Recombination analysis. (Top) schematic diagrams of FMDV’s ORF. The polyprotein encoded by the ORF is processed into several protein products by proteases (Diamonds; see Keys for the names of proteases). Based on the functions of mature proteins, the ORF can be divided into four main functional areas (L: turquoise; P1: red; P2: green; and P3: blue). L region encodes a leader protease (Lpro). The P1 region encodes four structural capsid proteins, VP1–4. The P2 and P3 regions encode several non-structure proteins, including 2A–C, and 3A–D. 3C and 3D are a viral protease (3Cpro) and an RNA-dependent RNA polymerase (3Dpol), respectively. (Bottom) number of inferred recombination breakpoints estimated per 200-nucleotide window. The tick marks above the plot show the locations of individual breakpoints inferred. Global and local 99% and 95% confidence intervals of the estimated recombination breakpoints are shown (see Keys). Regions with the inferred number of recombination breakpoints more than the 99% local confidence intervals are considered recombination hotspots. Four recombination hotspots were detected in total, indicated by vertical transparent strips. Vertical dotted lines are the locations at which the ORF alignment was split (Data S2–6).