a) Sites fixed for alternative alleles in the Congolese (C) and Upper Nile (N) taxa are enriched for high global F ST outlier SNPs in Lake Victoria. Of the 12,890 biallelic SNPs among six sympatric Lake Victoria species (shown in ( b)), 340 are outliers of high global F ST (LV outliers). We assigned SNPs to five different ancestry categories according to the presence or absence of the two alleles in the Congolese (C) and Upper Nile (N) lineage taxa. The grey bars show the proportion of LV outliers among all SNPs in each ancestry category. Total SNP counts in each category and P-values of two-sided Fisher’s exact tests are shown on top. Ancestry category (1) includes all SNPs for which only one of the two LV alleles was found in the Congolese and Upper Nile taxa together (novel LV allele or unsampled in parental lineages), (2) both LV alleles found in the Congolese taxa (polymorphic in LVRS even without Upper Nile hybridization), (3) only one allele found in Congolese but both alleles found in Upper Nile taxa (not available in LVRS without hybridization), and 4) Congolese and Upper Nile taxa each fixed for alternative LV alleles (not available in LVRS without hybridization) potentially including Bateson–Dobzhansky–Muller incompatibilities. Category 5 includes sites with similar initial allele frequency in Lake Victoria (16%) than sites fixed for alternative alleles in the parental lineages (category 4) to test if the enrichment in category 4 could simply be because of high initial allele frequency. ( b) Differential sorting of parental alleles between Lake Victoria cichlid species at LV outliers fixed for alternative alleles in the Congolese and Upper Nile lineage taxa (mean global F ST among LV species=0.52). Each square represents a SNP coloured according to the allele frequency in that species ranging from red (fixed for Congolese allele) to blue (fixed for Upper Nile allele). All except two sites (2+3 from the right) are located on different scaffolds of the Pundamilia nyererei reference genome. If known, chromosomal positions on the Oreochromis niloticus genome are shown below. At least 10 of the 22 chromosomes are involved in mosaic-like allele sorting between radiation species at loci that were fixed for alternative alleles in the parental lineages of the ancestral hybrid swarm (Photo credits: Oliver Selz, Ole Seehausen, Adrian Indermaur, ‘Teleos’, Uli Schliewen).