos, R. & Reynaud, B. (1996). Infectivity and complete nucleotide sequence of the genome of a genetically distinct strain of maize streak virus from Re´union Island. Arch Virol 141, 1637–1650. Pinner, M. S. & Markham, P. G. (1990). Serotyping and strain identification of maize streak virus isolates. J Gen Virol 71, 1635–1640. Pinner, M. S., Markham, P. G., Markham, R. H. & Dekker, E. L. (1988). Characterisation of maize streak virus – description of strains – symptoms. Plant Pathol 37, 74–87. Pita, J. S., Fondong, V. N., Sangar e´, A., Otim-Nape, G. W., Ogwal, S. & Fauquet, C. M. (2001). Recombination, pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of severe cassava mosaic disease in Uganda. J Gen Virol 82, 655–665. Posada, D. (2006). ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Res 34, W700–W703. Posada, D. & Crandall, K. A. (2001). Evaluation of methods for detecting recombination from DNA sequences: computer simula- tions. Proc Natl Acad Sci U S A 98, 13757–13762. Posada, D. & Crandall, K. A. (2002). The effect of recombination on the accuracy of phylogeny estimation. J Mol Evol 54, 396–402. Prasanna, H. C. & Rai, M. (2007). Detection and frequency of recombination in tomato-infecting begomoviruses of South and Southeast Asia. Virol J 4, 111. Schnippenkoetter, W. H., Martin, D. P., Hughes, F., Fyvie, M., Willment, J. A., James, D., von Wechmar, B. & Rybicki, E. P. (2001). The biological and genomic characterisation of three mastreviruses. Arch Virol 146, 1075–1088. Shepherd, D. N., Martin, D. P., Lefeuvre, P., Monjane, A. L., Owor, B. E., Rybicki, E. P. & Varsani, A. (2008a). A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue. J Virol Methods, doi:10.1016/j.jviromet.2007.12.014 2073