Figure 3

Sketch of the SMC algorithm with inversions for a sample of size 2. We sample one standard and one inverted chromosome. The dotted line separates the two chromosome classes; lineages to the left of the line belong to the standard class, lineages to the right to the inverted class. Each panel shows three steps: locating the recombination event, creating the floating lineage, and reattaching the floating lineage. Panel a shows a homokaryotypic recombination event, indicated by a crossmark, and the left part of a gene flux event, indicated by an open circle. Panel b shows the right part of the same gene flux event, indicated by a filled circle. Note that another gene flux event is necessary for coalescence. Bold lines show the reattached lineages.