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Figure S1. (A) Site frequency spectrum of Lake Victoria cichlids. The white and black bars represent H. pyrrhocephalus and H. sp. ‘macula,’ respectively. (B) Demographic model of Lake Victoria cichlids. See the section Demographic Model and Parameter Estimation for details. (C) Nucleotide and indel frequencies within five DRs. We amplified and determined the sequences, including fixed differences, of four DRs from 20 individuals each of H. sp. ‘macula’ and H. pyrrhocephalus. Positions indicate the positions from the first nucleotides of the determined sequences. The frequencies of nucleotides in the coding region of LWS were verified in a previous study (14). (PDF 155 kb)

Figure S2. Population genomic analyses using only male individuals. (A) Site frequency spectrum in H. pyrrhocephalus (white bars; 126,843 SNPs) and H. sp. ‘macula’ (black bars; 146,456 SNPs). Nucleotide diversity and Tajima’s D values were almost same as those in all samples. (B) Average FST values (±1 SD) against coverage for Pool-seq data as in Fig. 1b (5,662,990 SNPs). The blue and orange dots represent observed and simulated values under panmixia. (C) The spatial patterns of average nucleotide diversity within each species (πW; pink), average pairwise nucleotide divergence between species (πB; blue), and FST (green) in and around LWS gene as in Fig. 2b. The green arrows represent fixed nucleotide differences between species. (PDF 279 kb)

Figure S4. The origins of mutations in DRs. Three phylogenetic trees represent the accumulation of mutations in the common ancestral species of (A) Lake Victoria species, (B) Lake Victoria and riverine Haplochromis species, and (C) tribe Tropheini in Lake Tanganyika, Lakes Malawi, Victoria, and riverine Haplochromis species. The tree topologies constructed from sequences of each DR were consistent with (D) “Riverine origin” or (E) “Modern haplochromine origin.” Scale bars indicate the number of substitutions per site. (F) The LWS sequences were determined from three riverine species: H. sp. ‘katonga’ from Katonga, H. sp. ‘kitilda-rukwa’ from Kitilda-Rukwa, and H. sp. ‘muzu’ from Muzu. (PDF 554 kb)

Text S1. Supporting Text. (DOCX 572 kb)

Figure S3. The spatial patterns of average nucleotide diversity within species (πW; pink), average pairwise nucleotide divergence between species (πB; blue), and FST (green) in and around DRs. The green arrows represent fixed nucleotide differences between species. (PDF 1356 kb)