Fig. 1

a. The scheme illustrates an example of several duplication events in the genome, the resulting alignments and the network constructed based on those alignments. In every time step one duplication happens in the genome and a second copy is inserted in the genome nearby. Alignments appear not only between a copied region and its copy as expected, but also when a duplication overlaps one of existing duplicated regions (the second duplication event on the scheme). We call those alignments “secondary” alignments because they do not represent a duplication event between aligning regions. For the network construction we grouped sets of overlapping alignments into separate duplicated regions. Each duplicated region is represented with a node in the SD network. Edges are added if there exists an alignment between duplicated regions. Number of edges that a node has (node degree) represents a number of copies of a corresponding duplicated region. b. The network constructed based on SDs of the reference Human genome (SD network). The black circles and lines represent nodes and edges of the SD network. There are 6656 nodes and 16042 edges in the SD network in total. One can see that the SD network includes multiple small connected components and a distinctive giant component with 1325 nodes and 9678 edges in it