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Fig. S1 Proportion of outliers (FDR = 20%; prior odds 10) among all polymorphic SNPs between all species pairs for each of the three assemblies (see Table S1 for details on assemblies).

Fig. S2 Results of outlier scans assuming even prior odds for all pairwise comparisons among the five cichlid species.

Fig. S3 (a) Results of a structure analysis of the full dataset of 10 663 SNPs. (b) Maximum likelihood tree based on the full dataset.

Fig. S4 Results of structure analyses of three data subsets.

Table S1 Number of RAD loci and polymorphic sites obtained with different assembly and mapping criteria in 50 individuals from five cichlid species.

Table S2 Genetic diversity of five haplochromine species (Mbipia lutea, Mbipia mbipia, Pundamilia nyererei, Pundamilia sp. ‘pink anal fin’ and Pundamilia pundamilia) at Makobe Island, Southern Lake Victoria based on the M2 assembly.

Table S3 Neutral FST between all species pairs estimated based on 5331 intermediate SNPs (i.e. between lower and upper quartiles of a list of all SNPs arranged in order of increasing global FST).

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