, but due to its secondary structure it can be unambiguously aligned and there should also be sufficient characters that show some degree of variability to give reasonable resolution if data from closely related species are compared. Regardless of this, we were unable to find any correlation between s2m mutational patterns and host phylogenies. For instance, we were unable to assess whether the two copies of s2m found in the dog norovirus strains came from independent sources or if they are the result of some sort of duplication event and subsequent independent evolution ( Figure 1B and Table 1), and the phylogeny of the deltacoronovirus s2m sequences was poorly resolved and did not match the phylogeny of the hosts (data not shown). There seems to be a number of loci that 'permit' certain substitutions and that these mutate quite quickly, masking any phylogenetic signal.
Although our analyses did not address the function of s2m per se, we believe that our observations might provide some clues as to how s2m might evolve and provide a selective advantage to the host viruses. We believe that s2m must have some sort of 'autonomous' function that does not require complex interactions with other parts of the viral genome/transcriptome as there do not appear to be any conserved flanking regions in s2m viruses (proximity to coding region, adjacent reading frames, nucleotide motifs etc.). Neither do there appear to be any conserved amino acid motifs in any of the annotated open reading frames except the GDD core of the RNAdependent RNA polymerase when looking at protein sequence data from representatives from the four virus families (data not shown). The conserved nature of s2m might also imply that the s2m targets are homologous as all infected organisms are (relatively) closely related in an evolutionary perspective whereas the viruses are distantly related when looking both at molecular data and functionality (genome replication and transcription/ translation strategies). An intracellular target also seems plausible, as all s2m containing viruses replicate in the cytoplasm and this is where s2m is likely to be available for interactions with the cellular machinery. The observation that s2m can apparently be transferred between unrelated viruses and remain functional (under selection pressure to maintain sequence and structure) also suggests strongly that the target for s2m is host-specific and not viral. Based on structural similarities between micro RNA (miRNA) hairpins involved in gene regulation, we propose that s2m functions through a RNA interference (RNAi)-like mechanism, possibly targeting homologous sequence loci in infected organisms. Recent observations using a reverse genetics-based approach and a recombinant Sindbis virus indicate that the required cellular machinery for this to function should be in place in human cells [19], and this model would also be consistent with an additive effect, where more copies of s2m would allow the formation of more miRNA/protein complexes, resulting in a more profound effect on target gene regulation.
Based on the finding of s2m in what appears to be newly emerging viruses, such as SARS-CoV, we also believe that s2m still maintains its mobility and will play a role in the future of virus evolution.

Conclusions
The s2m sequence motif appears to be an active mobile genetic element that thus far can be found in four different families of + ssRNA viruses. It seems likely that s2m provides some kind of selective advantage for the viruses that contain the motif, and a possible function could be related to RNAi-like gene regulation of infected organisms.

Methods
All sequence data were downloaded from GenBank. Only accessions where continuous sequence information from the 3' end of the genome to the locus selected for phylogenetic analyses was available were used when investigating the evolutionary relationship between the (s2m-containing) viruses.
By using all the available sequence information from publications pertaining to s2m, several conserved sequences domains within s2m could be identified. These sequence motifs were used to perform nucleotide BLAST searches through the NCBI portal and >400 s2mcontaining sequences could be identified. The s2m motifs (43-44 nucleotides long) were individually extracted and aligned, and the following consensus sequence could be generated: CGNGG(N)CCACGNNGNGT(N)ANNANCG AGGGT(N)ACAG (N's in parenthesis indicate possible indels) for the conserved core region of s2m. This text string profile was used to search all viral sequences in GenBank using different combinations of the indicated indels and allowing for nucleotide substitutions.
All the alignments were constructed using the Clustal W algorithm [20] and manually edited using Bioedit (version 7.0.5.3; [21]). Only unambiguously aligned domains were included in the subsequent analyses. Phylogenetic analyses were performed using RAxML with the optimal GTR (General Time Reversible) with Gamma distribution model for amino acid substitution and 100 bootstrap replicates [22]. Minimally constrained trees were constructed to test whether trees with monophyly of s2m-containing sequences were significantly less likely than the optimal unconstrained tree. The primary constraint was to make all s2m-containing taxa monophyletic. If more than two s2m-containing clades were present alternate topologies were constructed in a pairwise manner to test topologies with two s2m clades constrained together. The optimal tree compatible with the constraint was calculated using RAxML with the above amino acid substitution model, followed by site likelihood calculation with RAxML. The Approximately Unbiased (AU) test was calculated using CONSEL [23].

Additional file
Additional file 1: List of s2m-containing sequences found in Genbank.
Additional file 2: Figure S1, S2, S3 and S4. For each virus family, the optimal tree with bootstrap support values is shown (identical to Figures 1, 2, 3 and 4). Each of the s2m-containing clades was numbered, from top to bottom without regard to taxonomy, and the total number of observed s2m gains was mapped onto the tree. Constraint trees were constructed to test a series of hypotheses for s2m gains. For example, all s2m-containing sequences were constrained to a single clade to see if a tree with only a single gain of the s2m sequence was significantly less likely given the alignment. Other less constrained trees were also constructed to test if trees with more than one s2m gain were also significantly less likely given the alignment. The specific constraints on s2m clades are shown in the table below. In all cases the differences in log likelihood and p-values for the different trees are shown in comparison to the most likely unconstrained tree. In addition to the Approximately Unbiased (AU) p-values, other test support values are also shown (np = bootstrap probablility, bp = bootstrap proportion, pp = posterior probability, kh = Kishino-Hasegawa, sh = Shimodaira-Hasegawa, wkh = weighted Kishino-Hasegawa, wsh = weighted Shimodaira-Hasegawa).Quick question about FAAB

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