Fig. 1

Illustration of genome evolution with rearrangements. a Starting from ancestral DNA, evolution with rearrangements results in derived sequences with deletions, duplications, and re-ordered fragments. Each colored block represents a piece of a chromosome, e.g., a few thousand basepairs. The blocks labeled n and s are similar repeated sequences (same color). b Comparison of derived sequence (vertical) to ancestral sequence (horizontal). The diagonal red lines show which ancestral basepair each basepair in the derived sequence is descended from: starting at a derived basepair, go horizontally to the right until hitting a red line, then go up vertically to find the ancestral basepair. The diagonal black line indicates a misleading (paralogous) similarity between the ancestral and derived sequences. c Comparison of the same derived sequence (vertical) to a derived reference genome (horizontal). Diagonal red lines show basepairs in the horizontal and vertical sequences that are descended from the same basepair in the most recent common ancestor of the sequences. The diagonal black line shows similar segments that are not descended from the same part of the most recent common ancestor