Additional file 4.

Figure S3. Distribution of recombination breakpoints detected within (A) DNA-A and (B) DNA-B sequences. All estimated breakpoint positions are indicated by small vertical lines at the top of the graph. A 200-nucleotide window was moved along the alignment one nucleotide at a time and the number of breakpoints detected within the window region was counted and plotted (solid line). The horizontal lines at the top of each graph indicate 99% and 95% confidence thresholds for globally significant breakpoint clusters. Light and dark grey areas respectively indicate local 99% and 95% breakpoint clustering thresholds, taking into account local regional differences in sequence diversity that influence the ability of different recombination detection methods to identify recombination breakpoints. Red areas indicate recombination hot-spots.

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De Bruyn et al. BMC Evolutionary Biology 2012 12:228   doi:10.1186/1471-2148-12-228