Network of genome affinities and underlying speciation tree for one replicate of the noLGT simulation. The network is based on the genome tree shown in Figure S2, using the wLP (panel A) and ndLP (panel B) methods. The edge color represents the distance in the tree measure, where black represents a distance of 0, and lighter colors represent larger distances up to 9 (lightest blue). The edge widths represent the degree of affinity between two nodes, corresponding to the weights obtained from the LP solution. Clades described in the main text are indicated with numbers 1-8, and genome 997 is highlighted with an asterisk.