begomoviruses being smaller than that detected in mastreviruses. The distribution of recombination break- points detectable in our mastrevirus dataset is consistent with proposals that breakpoint distributions observed in geminiviruses sampled from nature are strongly influenced by selective forces that eliminate recombinants with defective intra-genome interactions (Martin et al., 2005c; Lefeuvre et al., 2007b). It has been convincingly demon- strated that selection strongly favours the survival of geminivirus recombinants in which both intra-protein amino acid interactions (Lefeuvre et al., 2007b) and inter- genome region interactions (Martin et al., 2005c) remain undisrupted. Importantly, there are various lines of evidence that indicate that recombination breakpoints both at the 39 end of cp (Garcı´a-Andre´s et al., 2007a; Lefeuvre et al., 2007b) and within the SIR (Martin et al., 2005c; Martin & Rybicki, 2002) are particularly undisrup- tive of intra-genome interactions. MSV SIR sequences are extremely modular and can continue functioning properly even when transferred into genetic backgrounds very different from those in which they evolved (Martin & Rybicki, 2002). If the modestly sized recombination hot- spot at the 39 end of the begomovirus cp is caused by the coincident location of a site encoding a proportion of CP that tolerates recombination well at the same position as a transcription terminator that is biochemically predisposed to recombination (due to clashes between transcription and replication complexes), then it is reasonable to suspect that the placement of a highly modular intergenic region beside this site in mastreviruses is responsible for the larger size of this hot-spot in these viruses. Differences in the geographical distributions of MSV strains and variants We were interested in determining whether there were differences in MSV strain demographics in different parts of Africa analogous to those previously detected for cassava- infecting geminiviruses (Ndunguru et al., 2005; Bull et al., 2006). We therefore split the sampled viruses into southern African (isolates from Zimbabwe, South Africa and Mozambique; n570), West African (isolates from Nigeria MSV diversity in African grasses and Mali; n511), East African (isolates from Uganda, Rwanda, Burundi and Kenya; n510) and La Re´union (n58) groups and tested for differences in the strain compositions of these groups. Although there was a highly significant difference in the strain distributions across all four regions collectively (P58.361028, 4 [regions]611 [MSV strains] x2 test), separate pairwise comparisons between the regions indicated that these differences originated primarily from the West African population sample (Fig. 3). While the East African and southern African strain distributions were also significantly different, the West African strain distribution is clearly the most unique. The key differences between the sampled West African MSV population and those found elsewhere are the absence of any MSV-B isolates and the presence of MSV-G and -H isolates. This was a surprising result as we had anticipated that the mainland African MSV-populations would have similar structures, and that the La Re´union population would be distinct. Recent reports of large numbers of new geminivirus species, strains and variants unique to the Indian Ocean islands (Delatte et al., 2005; Lefeuvre et al., 2007a; Peterschmitt et al., 1996; Shepherd et al., 2008b) have indicated that they have been reasonably isolated with respect to the movement of geminiviruses. Conversely, the close relationships shared by MSV strain A isolates found in West Africa with those found elsewhere on the continent (Briddon et al. 1994; Martin et al., 2001) clearly indicate that the movement of at least some MSV strains either to or from West Africa is relatively frequent and largely unhindered. Our failure to sample any MSV-B isolates in West Africa and any MSV-G and -H isolates outside West Africa therefore suggests that there may be strain-specific differences in the continent-wide movement of MSV variants. To investigate this possibility further we compared the phylogenies of MSV-A and -B isolates (the two best sampled MSV strains) in the context of their regions of origin (Fig. 4). Both MSV-A and -B isolates from particular regions tend to group in phylogenetic trees with other isolates from the same region. However, all MSV-B isolates from particular regions form monophyletic groups (i.e. all viruses from, for example, southern Africa are more closely Fig. 3. MSV strain demographics in different parts of Africa and La R e´union. All virus isolates represented here were sampled from uncultivated grass species. Different strains are represented by different colours, and P values indicate regions with significantly different MSV-population structures (values in bold). http://vir.sgmjournals.org 2069