Fig. 3

Typical examples of RIP analyses of h-PHI-identified recombinant taxa. These examples come from M1001/P1024 and are representative of all RIP results among all four mother–child pairs investigated in this study (Additional file 2: Table S1). Panel a shows a result where the query sequence (h-PHI-identified recombinant taxon P1024-7C) does not have a significant similarity with any one detected non-recombinant maternal or child sequence in any part of the sequenced genome (2500 nt of env). Panel b shows an example where the h-PHI-identified recombinant taxon P1024-15D has one parent (P1024-17C) significantly more similar in part of the sequence (approximately nucleotide sites k = 700–2500) and likely one missing parent (sites 1–700) in the detected set of non-recombinant potential parents. Panels c and d show examples of results where >1 parent shows significant similarity to some part of the query sequence (P1024-3A to P1024-2C and P1024-11B, and P1024-10A to P1024-2C and P1024-19B). These latter two panels also show the situation where no parent is significantly more similar than the other potential parents because several are fairly similar (sites 1500–2500). The similarity, s(k), to each non-recombinant potential parent is displayed as a colored line, identified in the list to the right of the RIP result panels. Each RIP result also shows the best match in the corresponding color as the lower horizontal bar in the top of each panel, and if the match is significant, another colored bar on top of that is shown for the corresponding sites