a) The size distribution of putative ancestry blocks shows mostly small ancestry blocks and slightly larger Congolese (red) than Upper Nile blocks (blue). The plot shows the counts of ancestry blocks in different size categories summed up for five LVRS radiation species across all scaffolds calculated with 3 kb windows. As most blocks do not span multiple windows of 3 kb and many blocks cannot be clearly allocated to Congolese or Upper Nile ancestry (grey) ( Supplementary Fig. 8), the average ancestry block size is likely 3 kb or smaller, consistent with hybridization many thousands of years ago. ( b) Correlation of ancestry blocks between whole-genome sequenced LVRS members is high overall but decreases with phylogenetic distance. The boxplots show correlation of f d (ref. 78) in 10 kb windows between single individuals of conspecifics ( Pundamilia individuals of the same species), sister species ( Pu. pundamilia versus Pu. nyererei), more distantly related Lake Victoria (LVi) species ( Paralabidochromis flavus versus Pu. pundamilia and Pu. nyererei), Lake Kivu (LKi) species ( Pa. paucidens versus Harpagochromis vittatus) and Lake Victoria against Lake Kivu species. This suggests that all radiation member species share the same hybridization event in their ancient history but vary in how long after that event they remained part of the same recombining population. It also suggests that some of the admixture variation still segregates within individual species (indicated by the deviation from an f d correlation of 1 among conspecifics).