If this scenario was correct, then one would expect the different domains of the polyprotein to have a similar evolutionary history. From the phylogenetic analysis (Table 2) this seems to be confirmed for the MT, HEL and RdRp domains, but not for the AlkB domain. This indicates that the AlkB domain may not have co-evolved with the other domains, at least until relatively recently. This seems to be confirmed by looking at the degree of co-evolution, which was analysed by computing pairwise distances between alignment regions representing the relevant domains ( Figure 4 ). In the case of perfect co-evolution all points should fall on a diagonal. This seems to be the case for the MT, HEL and RdRp domains. However, the plot of the AlkB domain vs. these three domains for the same set of sequences does not show a similar correlation. Only some of the closely related sequence pairs in the upper right quadrant of the plot in Figure 4 show some degree of correlation for AlkB vs. RdRp. The most likely explanation seems to be that most of the AlkB domains have not coevolved with the other domains for any significant period of time. This seems to rule out the possibility of ancient integration of the AlkB domain, except if we assume that an ancient viral AlkB domain has frequently recombined with other AlkB domains. However, it is difficult to distinguish a scenario with frequent recombination of AlkB domains from de novo integration, and the net effect on the properties observed here would be the same.